Key: 6201 Medline: Authors: Ono S Title: Regulation of actin filament dynamics by actin depolymerizing factor/cofilin and actin-interacting protein 1: new blades for twisted filaments. Citation: Biochemistry 42: 13363-13370 2003 Type: REVIEW Genes: unc-60 unc-78 Abstract: Actin depolymerizing factor (ADF)/cofilin enhances turnover of actin filaments by severing and depolymerizing filaments. A number of proteins functionally interact with ADF/cofilin to modulate the dynamics of actin filaments. Actin-interacting protein 1 (AIP1) has emerged as a conserved WD-repeat protein that specifically enhances ADF/cofilin-induced actin dynamics. Interaction of AIP1 with actin was originally characterized by a yeast two-hybrid system. However, biochemical studies revealed its unique activity on ADF/cofilin-bound actin filaments. AIP1 alone has negligible effects on actin filament dynamics, whereas in the presence of ADF/cofilin, AIP1 enhances filament fragmentation by capping ends of severed filaments. Studies in model organisms demonstrated that AIP1 genetically interacts with ADF/cofilin and participates in several actin-dependent cellular events. The crystal structure of AIP1 revealed its unique structure with two seven-bladed beta-propeller domains. Thus, AIP1 is a new class of actin regulatory proteins that selectively enhances ADF/cofilin-dependent actin filament dynamics. ------------------- Key: 6202 Medline: 12937276 Authors: Galy V;Mattaj IW;Askjaer P Title: Caenorhabditis elegans nucleoporins Nup93 and Nup205 determine the limit of nuclear pore complex size exclusion in vivo. Citation: Molecular Biology of the Cell 14: 5104-5115 2003 Type: ARTICLE Genes: npp-1 npp-2 npp-3 npp-4 npp-5 npp-6 npp-7 npp-8 npp-9 npp-10 npp-11 npp-12 npp-13 npp-14 npp-15 npp-16 npp-17 npp-18 npp-19 npp-20 Abstract: Nuclear pore complexes (NPCs) span the nuclear envelope and mediate communication between the nucleus and the cytoplasm. To obtain insight into the structure and function of NPCs of multicellular organisms, we have initiated an extensive analysis of Caenorhabditis elegans nucleoporins. Of 20 assigned C. elegans nucleoporin genes, 17 were found to be essential for embryonic development either alone or in combination. In several cases, depletion of nucleoporins by RNAi caused severe defects in nuclear appearance. More specifically, the C. elegans homologs of vertebrate Nup93 and Nup205 were each found to be required for normal NPC distribution in the nuclear envelope in vivo. Depletion of Nup93 or Nup205 caused a failure in nuclear exclusion of nonnuclear macromolecules of similar to70 kDa without preventing active nuclear protein import or the assembly of the nuclear envelope. The defects in NPC exclusion were accompanied by abnormal chromatin condensation and early embryonic arrest. Thus, the contribution to NPC structure of Nup93 and Nup205 is essential for establishment of normal NPC function and for ------------------- Key: 6203 Medline: 14628056 Authors: Sijen T;Plasterk RHA Title: Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Citation: Nature 426: 310-314 2003 Type: ARTICLE Genes: mut-7 mut-14 mut-16 pie-1 rde-1 rde-4 unc-22 Abstract: Transposable elements are stretches of DNA that can move and multiply within the genome of an organism. The Caenorhabditis elegans genome contains multiple Tc1 transposons that jump in somatic cells, but are silenced in the germ line(1-3). Many mutants that have lost this silencing have also lost the ability to execute RNA interference (RNAi)(2,3), a process whereby genes are suppressed by exposure to homologous double-stranded RNA ( dsRNA). Here we show how RNAi causes transposon silencing in the nematode germ line. We find evidence for transposon-derived dsRNAs, in particular to the terminal inverted repeats, and show that these RNAs may derive from read-through transcription of entire transposable elements. Small interfering RNAs of Tc1 were detected. When a germline-expressed reporter gene is fused to a stretch of Tc1 sequence, this transgene is silenced in a manner dependent on functional mutator genes (mut-7, mut-16 and pk732). These results indicate that RNAi surveillance is triggered by fortuitous read-through transcription of dispersed Tc1 copies, which can form dsRNA as a result of 'snap-back' of the terminal inverted repeats. RNAi mediated by this dsRNA silences transposase gene expression. ------------------- Key: 6204 Medline: 12905072 Authors: Kuervers LM;Jones CL;O'Neil NJ;Baillie DL Title: The sterol modifying enzyme LET-767 is essential for growth, reproduction and development in Caenorhabditis Citation: Molecular Genetics & Genomics 270: 121-131 2003 Type: ARTICLE Genes: let-767 sDf125 Abstract: The let-767 gene encodes a protein that is similar to mammalian steroid enzymes that are responsible for the reduction of 17-beta hydroxysteroid hormones. Caenorhabditis elegans is incapable of the de novo synthesis of cholesterol. Therefore, this free-living nematode must extract cholesterol from its environment and modify it to form steroid hormones that are necessary for its survival. C. elegans is unable to survive in the absence of supplemental cholesterol, and is therefore sensitive to cholesterol limitation. We show that a mutation in let-767 results in hypersensitivity to cholesterol limitation, supporting the hypothesis that LET-767 acts on a sterol derivative. Furthermore, let-767 mutants exhibit defects in embryogenesis, female reproduction and molting. Although ecdysone is the major molting hormone in insects, there is as yet no evidence for ecdysone synthesis in C. elegans, suggesting that a different hormone is required for molting in C. elegans. Our results suggest that LET-767 modifies a sterol hormone that is required both for embryogenesis and for later ------------------- Key: 6205 Medline: Authors: Dolinski CM;Baldwin JG Title: Fine structure of the stoma of Bunonema sp. and Teratorhabditis palmarum (Nematoda) and its phylogenetic significance. Citation: Journal of Nematology 35: 244-251 2003 Type: ARTICLE Genes: Abstract: Fine structure of the stoma, including the cheilostom, gymnostom, and stegostom of Bunonema sp. and Teratorhabditis palmarum was compared with Caenorhabditis elegans to consider fine structural characters that may, be phylogenetically informative. The stegostom, enclosed by the anterior end of the pharynx, includes a triradiate lumen surrounded by radial cells (interradial or pairs of adradial cells) repeated in the dorsal and subventral sectors; in Rhabditina, typically the stegostom includes anteriorly two sets of epithelia] and posteriorly two sets of muscular radial cells. These muscle cells are anteriorly m1 and posteriorly m2. In Bunonema sp., unlike T. palmarum and C. elegans, the stegostom has a third set of interradial epithelial cells. In Bunonema sp., m1 is expressed by three interradial cells, whereas in T palmarum and C elegans m1 is three pairs of adradial muscle cells (i.e., six cells). I it all three taxa m2 is expressed as three pairs of adradial muscle cells. Posterior processes of adjacent adradial cells fuse, and closely apposed nuclei may present a figure-eight shape. However, in Bunonema the three interradial m I cells each have a long posterior process enclosing two separate round nuclei. In combination with additional characters, these diverse stoma features may prove phylogenetically informative. Specifically, the radial epithelia] cells of the stegostom appear to be a synapomorphy consistent with a bunonemid-diplogastrid-rhabditid clade, whereas a thickening in the dorsal sector of the stoma cuticle lining is interpreted as a synapomorphy supporting a ------------------- Key: 6206 Medline: Authors: Hartman P;Belmont P;Zuber S;Ishii N;Anderson J Title: Relationship between catalase and life span in recombinant inbred strains of Caenorhabditis elegans. Citation: Journal of Nematology 35: 314-319 2003 Type: ARTICLE Genes: Abstract: Johnson and Wood constructed recombinant inbred strains of Caenorhabditis elegans with life spans ranging from 10 to 31 days. Using these strains, we have demonstrated previously that hyperoxia and methyl viologen inhibited development at rates inversely correlated with life span. The growth rates of the short-lived recombinant inbred strains were more profoundly inhibited by oxidative stress than were those of the long-lived strains. Here we report a positive correlation between life span and catalase levels in these same strains. Specifically, when compared to short-lived strains at 10 days after fertilization, the long-lived strains possessed higher levels of total enzymatic catalase. Northern blots indicated a similar relationship between life span and clt-1mRNA (the cytosolic catalase). This suggests that at least some of the polygenes that influence life span are also responsible for regulating gene expression of catalase, an important defense component against oxidative stress. ------------------- Key: 6207 Medline: 14627270 Authors: Caldwell KN;Anderson GL;Williams PL;Beuchat LR Title: Attraction of a free-living nematode, Caenorhabditis elegans, to foodborne pathogenic bacteria and its potential as a vector of Salmonella Poona for preharvest contamination of cantaloupe. Citation: Journal of Food Protection 66: 1964-1971 2003 Type: ARTICLE Genes: Abstract: Caenorhabditis elegans was studied to determine the potential role of free-living microbivorous nematodes as vectors for preharvest contamination of fruits and vegetables with foodborne pathogens. The propensity of C. elegans to be attracted to seven strains of Escherichia coli O157:H7, eight serotypes of Salmonella, six strains of Listeria monocytogenes, and cantaloupe juice was investigated. Twenty to 30 adult worms were placed on the surface of K agar midway between a 24-h bacterial colony and 10 mul of uninoculated tryptic soy broth (TSB) or cantaloupe juice positioned 1.5 cm apart. The numbers of nematodes that migrated to the colony, to the TSB, and to the cantaloupe juice within 5, 10, 15, and 20 min at 21degreesC were determined, and then the plates were incubated at 37degreesC for up to 7 days to determine the ability of C. elegans to survive and reproduce in bacterial colonies. The nematode was attracted to colonies of all test pathogens and survived and reproduced within colonies for up to 7 days. C. elegans was not attracted to cantaloupe juice. The potential of C. elegans to serve as a vector for the transport of Salmonella Poona to cantaloupe rinds was investigated. Adult worms that had been immersed in a suspension of Salmonella Poona were deposited 1 or 3 cm below the surface of soil on which a piece of cantaloupe rind was placed. The rind was analyzed for the presence of Salmonella Poona after 1, 3, 7, and 10 days at 21degreesC. The presence of Salmonella Poona was evident more quickly on rinds positioned on soil beneath which C. elegans inoculated with Salmonella Poona was initially deposited than on rinds positioned on soil beneath which Salmonella Poona alone was deposited. The time required to detect Salmonella Poona on rinds was longer when the rind was placed 3 cm above the inoculum than when the rind was placed 1 cm above the inoculum. Free-living nematodes may play a role in the preharvest dispersal of incidental human pathogens in soil to the surfaces of raw fruits and vegetables in contact with soil during development and maturation, as evidenced by the behavior of C. elegans as a ------------------- Key: 6208 Medline: 12954633 Authors: Harding A;Hsu V;Kornfeld K;Hancock JF Title: Identification of residues and domains of Raf important for function in vivo and in vitro. Citation: Journal of Biological Chemistry 278: 45519-45527 2003 Type: ARTICLE Genes: lin-45 Abstract: Random mutagenesis and genetic screens for impaired Raf function in Caenorhabditis elegans were used to identify six loss-of-function alleles of lin-45 raf that result in a substitution of a single amino acid. The mutations were classified as weak, intermediate, and strong based on phenotypic severity. We engineered these mutations into the homologous residues of vertebrate Raf-1 and analyzed the mutant proteins for their underlying biochemical defects. Surprisingly, phenotype strength did not correlate with the catalytic activity of the mutant proteins. Amino acid substitutions Val-589 and Ser-619 severely compromised Raf kinase activity, yet these mutants displayed weak phenotypes in the genetic screen. Interestingly, this is because these mutant Raf proteins efficiently activate the MAPK (mitogen-activated protein kinase) cascade in living cells, a result that may inform the analysis of knockout mice. Equally intriguing was the observation that mutant proteins with non-functional Ras-binding domains, and thereby deficient in Ras-mediated membrane recruitment, displayed only intermediate strength phenotypes. This confirms that secondary mechanisms exist to couple Ras to Raf in vivo. The strongest phenotype in the genetic screens was displayed by a S508N mutation that again did not correlate with a significant loss of kinase activity or membrane recruitment by oncogenic Ras in biochemical assays. Ser-508 lies within the Raf-1 activation loop, and mutation of this residue in Raf-1 and the equivalent Ser-615 in B-Raf revealed that this residue regulates Raf binding to MEK. Further characterization revealed that in response to activation by epidermal growth factor, the Raf-S508N mutant protein displayed both reduced catalytic activity and aberrant activation kinetics: characteristics that may explain the C. elegans phenotype. ------------------- Key: 6209 Medline: 14597199 Authors: Kostic I;Li S;Roy R Title: cki-1 links cell division and cell fate acquisition in the C. elegans somatic gonad. Citation: Developmental Biology 263: 242-252 2003 Type: ARTICLE Genes: cdh-3 cki-1 glp-1 lag-2 lin-3 Abstract: The formation of a complex multicellular organism requires the precise specification of many diverse cell types at the correct time and position throughout development. This may be achieved by coordinating cell fate specification processes with progression through the cell cycle. Here, we show that the extra distal tip cells (DTCs) associated with the loss of cki-1, a Caenorhabditis elegans homologue of the cyclin-dependent kinase inhibitor p27, do not arise from duplications of pre-existing DTCs, but that they are formed from another cell type within the somatic gonad. Results from our laser microsurgery experiments suggest that the extra DTCs are caused by aberrant somatic gonadal precursor cell divisions in the absence of cki-1, resulting in abnormal daughter cell fates. cki-1(RNAi) animals also possess extra anchor cells and ectopic gonad arms with variable sheath cell numbers and positioning. In addition, cki-1 (RNAi) animals display an endomitotic oocyte (Emo) phenotype. Our results uncover a novel role of this CKI in cell fate acquisition, either by directly influencing specification, or through a more conventional role in appropriately linking cell cycle phase with this process. ------------------- Key: 6210 Medline: 14597206 Authors: Hapiak V;Hresko MC;Schriefer LA;Saiyasisongkhram K;Bercher M;Plenefisch J Title: mua-6, a gene required for tissue integrity in Caenorhabditis elegans, encodes a cytoplasmic intermediate filament. Citation: Developmental Biology 263: 330-342 2003 Type: ARTICLE Genes: ifa-2 mua-6 mnDf4 mnDf41 Abstract: Locomotion in Caenorhabditis elegans requires force transmission through a network of proteins linking the skeletal muscle, via an intervening basal lamina and epidermis (hypodermis), to the cuticle. Mutations in mua-6 result in hypodermal rupture, muscle detachment from the bodywall, and progressive paralysis. It is shown that mua-6 encodes the cytoplasmic intermediate filament (cIF) A2 protein and that a MUA-6/IFA-2::GFP fusion protein that rescues the presumptive mua-6 null allele localizes to hypodermal hemidesmosomes. This result is consistent with what is known about the function of cIFs in vertebrates. Although MUA-6/IFA-2 is expressed embryonically, and plays an essential postembryonic role in tissue integrity, it is not required for embryonic development of muscle-cuticle linkages nor for the localization of other cIFs or hem ides mosome-associated proteins in the embryo. Finally, the molecular lesion in the mua-6(rh85) allele suggests that the head domain of the MUA-6/IFA-2 is dispensable for its function. ------------------- Key: 6211 Medline: Authors: Morck C;Axang C;Pilon M Title: Erratum to "A genetic analysis of axon guidance in the C. elegans pharynx" Citation: Developmental Biology 263: 367-368 2003 Type: CORRECT Genes: efn-2 efn-3 smp-1 smp-2 Abstract: The publisher regrets that several corrections requested by the author were not made. ------------------- Key: 6212 Medline: 14645848 Authors: Wang X;Wu YC;Fadok VA;Lee MC;Gengyo-Ando K;Cheng LC;Ledwich D;Hsu PK;Chen JY;Chou BK;Henson P;Mitani S;Xue D Title: Cell corpse engulfment mediated by C. elegans phosphatidylserine receptor through CED-5 and CED-12. Citation: Science 302: 1563-1566 2003 Type: ARTICLE Genes: ced1 ced-2 ced-5 ced-6 ced-7 ced-10 ced-12 psr-1 Abstract: During apoptosis, phosphatidylserine, which is normally restricted to the inner lea. et of the plasma membrane, is exposed on the surface of apoptotic cells and has been suggested to act as an "eat-me" signal to trigger phagocytosis. It is unclear how phagocytes recognize phosphatidylserine. Recently, a putative phosphatidylserine receptor (PSR) was identified and proposed to mediate recognition of phosphatidylserine and phagocytosis. We report that psr-1, the Caenorhabditis elegans homolog of PSR, is important for cell corpse engulfment. In vitro PSR-1 binds preferentially phosphatidylserine or cells with exposed phosphatidylserine. In C. elegans, PSR-1 acts in the same cell corpse engulfment pathway mediated by intracellular signaling molecules CED-2 ( homologous to the human CrkII protein), CED-5 (DOCK180), CED-10 (Rac GTPase), and CED-12 (ELMO), possibly through direct interaction with CED-5 and CED-12. Our findings suggest that PSR-1 is likely an upstream receptor for the signaling pathway containing CED-2, CED-5, CED-10, and CED-12 proteins and plays an important role in recognizing phosphatidylserine during phagocytosis. ------------------- Key: 6213 Medline: 14622579 Authors: Schuske KR;Richmond JE:Matthies DS;Davis WS;Runz S;Rube DA;van der Bliek AM;Jorgensen EM Title: Endophilin is required for synaptic vesicle endocytosis by localizing synaptojanin. Citation: Neuron 40: 749-762 2003 Type: ARTICLE Genes: dyn-1 unc-26 unc-57 Abstract: Endophilin is a membrane-associated protein required for endocytosis of synaptic vesicles. Two models have been proposed for endophilin: that it alters lipid composition in order to shape membranes during endocytosis, or that it binds the polyphosphoinositide phosphatase synaptojanin and recruits this phosphatase to membranes. In this study, we demonstrate that the unc-57 gene encodes the Caenorhabditis elegans ortholog of endophilin A. We demonstrate that endophilin is required in C. elegans for synaptic vesicle recycling. Furthermore, the defects observed in endophilin mutants closely resemble those observed in synaptojanin mutants. The electrophysiological phenotype of endophilin and synaptojanin double mutants are virtually identical to the single mutants, demonstrating that endophilin and synaptojanin function in the same pathway. Finally, endophilin is required to stabilize expression of synaptojanin at the synapse. These data suggest that endophilin is an adaptor protein required to localize and stabilize synaptojanin at membranes during synaptic vesicle recycling. ------------------- Key: 6214 Medline: 12885961 Authors: Ganko EW;Bhattacharjee V;Schliekelman P;McDonald JF Title: Evidence for the contribution of LTR retrotransposons to C. elegans gene evolution. Citation: Molecular Biology and Evolution 20: 1925-1931 2003 Type: ARTICLE Genes: Abstract: LTR retrotransposons may be important contributors to host gene evolution because they contain regulatory and coding signals. In an effort to assess the possible contribution of LTR retrotransposons to C. elegans gene evolution, we searched upstream and downstream of LTR retrotransposon sequences for the presence of predicted genes. Sixty-three percent of LTR retrotransposon sequences (79/124) are located within 1 kb of a gene or within gene boundaries. Most gene-retrotransposon associations were located along the chromosome arms. Our results are consistent with the hypothesis that LTR retrotransposons have contributed to the structural and/or regulatory evolution of genes in C. elegans. ------------------- Key: 6215 Medline: 14600234 Authors: Joshua GWP;Karlyshev AV;Smith MP;Isherwood KE;Titball RW;Wren BW Title: A Caenorhabditis elegans model of Yersinia infection: biofilm formation on a biotic surface. Citation: Microbiology 149: 3221-3229 2003 Type: ARTICLE Genes: Abstract: To investigate Yersinia pathogenicity and the evolutionary divergence of the genus, the effect of pathogenic yersiniae on the model organism Caenorhabditis elegans was studied. Three strains of Yersinia pestis, including a strain lacking pMT1, caused blockage and death of C. elegans; one strain, lacking the haemin storage (hms) locus, caused no effect. Similarly, 15 strains of Yersinia enterocolitica caused no effect. Strains of Yersinia pseudotuberculosis showed different levels of pathogenicity. The majority of strains (76%) caused no discernible effect; 5% caused a weak infection, 9(.)5% an intermediate infection, and 9(.)5% a severe infection. There was no consistent relationship between serotype and severity of infection; nor was there any relationship between strains causing infection of C. elegans and those able to form a biofilm on an abiotic surface. Electron microscope and cytochemical examination of infected worms indicated that the infection phenotype is a result of biofilm formation on the head of the worm. Seven transposon mutants of Y. pseudotuberculosis strain YPIII pIB1 were completely or partially attenuated; mutated genes included genes encoding proteins involved in haemin storage and lipopolysaccharide biosynthesis. A screen of 15 defined C. elegans mutants identified four where mutation caused (complete) resistance to infection by Y. pseudotuberculosis YPIII pIB1. These mutants, srf-2, srf-3, srf-5 and the dauer pathway gene daf-1, also exhibit altered binding of lectins to the nematode surface. This suggests that biofilm formation on a biotic surface is an interactive process involving both bacterial and invertebrate control mechanisms. ------------------- Key: 6216 Medline: 14610052 Authors: O'Toole ET;McDonald K;Mantler J;McIntosh JR;Hyman AA;Muller-Reichert T Title: Morphologically distinct microtubule ends in the mitotic centrosome of Caenorhabditis elegans. Citation: Journal of Cell Biology 163: 451-456 2003 Type: ARTICLE Genes: Abstract: During mitosis, the connections of microtubules (MTs) to centrosomes and kinetochores are dynamic. From in vitro studies, it is known that the dynamic behavior of MTs is related to the structure of their ends, but we know little about the structure of MT ends in spindles. Here, we use high-voltage electron tomography to study the centrosome- and kinetochore-associated ends of spindle MTs in embryonic cells of the nematode, Caenorhabditis elegans. Centrosome-associated MT ends are either closed or open. Closed MT ends are more numerous and are uniformly distributed around the centrosome, but open ends are found preferentially on kinetochore-attached MTs. These results have structural implications for models of MT interactions with centrosomes. ------------------- Key: 6217 Medline: 13129931 Authors: Guo J;Lemire BD Title: The ubiquinone-binding site of the Saccharomyces cerevisiae succinate-ubiquinone oxidoreductase is a source of superoxide. Citation: Journal of Biological Chemistry 278: 47629-47635 2003 Type: ARTICLE Genes: mev-1 Abstract: The mitochondrial succinate dehydrogenase (SDH) is a tetrameric iron-sulfur flavoprotein of the Krebs cycle and of the respiratory chain. A number of mutations in human SDH genes are responsible for the development of paragangliomas, cancers of the head and neck region. The mev-1 mutation in the Caenorhabditis elegans gene encoding the homolog of the SDHC subunit results in premature aging and hypersensitivity to oxidative stress. It also increases the production of superoxide radicals by the enzyme. In this work, we used the yeast succinate dehydrogenase to investigate the molecular and catalytic effects of paraganglioma- and mev-1-like mutations. We mutated Pro-190 of the yeast Sdh2p subunit to Gln (P190Q) and recreated the C. elegans mev-1 mutation by converting Ser-94 in the Sdh3p subunit into a glutamate residue (S94E). The P190Q and S94E mutants have reduced succinate-ubiquinone oxidoreductase activities and are hypersensitive to oxygen and paraquat. Although the mutant enzymes have lower turnover numbers for ubiquinol reduction, larger fractions of the remaining activities are diverted toward superoxide production. The P190Q and S94E mutations are located near the proximal ubiquinone-binding site, suggesting that the superoxide radicals may originate from a ubisemiquinone intermediate formed at this site during the catalytic cycle. We suggest that certain mutations in SDH can make it a significant source of superoxide production in mitochondria, which may contribute directly to disease progression. Our data also challenge the dogma that superoxide production by SDH is a flavin-mediated event rather than a quinone-mediated one. ------------------- Key: 6218 Medline: 14622138 Authors: Sasagawa Y;Urano T;Kohara Y;Takahashi H;Higashitani A Title: Caenorhabditis elegans RBX1 is essential for meiosis, mitotic chromosomal condensation and segregation, and cytokinesis. Citation: Genes to Cell 8: 857-872 2003 Type: ARTICLE Genes: glc-7 gld-1 rbx-1 Abstract: Background: The RING-H2 finger protein RBX1 (ROC1/HRT1) is a common subunit of SKP1-CDC53/CUL1-F-box (SCF), other cullins and von Hippel-Lindau (VHL) tumour suppressor E3 ubiquitin ligase complexes. RBX1 protein sequences are highly conserved in various species, including yeasts, Drosophila melanogaster, mice and humans. In Saccharomyces cerevisiae, RBX1 is essential for the G1/S transition. Results: Caenorhabditis elegans RBX1 is strongly expressed in early embryos and in the gonad, including meiotic cells. Depletion of RBX1 by RNA-mediated interference (RNAi) caused pronounced defects in the first meiotic division. Several irregular phenotypes were identified in embryos that escaped from meiotic arrest: defects in mitotic chromosomal condensation and segregation, abnormal chromosome bridges, giant nuclei, abnormal cortical protrusion, multinucleate cells and defects in germ cell proliferation. Moreover, histone H3 phosphorylation at Ser(10) and Ser(28) was significantly reduced in these embryos. The histone H3 phosphorylation defect of embryos was rescued by the additional depletion of protein phosphatase 1 (GLC7alpha/beta) by RNAi. Conclusion: These results indicate that the RBX1 protein participates in diverse functions relevant to chromosome metabolism and ------------------- Key: 6219 Medline: 14630941 Authors: Kamikura DM;Cooper JA Title: Lipoprotein receptors and a disabled family cytoplasmic adaptor protein regulate EGL-17/FGF export in C. elegans. Citation: Genes & Development 17: 2798-2811 2003 Type: ARTICLE Genes: apm-1 apt-2 apt-4 apt-5 apt-6 apt-10 dab-1 egl-17 let-23 lrp-1 lrp-2 rme-2 unc-101 Abstract: Growth factors and morphogens need to be secreted to act on distant cells during development and in response to injury. Here, we report evidence that efficient export of a fibroblast growth factor (FGF), EGL-17, from the Caenorhabditis elegans developing vulva requires the lipoprotein receptor-related proteins Ce-LRP-1 and Ce-LRP-2 and a cytoplasmic adaptor protein, Ce-DAB-1 (Disabled). Lipoprotein receptors are transmembrane proteins best known for their roles in endocytosis. Ce-LRP-1 and Ce-LRP-2 possess a conserved intraluminal domain that can bind to EGL-17, as well as a cytosolic FXNPXY motif that can bind to Ce-DAB-1. Ce-DAB-1 contains signals that confer subcellular localization to Golgi-proximal vesicles. These results suggest a model in which Ce-DAB-1 coordinates selection of receptors and cargo, including EGL-17, for transport through the secretory pathway. ------------------- Key: 6220 Medline: 14604799 Authors: Astolfi P;Bellizzi D;Sgaramella V Title: Frequencey and coverage of trinucleotide repeats in eukaryotes. Citation: Gene 317: 117-125 2003 Type: ARTICLE Genes: Abstract: In the aim to assess whether the tri-repeat shortage reported in vertebrates affects specific motifs, such as those causing neuromuscular diseases in man, we detected approximate di-, tri- and tetra-repeats (STR) longer than 25 bases in human chromosomes 21 and 22, and in some model organisms (M. musculus, D. melanogaster, C elegans, A. thaliana and S. cerevisiae). We found that overall STR are more represented in mouse and in man than in the other organisms. However, tri-repeats are less represented than di- and tetra- in man and mouse, but show intermediate values between di- and tetra- in the other organisms. In man, ACG shows the lowest both frequency and coverage, ATC the highest coverage and AAT the highest frequency. In general, coverage and frequency of tri-repeats are linearly related, except for ACC, ATC, AAG, AGG motifs in man and AAG, AGG in mouse, which exhibit unexpectedly long repeats. Often their copy numbers exceed that found responsible for the dynamic mutations, set at around 40. The shortage in frequency and coverage of tri- vs. di- and tetra-repeats observed in man and mouse can be ascribed to a subset of the remaining tri-repeat motifs, but among them those recognized as dynamically mutable (AAG, AGC and CCG) are not the least represented. Possible constraints in tri-repeat expansion seem to be structural and conserved along the evolutionary scale: a motif-specific relaxation of the relevant controls may be responsible for the occasional expansions found in mouse and man. ------------------- Key: 6221 Medline: Authors: Chen C;Dewaele S;Braeckman B;Desmyter L;Verstraelen J;Borgonie G;Vanfleteren J;Contreras R Title: A high-throughput screening system for genes extending life-span. Citation: Experimental Gerontology 38: 1051-1063 2003 Type: ARTICLE Genes: Abstract: We developed a high-throughput functional genomic screening system that allows identification of genes prolonging life-span in the baker's yeast Saccharomyces cerevisiae. The method is based on isolating yeast mother cells with extended number of cell divisions as indicated by the increased number of bud scars on their surface. Fluorescently labelled Wheat Germ Agglutinin was used for specific staining of chitin, a major component of bud scars. Screening of a human HepG2 cDNA expression library in yeast resulted in the isolation of 12 yeast transformants with a potentially prolonged life-span. The transgene in one of the lines was identified as ferritin light chain (FTL) and studied in more detail. Yeast cells containing FTL showed an enhanced iron and H2O2 resistance, a reduced cell death rate and an increased number of cell divisions. Overexpression of FTL in the nematode Caenorhabditis elegans resulted in a life-span increase of 8% confirming our yeast observations in a multicellular organism. Our data demonstrate that this method permits a fast screening of libraries for hunting genes involved in ------------------- Key: 6222 Medline: 14629117 Authors: Izeta A;Malcomber S;O'Rourke D;Hodgkin J;O'Hare P Title: A C-terminal targeting signal controls differential compartmentalisation of Caenorhabditis elegans host cell factor (HCF) to the nucleus or mitochondria. Citation: European Journal of Cell Biology 82: 495-504 2003 Type: ARTICLE Genes: Abstract: HCF-1 (host cell factor 1) is a human protein originally identified as a component of the VP16 transcription complex. A related protein HCF-2 is also present in humans and while at least HCF-1 appears to be required for normal cell growth there is currently little information on the precise cellular role(s) of these proteins. C. elegans contains a single HCF orthologue (CeHCF) which is very closely related to human HCF-2. To contribute to an understanding of the activities of these proteins here we analyse the subcellular localisation of the CeHCF protein in live transgenic worms and in mammalian cells. We constructed a green fluorescent protein (GFP) fusion of CeHCF and studied localisation after ectopic expression under the control of a heat shock protein promoter. The CeHCF-GFP protein accumulated in the cell nuclei at every stage of development and in a wide variety of cell types. Nuclear accumulation with nucleolar sparing was evident on the larvae and adult stages, but not earlier in development in which the protein accumulated diffusely in the nucleoplasm. Surprisingly the same protein accumulated in the mitochondria of a stable HeLa cell lines suggesting a differential localisation of CeHCF in mammalian cells. Furthermore, when overexpressed in transient transfection the CeHCF accumulated in both nuclear and mitochondrial compartments. We have refined the targeting determinants of CeHCF to the last 23 amino acids at the extreme C-terminus and show that they contain interdigitated amino acids involved in both nuclear and mitochondrial targeting. This novel targeting signal is sufficient to redirect HCF-2 into mitochondria. It can also be transferred to an unrelated protein, resulting in its targeting to both the ------------------- Key: 6223 Medline: 14602075 Authors: Schaner CE;Deshpande G;Schedl PD;Kelly WG Title: A conserved chromatin architecture marks and maintains the restricted germ cell lineage in worms and flies. Citation: Developmental Cell 5: 747-757 2003 Type: ARTICLE Genes: emb-4 hda-1 let-418 mep-1 mes-2 mes-3 mes-4 mes-6 mex-1 nos-1 nos-2 pie-1 Abstract: In C. elegans, mRNA production is initially repressed in the embryonic germline by a protein unique to C. elegans germ cells, PIE-1. PIE-1 is degraded upon the birth of the germ cell precursors, Z2 and Z3. We have identified a chromatin-based mechanism that succeeds PIE-1 repression in these cells. A subset of nucleosomal histone modifications, methylated lysine 4 on histone H3 (H3meK4) and acetylated lysine 8 on histone H4 (H4acetylK8), are globally lost and the DNA appears more condensed. This coincides with PIE-1 degradation and requires that germline identity is not disrupted. Drosophila pole cell chromatin also lacks H3meK4, indicating that a unique chromatin architecture is a conserved feature of embryonic germ cells. Regulation of the germline-specific chromatin architecture requires functional nanos activity in both organisms. These results indicate that genome-wide repression via a nanos-regulated, germ cell-specific chromatin organization is a conserved feature of germline maintenance during embryogenesis. ------------------- Key: 6224 Medline: 14614844 Authors: Goldstein B Title: Asymmetric division: AGS proteins position the spindle. Citation: Current Biology 13: R879-R880 2003 Type: REVIEW Genes: Abstract: Many cells divide asymmetrically by shifting their division machinery toward a specific region of the cell cortex, but little is known about how this occurs. Three recent papers have implicated activators of heterotrimeric G protein signaling in this process in Caenorhabditis elegans. ------------------- Key: 6225 Medline: Authors: Woo JS;Jung JS;Ha NC;Shin J;Kim KH;Lee W;Oh BH Title: Unique structural features of a BCL-2 family protein CED-9 and biophysical characterization of CED-9/EGL-1 interactions. Citation: Cell Death and Differentiation 10: 1310-1319 2003 Type: ARTICLE Genes: ced-9 egl-1 Abstract: The interactions between B-cell lymphoma 2 (BCL-2) family members are known to be mediated through the binding of the BH3 domain of a proapoptotic member to the BH3-binding groove of an antiapoptotic member. We determined the crystal structure of antiapoptotic CED-9, which reveals a unique C-terminal helix altering the common BH3-binding region. A coexpression system to produce CED-9 in complex with proapoptotic EGL-1 enabled us to show that the binding of EGL-1 to CED-9 is extremely stable, raising the melting temperature (T-M) of CED-9 by 25degreesC, and that the binding surface of CED-9 extends beyond the BH3-binding region and reaches the BH4 domain. Consistently, the T-M and a H-1-N-15 correlation NMR spectrum of CED-9 in complex with EGL-1 are drastically different from those of CED-9 in complex with the EGL-1 BH3 peptide. The data suggest that the recognition between other BCL-2 family members may also involve much wider protein surfaces than is previously thought. ------------------- Key: 6226 Medline: 14622602 Authors: Libina N;Berman JR;Kenyon C Title: Tissue-specific activities of C. elegans DAF-16 in the regulation of lifespan. Citation: Cell 115: 489-502 2003 Type: ARTICLE Genes: daf-2 daf-16 ges-1 mes-1 myo-3 sod-3 unc-119 Abstract: In C. elegans, the transcription factor DAF-16 promotes longevity in response to reduced insulin/IGF-1 signaling or germline ablation. In this study, we have asked how different tissues interact to specify the life-span of the animal. We find that several tissues act as signaling centers. In particular, DAF-16 activity in the intestine, which is also the animal's adipose tissue, completely restores the longevity of daf-16(-) germline-deficient animals, and increases the lifespans of daf-16(-) insulin/IGF-1-pathway mutants substantially. Our findings indicate that DAF-16 may control two types of downstream signals: DAF-16 activity in signaling cells upregulates DAF-16 in specific responding tissues, possibly via regulation of insulin-like peptides, and also evokes DAF-16-independent responses. We suggest that this network of tissue interactions and feedback regulation allows the tissues to equilibrate and fine-tune their expression of downstream genes, which, in turn, coordinates their rates of aging within the animal. ------------------- Key: 6227 Medline: 14618537 Authors: Friedenberg NA Title: Determinism in a transient assemblage: the roles of dispersal and local competition. Citation: American Naturalist 162: 586-596 2003 Type: ARTICLE Genes: Abstract: Both dispersal and local competitive ability may determine the outcome of competition among species that cannot coexist locally. I develop a spatially implicit model of two-species competition at a small spatial scale. The model predicts the relative fitness of two competitors based on local reproductive rates and regional dispersal rates in the context of the number, size, and extinction probability of habitat patches in the landscape. I test the predictions of this model experimentally using two genotypes of the bacteriophagous soil nematode Caenorhabditis elegans in patchy microcosms. One genotype has higher fecundity while the other is a better disperser. With such a fecundity-dispersal trade-off between competitors, the model predicts that relative fitness will be affected most by local population size when patches do not go extinct and by the number of patches when there is a high probability of patch extinction. The microcosm experiments support the model predictions. Both approaches suggest that competitive dominance in a patchily distributed transient assemblage will depend upon the architecture and predictability of the environment. These mechanisms, operating at a small scale with high spatial admixture, may be embedded in a larger metacommunity process. ------------------- Key: 6228 Medline: Authors: Nagai K;Sunazuka T;Shiomi K;Harder A;Turberg A;Omura S Title: Synthesis and biological activities of novel 4"-alkylidene avermectin derivatives. Citation: Bioorganic & Medicinal Chemistry Letters 13: 3943-3946 2003 Type: ARTICLE Genes: Abstract: Horner-Emmons reaction of 4"-dehydro-5-O-TBDMS-avermectin B-1a with a variety of phosphorus ylides using LHMDS gave novel 4"-alkylidene avermectin derivatives in high yields. Further modifications led to derivatives bearing diverse functional groups. The new avermectin derivatives showed potent growth inhibitory activity against Artemia salina and Caenorhabditis elegans. ------------------- Key: 6229 Medline: 12944392 Authors: Griffitts JS;Huffman DL;Whitacre JL;Barrows BD;Marroquin LD;Muller R;Brown JR;Hennet T;Esko JD;Aroian RV Title: Resistance to a bacterial toxin is mediated by removal of a conserved glycosylation pathway required for toxin-host interactions. Citation: Journal of Biological Chemistry 278: 45594-45602 2003 Type: ARTICLE Genes: bre-2 bre-3 bre-4 bre-5 Abstract: Crystal (Cry) proteins made by the bacterium Bacillus thuringiensis are pore-forming toxins that specifically target insects and nematodes and are used around the world to kill insect pests. To better understand how pore-forming toxins interact with their host, we have screened for Caenorhabditis elegans mutants that resist Cry protein intoxication. We find that Cry toxin resistance involves the loss of two glycosyltransferase genes, bre-2 and bre-4. These glycosyltransferases function in the intestine to confer susceptibility to toxin. Furthermore, they are required for the interaction of active toxin with intestinal cells, suggesting they make an oligosaccharide receptor for toxin. Similarly, the bre-3 resistance gene is also required for toxin interaction with intestinal cells. Cloning of the bre-3 gene indicates it is the C. elegans homologue of the Drosophila egghead (egh) gene. This identification is striking given that the previously identified bre-5 has homology to Drosophila brainiac (brn) and that egh-brn likely function as consecutive glycosyltransferases in Drosophila epithelial cells. We find that, like in Drosophila, bre-3 and bre-5 act in a single pathway in C. elegans. bre-2 and bre-4 are also part of this pathway, thereby extending it. Consistent with its homology to brn, we demonstrate that C. elegans bre-5 rescues the Drosophila brn mutant and that BRE-5 encodes the dominant UDP-GlcNAc:Man GlcNAc transferase activity in C. elegans. Resistance to Cry toxins has uncovered a four component glycosylation pathway that is functionally conserved between nematodes and insects and that provides the basis of the dominant mechanism of resistance in C. ------------------- Key: 6230 Medline: 14580264 Authors: Szewczyk N;Kozak E;Conley CA Title: Chemically defiend medium and Caenorhabditis elegans. Citation: BMC Biotechnology 3: - 2003 Type: ARTICLE Genes: Abstract: Background: C. elegans has been established as a powerful genetic system. Use of a chemically defined medium (C. elegans Maintenance Medium (CeMM)) now allows standardization and systematic manipulation of the nutrients that animals receive. Liquid cultivation allows automated culturing and experimentation and should be of use in large-scale growth and screening of animals. Results: We find that CeMM is versatile and culturing is simple. CeMM can be used in a solid or liquid state, it can be stored unused for at least a year, unattended actively growing cultures may be maintained longer than with standard techniques, and standard C. elegans protocols work well with animals grown in defined medium. We also find that there are caveats to using defined medium. Animals in defined medium grow more slowly than on standard medium, appear to display adaptation to the defined medium, and display altered growth rates as they change the composition of the defined medium. Conclusions: As was suggested with the introduction of C. elegans as a potential genetic system, use of defined medium with C. elegans should prove a powerful tool. ------------------- Key: 6231 Medline: 14657490 Authors: Tonkin LA;Bass BL Title: Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Citation: Science 302: 1725- 2003 Type: ARTICLE Genes: adr-1 adr-2 rde-1 rde-4 Abstract: Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine (A) to inosine (I) within double-stranded RNA (dsRNA). ADARs are found in metazoa where they are highly expressed in neuronal tissues. Drosophila melanogaster and Caenorhabditis elegans strains lacking all ADAR activity are viable but exhibit behavioral defects, whereas mice lacking ADARs die embryonically or shortly after birth. ------------------- Key: 6232 Medline: 14657502 Authors: Shibata Y;Branicky R;Landaverde IO;Hekimi S Title: Redox regulation of germline and vulval development in Caenorhabditis elegans. Citation: Science 302: 1779-1782 2003 Type: ARTICLE Genes: ark-1 clk-1 dsc-4 itr-1 let-60 lin-1 sid-1 sod-1 sod-2 sod-3 sod-4 vit-2 vit-3 vit-4 vit-5 vit-6 Abstract: In vitro studies have indicated that reactive oxygen species (ROS) and the oxidation of signaling molecules are important mediators of signal transduction. We have identified two pathways by which the altered redox chemistry of the clk-1 mutants of Caenorhabditis elegans acts in vivo on germline development. One pathway depends on the oxidation of an analog of vertebrate low density lipoprotein (LDL) and acts on the germline through the Ack-related tyrosine kinase (ARK-1) kinase and inositol trisphosphate (IP3) signaling. The other pathway is the oncogenic ras signaling pathway, whose action on germline as well as vulval development appears to be modulated by ------------------- Key: 6233 Medline: Authors: Hu JY;Fan Y;Lin YH;Zhang HB;Ong SL;Dong N;Xu JL;Ng WJ;Zhang LH Title: Microbial diversity and prevalence of virulent pathogens in biofilms developed in a water reclamation system. Citation: Research in Microbiology 154: 623-629 2003 Type: ARTICLE Genes: Abstract: Bacterial biofilm is a common phenomenon in both natural and engineered systems which often becomes a source of contamination and microbially influenced corrosion. It is thought that formation of biofilm in the monoculture of several bacterial species is regulated by acylhomoserine lactone (AHL) quorum-sensing signals. In this study, we investigated the microbial diversity and existence of AHL-producing and AHL-degrading bacterial species in the biofilm samples from a water reclamation system located in a tropical environment. 16S ribosomal DNA sequencing analysis indicated the presence of at least 11 bacterial species, including the frequently encountered bacterial pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae, and several rare pathogens. We showed that only two groups of isolates, belonging to P. aertuginosa and Enterobacter agglomerans, produced AHL signals. We also found that three bacterial isolates, i.e., Agrobacterium tumefaciens XJOL Bacillus cereus XJO8, and Ralstonia sp. XJ12, expressed AHL degradation enzymes. Furthermore, we showed that P. aeruginosa isolate HL43 was virulent against animal model Caenorhabditis elegans and released 2-6-fold more pyocyanin cytotoxin than P auruginosa strains PA01 and PA14, the two commonly used laboratory strains. These data indicate the complexity and importance of biofilm research in water reclamation. ------------------- Key: 6234 Medline: 14612577 Authors: Santi CM;Yuan A;Fawcett G;Wang ZW;Butler A;Nonet ML;Wei A;Rojas P;Salkoff L Title: Dissection of K+ currents in Caenorhabditis elegans muscle cells by genetics and RNA interference. Citation: Proceedings of the National Academy of Sciences USA 100: 14391-14396 2003 Type: ARTICLE Genes: slo-2 Abstract: GFP-promoter experiments have previously shown that at least nine genes encoding potassium channel subunits are expressed in Caenorhabditis elegans muscle. By using genetic, RNA interference, and physiological techniques we revealed the molecular identity of the major components of the outward K+ currents in body wall muscle cells in culture. We found that under physiological conditions, outward current is dominated by the products of only two genes, Shaker (Kv1) and Shal (Kv4), both expressing voltage-dependent potassium channels. Other channels may be held in reserve to respond to particular circumstances. Because GFP-promoter experiments indicated that slo-2 expression is prominent, we created a deletion mutant to identify the SLO-2 current in vivo. In both whole-cell and single-channel modes, in vivo SLO-2 channels were active only when intracellular Ca2+ and Cl- were raised above normal physiological conditions, as occurs during hypoxia. Under such conditions, SLO-2 is the largest outward current, contributing up to 87% of the total current. Other channels are present in muscle, but our results suggest that they are unlikely to contribute a large outward component under physiological conditions. However, they, too, may contribute currents conditional on other factors. Hence, the picture that emerges is of a complex membrane with a small number of household conductances functioning under normal circumstances, but with additional conductances that are activated during unusual ------------------- Key: 6235 Medline: 14636565 Authors: Shi Y;Blackwell TK Title: A two-tiered transcription regulation mechanism that protects germ cell identity. Citation: Molecular Cell 12: 1062-1064 2003 Type: REVIEW Genes: pie-1 nos-1 nos-2 Abstract: In the November issue of Developmental Cell, Schaner and colleagues (2003) describe remarkable versatility in how the embryonic germ lineage blocks differentiation: in early C. elegans germ cell precursors transcription is silenced but chromatin remains open, and then after lineage restriction a conserved inhibitory chromatin architecture ------------------- Key: 6236 Medline: 14551256 Authors: Roberts B;Clucas C;Johnstone IL Title: Loss of SEC-23 in Caenorhabditis elegans causes defects in oogenesis, morphogenesis, and extracellular matrix secretion. Citation: Molecular Biology of the Cell 14: 4414-4426 2003 Type: ARTICLE Genes: col-12 dpy-7 emo-1 glp-1 rme-2 sec-23 Abstract: SEC-23 is a component of coat protein complex II (COPII)-coated vesicles involved in the endoplasmic reticulum-to-Golgi transport pathway of eukaryotes. During postembryonic life, Caenorhabditis elegans is surrounded by a collagenous exoskeleton termed the cuticle. From a screen for mutants defective in cuticle secretion, we identified and characterized a sec-23 mutant of C. elegans. By sequence homology, C. elegans has only the single sec-23 gene described herein. In addition to the cuticle secretion defect, mutants fail to complete embryonic morphogenesis. However, they progress through the earlier stages of embryogenesis, including gastrulation, and achieve substantial morphogenesis before death. We demonstrated a maternal component of SEC-23 function sufficient for progression through the earlier stages of embryogenesis and explaining the limited phenotype of the zygotic mutant. By RNA-mediated interference, we investigated the effects of perturbing COPII function during various postembryonic stages. During larval stages, major defects in cuticle synthesis and molting were observed. In the adult hermaphrodite, reduction of SEC-23 function by RNA-mediated interference caused a rapid onset of sterility, with defects in oogenesis including early maturation of the germline nuclei, probably a result of the observed loss of the GLP-1 receptor from the membrane surfaces adjacent to the developing germline nuclei. ------------------- Key: 6237 Medline: 12937270 Authors: Wright AJ;Hunter CP Title: Mutations in a beta-tubulin disrupt spindle orientation and microtubule dynamics in the early Caenorhabditis elegans embryo. Citation: Molecular Biology of the Cell 14: 4512-4525 2003 Type: ARTICLE Genes: tba-1 tba-2 tbb-1 tbb-2 nDf12 sDf121 sDf130 Abstract: The early Caenorhabditis elegans embryo contains abundant transcripts for two alpha- and two beta-tubulins, raising the question of whether each isoform performs specialized functions or simply contributes to total tubulin levels. Our identification of two recessive, complementing alleles of a beta-tubulin that disrupt nuclear-centrosome centration and rotation in the early embryo originally suggested that this tubulin, tbb-2, has specialized functions. However, embryos from tbb-2 deletion worms do not have defects in nuclear-centrosome centration and rotation suggesting that the complementing alleles are not null mutations. Both complementing alleles have distinct effects on microtubule dynamics and show allele-specific interactions with the two embryonically expressed alpha-tubulins: One of the alleles causes microtubules to be cold stable and resistant to the microtubule-depolymerizing drug benomyl, whereas the other causes cell cycle-specific defects in microtubule polymerization. Gene-specific RNA interference targeting all four embryonically expressed tubulin genes singly and in all double combinations showed that the tubulin isoforms in the early embryo are largely functionally redundant with the exception of tbb-2. tbb-2 is required for centrosome stabilization during anaphase of the first cell division, suggesting that tbb-2 may be specialized for interactions ------------------- Key: 6238 Medline: 14615205 Authors: Ruiz-Diez B;Sanchez P;Baquero F;Martinez JL;Navas A Title: Differential interactions within the Caenorhabditis elegans-Pseudomonas aeruginosa pathogenesis model. Citation: Journal of Theoretical Biology 225: 469-476 2003 Type: ARTICLE Genes: Abstract: A pathogenesis model based on the interaction between Caenorhabditis elegans and bacterial opportunistic pathogens has recently been developed. In the case of Pseudomonas aeruginosa, the model is based on three different modes of nematode killing (fast killing, slow killing and lethal paralysis) by virulent bacteria that has been incubated in different nutrient media. Using parametric statistics and Probit analysis, we test the reliability of the three different killing systems with respect to bacterial virulence. To accomplish this, we use three P. aeruginosa strains, each with a different level of virulence and one strain of non-virulent Escherichia coli. Probit function proved to be effective in quantifying the virulence of P. aeruginosa. The results of the killing curve analysis using the Probit function demonstrates that the slow-killing test is the most reliable method for quantifying virulence using the C elegans model of bacterial pathogenesis. Although the greatest virulence differences are observed after long periods of incubation, the Probit analysis clearly shows that the death kinetics of C elegans depend on the first hours of nematode/bacteria interaction. In contrast, fast killing seems to be non-specific, at least under our experimental conditions, since the killing rates of virulent P. aeruginosa and non-virulent E coli strains were indistinguishable. ------------------- Key: 6239 Medline: 14638858 Authors: Al-Bassam J;Cui Y;Klopfenstein D;Carragher BO;Vale RD;Milligan RA Title: Distinct conformations of the kinesin Unc104 neck regulate a monomer to dimer motor transition. Citation: Journal of Cell Biology 163: 743-753 2003 Type: ARTICLE Genes: unc-104 Abstract: Caenhorhabditis elegans Unc104 kinesin transports synaptic vesicles at rapid velocities. Unc104 is primarily monomeric in solution, but recent motility studies suggest that it may dimerize when concentrated on membranes. Using cryo-electron microscopy, we observe two conformations of microtubule-bound Unc104: a monomeric state in which the two neck helices form an intramolecular, parallel coiled coil; and a dimeric state in which the neck helices form an intermolecular coiled coil. The intramolecular folded conformation is abolished by deletion of a flexible hinge separating the neck helices, indicating that it acts as a spacer to accommodate the parallel coiled-coil configuration. The neck hinge deletion mutation does not alter motor velocity in vitro but produces a severe uncoordinated phenotype in transgenic C elegans, suggesting that the folded conformation plays an important role in motor regulation. We suggest that the Unc104 neck regulates motility by switching from a self-folded, repressed state to a dimerized conformation that can support fast processive movement. ------------------- Key: 6240 Medline: 14517217 Authors: Burgess J;Hihi AK;Benard CY;Branicky R;Hekimi S Title: Molecular mechanism of maternal rescue in the clk-1 mutants of Caenorhabditis elegans. Citation: Journal of Biological Chemistry 278: 49555-49562 2003 Type: ARTICLE Genes: clk-1 daf-2 Abstract: The clk-1 mutants of Caenorhabditis elegans display an average slowing down of physiological rates, including those of development, various behaviors, and aging. clk-1 encodes a hydroxylase involved in the biosynthesis of the redox-active lipid ubiquinone (co-enzyme Q), and in clk-1 mutants, ubiquinone is replaced by its biosynthetic precursor demethoxyubiquinone. Surprisingly, homozygous clk-1 mutants display a wild-type phenotype when issued from a heterozygous mother. Here, we show that this maternal effect is the result of the persistence of small amounts of maternally derived CLK-1 protein and that maternal CLK-1 is sufficient for the synthesis of considerable amounts of ubiquinone during development. However, gradual depletion of CLK-1 and ubiquinone, and expression of the mutant phenotype, can be produced experimentally by developmental arrest. We also show that the very long lifespan observed in daf-2 clk-1 double mutants is not abolished by the maternal effect. This suggests that, like developmental arrest, the increased lifespan conferred by daf-2 allows for depletion of maternal CLK-1, resulting in the expression of the synergism between clk-1 and daf-2. Thus, increased adult longevity can be uncoupled from the early mutant phenotypes, indicating that it is possible to obtain an increased adult lifespan from the late inactivation of ------------------- Key: 6241 Medline: 14623111 Authors: Im SH;Lee J Title: Identification of HMG-5 as a double-stranded telomeric DNA-binding protein in the nematode Caenorhabditis elegans. Citation: FEBS Letters 554: 455-461 2003 Type: ARTICLE Genes: ceh-37 hmg-5 Abstract: Many protein components of telomeres, the multifunctional DNA-protein complexes at the ends of eukaryotic chromosomes, have been identified in diverse species ranging from yeast to humans. In Caenorhabditis elegans, CEH-37 has been identified by a yeast one hybrid screen to be a double-stranded telomere-binding protein. However, the role of CEH-37 in telomere function is unclear because a deletion mutation in this gene does not cause severe telomere defects. This observation raises the possibility of the presence of genetic redundancy. To identify additional double-stranded telomere-binding proteins in C. elegans, we used a different approach, namely, a proteomic approach. Affinity chromatography followed by Finnigan LCQ ion trap mass spectrometer analysis allowed us to identify several candidate proteins. We further characterized one of these, HMG-5, which is encoded by F45E4.9. HMG-5 bound to double-stranded telomere in vitro as shown by competition assays. At least two telomeric DNA repeats were needed for this binding. HMG-5 was expressed in the nuclei of the oocytes and all embryonic cells, but not in the hatched larvae or adults. HMG-5 mainly localized to the chromosomal ends, indicating that HMG-5 also binds to telomeres in vivo. These observations suggest that HMG-5 may participate, together with CEH-37, in early embryogenesis by acting at the telomeres. ------------------- Key: 6242 Medline: 14659008 Authors: Gupta BP;Sternberg PW Title: The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans. Citation: Genome Biology 4: 16-19 2003 Type: ARTICLE Genes: Abstract: The publication of the draft genome sequence of Caenorhabditis briggsae improves the annotation of the genome of its close relative Caenorhabditis elegans and will facilitate comparative genomics and the study of the evolutionary changes during development. ------------------- Key: 6243 Medline: Authors: Tominaga N;Kohra S;Iguchi T;Arizono K Title: A multi-generation sublethal assay of phenols using the nematode Caenorhabditis elegans. Citation: Journal of Health Science 49: 459-463 2003 Type: ARTICLE Genes: Abstract: ------------------- Key: 6244 Medline: Authors: Page AP;Winter AD Title: Enzymes involved in the biogenesis of the nematode cuticle. Citation: Advances in Parasitology 53: 85-148 2003 Type: REVIEW Genes: bli-1 bli-2 bli-4 col-12 col-13 col-19 cut-1 cut-2 cyp-9 dpy-2 dpy-3 dpy-6 dpy-7 dpy-8 dpy-10 dpy-11 dpy-13 dpy-17 dpy-18 kpc-4 let-268 lin-29 lon-3 lrp-1 nhr-23 nhr-25 nhr-77 nhr-81 nhr-82 pdi-1 pdi-2 pdi-3 phy-1 phy-2 phy-3 phy-4 rol-6 rol-8 sqt-1 sqt-3 Abstract: Nematodes include species that are significant parasites of man, his domestic animals and crops, and cause chronic debilitating diseases in the developing world; such as lymphatic filariasis and river blindness caused by filarial species. Around one third of the World's population harbour parasitic nematodes; no vaccines exist for prevention of infection, limited effective drugs are available and drug resistance is an ever-increasing problem. A critical structure of the nematode is the protective cuticle, a collagen-rich extracellular matrix (ECM) that forms the exoskeleton, and is critical for viability. This resilient structure is synthesized sequentially five times during nematode development and offer protection from the environment, including the hosts' immune response. The detailed characterization of this complex structure; its components, and the means by which they are synthesized, modified, processed and assembled will identify targets that may be exploited in the future control of parasitic nematodes. This review will focus on the nematode cuticle. This structure is predominantly composed of collagens, a class of proteins that are modified by a range of co- and post-translational modifications prior to assembly into higher order complexes or ECMs. The collagens and their associated enzymes have been comprehensively characterized in vertebrate systems and some of these studies will be addressed in this review. Conversely, the biosynthesis of this class of essential structural proteins has not been studied in such detail in the nematodes. As with all morphogenetic, functional and developmental studies in the Nematoda phylum, the free-living species Caenorhabditis elegans has proven to be invaluable in the characterization of the cuticle and the cuticle collagen gene family, and is now proving to be an excellent model in the study of cuticle collagen biosynthetic enzymes. This model system will be the main ------------------- Key: 6245 Medline: Authors: Powell-Coffman JA Title: bHLH-PAS proteins in C. elegans. Citation: PAS Proteins: Regulators and Sensor of Development and Physiology. Kluwer Academic Publisher, Norwell. : 51-68 Type: REVIEW Genes: aha-1 ahr-1 daf-2 egl-9 hif-1 vhl-1 Abstract: During development and homeostasis, individual cells must divide, differentiate, migrate, adapt to the environment, or die at the appropriate times and places. A key to deciphering the molecular mechanisms by which cells make these decisions is to characterize the regulation and function of the proteins that regulate important changes in gene expression. The family of transcription factors that contain basic-helix-loop-helix and PAS motifs has been shown to control many critical developmental events and to mediate responses to certain environmental stimuli. For example, bHLH-PAS proteins play central roles in the development of specific neural tissues and vasculature, and they are core components of the molecular clock that govern circadian rhythms. bHLH-PAS proteins are also integral to the pathways that sense and respond to hypoxia (low oxygen) and certain xenobiotics (1). Phylogenetic analyses suggest that bHLH-PAS genes arose early in animal development, and in some cases, the functions of individual genes are largely conserved across phyla. This review describes the bHLH-PAS gene family in a genetic model organism, the nematode Caenorhabditis elegans. ------------------- Key: 6246 Medline: 14560955 Authors: Long X;Muller F;Avruch J Title: TOR action in mammalian cells and in Caenorhabditis Citation: Current Trends in Microbiology 279: 115-138 2003 Type: REVIEW Genes: Abstract: The p70 S6 kinase (p70 S6K) was the first signaling element in mammalian cells shown to be inhibited by rapamycin. The activity of the p70 S6K in mammalian cell is upregulated by extracellular amino acids (especially leucine) and by signals from receptor tyrosine kinases (RTKs), primarily through activation of the type 1A PI-3 kinase. The amino acid-/rapamycin-sensitive input and the PI-3 kinase input are co-dominant but largely independent, in that deletion of the amino-terminal and carboxy-terminal noncatalytic sequences flanking the p70 S6K catalytic domain renders the kinase insensitive to inhibition by both rapamycin and by withdrawal of amino acids, whereas this p70 S6K mutant remains responsive to activation by RTKs and to inhibition by wortmannin. At a molecular level, this dual control of p70 S6K activity is attributable to phosphorylation of the two p70 S6K sites: The Ptd Ins 3,4,5P(3)-dependent kinase1 (PDK1) phosphorylates p70 S6K at a Thr on the activation loop, whereas mTOR phosphorylates a Thr located in a hydrophobic motif carboxyterminal to the catalytic domain. Together these two phosphorylations engender a strong, positively cooperative activation of p70 S6K, so that each is indispensable for physiologic regulation. Like RTKs, the p70 S6K appears early in metazoan evolution and comes to represent an important site at which the more ancient, nutrient-responsive TOR pathway converges with the RTK/PI-3 kinase pathway in the control of cell growth. Dual regulation of p70 S6K is seen in Drosophila; however, this convergence is not yet evident in Caenorhabditis elegans, wherein nutrient activation of the insulin receptor (InsR) pathway negatively regulates dauer development and longevity, whereas the TOR pathway regulates overall mRNA translation through effectors distinct from p70 S6K, as in yeast. The C. elegans TOR and InsR pathways show none of the cross- or convergent regulation seen in mammalian cells. The nature of the elements that couple nutrient sufficiency to TOR activity remain to be discovered, and the mechanisms by which RTKs influence TOR activity in mammalian cells require further study. One pathway for RTK control involves the tuberous sclerosis complex, which is absent in C. elegans, but of major importance in Drosophila ------------------- Key: 6247 Medline: 12954713 Authors: Yu H;Pretot RF;Burglin TR;Sternberg PW Title: Distinct roles of transcription factors EGL-46 and DAF-19 in specifying the functionality of a polycystin-expressing sensory neuron necessary for C. elegans male vulva location behavior. Citation: Development 130: 5217-5227 2003 Type: ARTICLE Genes: ceh-26 daf-19 egl-44 egl-46 lov-1 nlp-8 osm-5 osm-6 pdk-2 Abstract: Caenorhabditis elegans polycystins LOV-1 and PKD-2 are expressed in the male-specific HOB neuron, and are necessary for sensation of the hermaphrodite vulva during mating. We demonstrate that male vulva location behavior and expression of lov-1 and pkd-2 in the ciliated sensory neuron HOB require the activities of transcription factor EGL-46 and to some extent also EGL-44. This EGL-46-regulated program is specific to HOB and is distinct from a general ciliogenic pathway functioning in all ciliated neurons. The ciliogenic pathway regulator DAF-19 affects downstream components of the HOB-specific program indirectly and is independent of EGL-46 activity. The sensory function of HOB requires the combined action of ------------------- Key: 6248 Medline: 14647365 Authors: Blaxter M Title: Two worms are better than one. Citation: Nature 426: 395-396 2003 Type: REVIEW Genes: Abstract: The genome of the microscopic worm Caenorhabditis briggsae has been sequenced, and show some remarkable differences from the genome of the better known - and physically similar - C. elegans. ------------------- Key: 6249 Medline: 14635135 Authors: Symersky J;Li S;Carson M;Luo D;Luan CH;Luo M Title: Structural genomics of Caenorhabditis elegans: structure of dihydropteridine reductase. Citation: Proteins: Structure, Function, and Genetics 53: 944-946 Type: ARTICLE Genes: Abstract: The biosynthesis of catecholamnes includes hydroxylation of the aromatic amino acids phenylalanin, tyrosine, and tryptophan. Corresponding hydroxylases use tetrahydrobiopterin (BH4), which is oxidized to a quinonoid form of dihydrobiopterin. ------------------- Key: 6250 Medline: 14635136 Authors: Symersky J;Lin G;Li S;Qiu S;Carson M;Schormann N;Luo M Title: Structural genomics of Caenorhabditis elegans: crystal structure of calmodulin. Citation: Proteins: Structure, Function, and Genetics 53: 947-949 Type: ARTICLE Genes: Abstract: Calmodulin (CaM), a conserved eucaryotic protein, can bind specifically to a large number of intracellular proteins and modulate their activity in response to the Ca2+ concentration. This small 17-kDa acidic protein belongs to a family of homologous calcium-binding proteins that bind Ca2+ through the EF-hand motif (e.g., parvalbumin or troponin C). A compact, calcium-free, apo form of CaM is converted to an extended dumbbell-shaped form on binding Ca2+. ------------------- Key: 6251 Medline: 14581619 Authors: Liedtke W;Tobin DM;Bargmann CI;Friedman JM Title: Mammalian TRPV4 (VR-OAC) directs behavioral responses to osmotic and mechanical stimuli in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 100: 14531-14536 2003 Type: ARTICLE Genes: elt-2 glr-1 ocr-2 odr-1 odr-3 osm-9 osm-10 sra-6 Abstract: All animals detect osmotic and mechanical stimuli, but the molecular basis for these responses is incompletely understood. The vertebrate transient receptor potential channel vanilloid subfamily 4 (TRPV4) (VR-OAC) cation channel has been suggested to be an osmo/mechanosensory channel. To assess its function in vivo, we expressed TRPV4 in Caenorhabditis elegans sensory neurons and examined its ability to generate behavioral responses to sensory stimuli. C elegans ASH neurons function as polymodal sensory neurons that generate a characteristic escape behavior in response to mechanical, osmotic, or olfactory stimuli. These behaviors require the TRPV channel OSM-9 because osm-9 mutants do not avoid nose touch, high osmolarity, or noxious odors. Expression of mammalian TRPV4 in ASH neurons of osm-9 worms restored avoidance responses to hypertonicity and nose touch, but not the response to odorant repellents. Mutations known to reduce TRPV4 channel activity also reduced its ability to direct nematode avoidance behavior. TRPV4 function in ASH required the endogenous C. elegans osmotic and nose touch avoidance genes ocr-2, odr-3, osm-10, and glr-1, indicating that TRPV4 is integrated into the normal ASH sensory apparatus. The osmotic and mechanical avoidance responses of TRPV4- expressing animals were different in their sensitivity and temperature dependence from the responses of wild-type animals, suggesting that the TRPV4 channel confers its characteristic properties on the transgenic animals' behavior. These results provide evidence that TRPV4 can function as a component of an osmotic/mechanical sensor in ------------------- Key: 6252 Medline: 14668850 Authors: Vellai T;Takacs-Vellai K;Zhang Y;Kovacs AL;Orosz L;Muller F Title: Influence of TOR kinase on lifespan in C. elegans. Citation: Nature 426: 620- 2003 Type: ARTICLE Genes: daf-2 daf-16 let-363 Abstract: The group of enzymes known as TOR (for 'target of rapamycin') kinases regulates cell growth and proliferation in response to nutrients and hormone-dependent mitogenic signals. Here we show that TOR deficiency in the nematode Caenorhabditis elegans more than doubles its natural lifespan. This new function for TOR signalling in ageing control may represent a link between nutrition, metabolism and longevity. ------------------- Key: 6253 Medline: 14656969 Authors: Cutter AD;Payseur BA;Salcedo T;Estes AM;Good JM;Wood E;Hartl T;Maughan H;Strempel J;Wang BM;Bryan AC;Dellos M Title: Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans. Citation: Genome Research 13: 2651-2657 2003 Type: ARTICLE Genes: Abstract: Understanding genome-wide links between genotype and phenotype has generally been difficult due to both the complexity of phenotypes, and until recently, inaccessibility to large numbers of genes that might underlie a trait. To address this issue, we establish the association between particular RNAi phenotypes in Caenorhabditis elegans and sequence characteristics of the corresponding proteins and DNA. We find that genes showing RNAi phenotypes are long and highly expressed with little noncoding DNA and high rates of synonymous site substitution (K.). In addition, genes conferring RNAi phenotypes have significantly lower rates of nonsynonymous site substitution (K-A). Collectively, these sequence features explain nearly 20% of the difference between the sets of loci that display or lack a RNAi-mediated effect, and reflect aspects both of the RNA! mechanism and the biological function of the genes. For example, the particularly low rate of evolution of genes in the sterility RNAi phenotype class suggests a role of C elegans life history in shaping these patterns of sequence and expression characteristics on phenotypes. This approach also allows prediction of a set of heretofore-uncharacterized loci for which we expect future RNAi studies to reveal phenotypic effects (i.e., false ------------------- Key: 6254 Medline: 14653817 Authors: Mohrlen F;Hutter H;Zwilling R Title: The astacin protein family in Caenorhabditis elegans. Citation: European Journal of Biochemistry 270: 4909-4920 2003 Type: ARTICLE Genes: nas-1 nas-2 nas-3 nas-4 nas-5 nas-6 nas-7 nas-8 nas-9 nas-10 nas-11 nas-12 nas-13 nas-14 nas-15 nas-16 nas-17 nas-18 nas-19 nas-20 nas-21 nas-22 nas-23 nas-24 nas-25 nas-26 nas-27 nas-28 nas-29 nas-30 nas-31 nas-32 nas-33 nas-34 nas-35 nas-36 nas-37 nas-38 nas-39 nas-40 Abstract: In the nematode Caenorhabditis elegans, 40 genes code for astacin-like proteins (nematode astacins, NAS). The astacins are metalloproteases present in bacteria, invertebrates and vertebrates and serve a variety of physiological functions like digestion, hatching, peptide processing, morphogenesis and pattern formation. With the exception of one distorted pseudogene, all the other C. elegans astacins are expressed and are evidently functional. For 13 genes we found splicing patterns differing from the Genefinder predictions in WormBase, sometimes markedly. The GFP expression pattern for NAS-4 shows a specific localization in anterior pharynx cells and in the whole digestive tract (as the secreted form). In contrast, NAS-7 is found in the head of adult hermaphrodites, but not in pharynx cells or in the lumen of the digestive tract. In embryos, NAS-7 fluorescence becomes detectable just before hatching. In C. elegans astacins, three basic structural and functional moieties can be discerned: a prepro portion, the central catalytic chain and long C-terminal extensions with presumably regulatory functions. Within the regulatory moiety, EFG-like, CUB, SXC, and ISP-1 domains can be distinguished. Based on structural differences of the regulatory unit we established six NAS subgroups, which seemingly represented different functional and evolutionary clusters. This pattern deduced exclusively from the domain arrangement in the regulatory moiety is perfectly reflected in an evolutionary tree constructed solely from amino acid sequence information of the catalytic chain. Related catalytic chains tend to have related regulatory ------------------- Key: 6255 Medline: 14713049 Authors: Boyd WA;Cole RD;Anderson GL;Williams PL Title: The effects of metals and food availability on the behavior of Caenorhabditis elegans. Citation: Environmental Toxicology & Chemistry 22: 3049-3055 2003 Type: ARTICLE Genes: Abstract: Caenorhabdiris elegons, a nonparasitic soil nematode, was used to assess the combined effects of metal exposures and food availability on behavior. Movement was monitored using a computer tracking system after exposures to Cu, Pb, or Cd while feeding was measured as a change in optical density (DeltaOD) of bacteria suspensions over the exposure period. After 24-h exposures at hig and low bacteria concentrations. movement was decreased in a concentration-dependent fashion by Pb and Cd but feeding reductions were not directly proportional to exposure concentrations. Copper exposure induced concentration-dependent declines in feeding and movement regardless of bacteria concentration. The impact of 24-h metal exposures was apparently reduced by increasing food availability. Therefore, exposures were shortened to 4 It in an attempt to minimize starvation effects on movement. Although nematodes were immobilized following 24 h of food depravation, worms deprived of food during the 4-h exposure continued to feed and move after exposure. A bead-ingestion assay after 4-h exposures was also used as an additional means of assessing the effects of metals on feeding behavior. Ingestion was significantly reduced by all concentrations of metals tested, indicating its sensitivity as a sublethal assay. Feeding (AOD) during exposures exhibited similar trends as ingestion but was slightly less sensitive. while movement was the least sensitive assay of 4-h metal exposures to C. elegans. Assessment of multiple sublethal endpoints allowed for the determination of the separate and interactive effects of metals and food ------------------- Key: 6256 Medline: 14654017 Authors: Blackwell TK;Walker AK Title: Transcription elongation: TLKing to chromatin? Citation: Current Biology 13: R915-R916 2003 Type: REVIEW Genes: tlk-1 Abstract: The tousled-like kinases have been implicated in chromatin deposition, but surprising new findings in Caenorhabditis elegans indicate they have a role in transcription elongation. Are these apparently distinct functions of tousled-like kinases related? ------------------- Key: 6257 Medline: 14630038 Authors: Fostel JL;Coste LB;Jacobson LA Title: Degradation of transgene-coded and endogenous proteins in the muscles of Caenorhabditis elegans. Citation: Biochemical and Biophysical Research Communications 312: 173-177 2003 Type: ARTICLE Genes: Abstract: To develop reporter systems to study the regulation of protein degradation in innervated muscle, we have used strains of the nematode Caenorhabditis elegans containing transgenes that fuse lacZ or green fluorescent protein (GFP) coding regions to muscle-specific promoter/enhancer regions, such that the fusion proteins are expressed exclusively in body-wall and vulval muscle cells. The starvation-induced degradation of the beta-galactosidase reporter protein is quantitatively similar to that of two endogenous muscle proteins, arginine kinase and adenylate kinase. A soluble GFP in the muscle cytosol is degraded during starvation, but when GFP is fused to a full-length myosin heavy chain and incorporated into myofibrils, it is resistant to starvation-induced degradation. This suggests that under some conditions soluble muscle proteins may be extensively catabolized in preference to the proteins of the contractile fibers. ------------------- Key: 6258 Medline: Authors: Scholey JM Title: Intraflagellar transport. Citation: Annual Review of Cell & Developmental Biology 19: 423-443 2003 Type: REVIEW Genes: Abstract: It has been a decade since a novel form of microtubule (MT)-based motility, i.e., intraflagellar transport (IFT), was discovered in Chlamydomonas flagella. Subsequent research has supported the hypothesis that IFT is required for the assembly and maintenance of all cilia and flagella and that its underlying mechanism involves the transport of nonmembrane-bound macromolecular protein complexes (IFT particles) along axonemal MTs beneath the ciliary membrane. IFT requires the action of the anterograde kinesin-H motors and the retrograde IFT-dynein motors to transport IFT particles in opposite directions along the MT polymer lattice from the basal body to the tip of the axoneme and back again. A rich diversity of biological processes has been shown to depend upon IFT, including flagellar length control, cell swimming, mating and feeding, photoreception, animal development, sensory perception, chemosensory behavior, and lifespan control. These processes reflect the varied roles of cilia and flagella in motility and sensory signaling. ------------------- Key: 6259 Medline: Authors: Lai EC Title: microRNAs: Runts of the genome assert themselves. Citation: Current Biology 13: R925-R936 2003 Type: REVIEW Genes: let-7 lin-4 lin-14 Abstract: microRNAs form an abundant class of 21-22 nucleotide, non-coding RNA that is common to diverse species of multicellular life. Although they are currently the subject of intense, directed study, the path toward their discovery has been dominated by chance and serendipity. In this review, I examine how these tiny molecules have risen from genetic obscurity to scientific stardom, and discuss the emerging biological functions of these novel ------------------- Key: 6260 Medline: 14685240 Authors: Johnston RJ;Hobert O Title: A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Citation: Nature 426: 845-849 2003 Type: ARTICLE Genes: ceh-36 cog-2 gcy-5 gcy-6 gcy-7 lim-6 lsy-6 Abstract: How left/right functional asymmetry is layered on top of an anatomically symmetrical nervous system is poorly understood. In the nematode Caenorhabditis elegans, two morphologically bilateral taste receptor neurons, ASE left (ASEL) and ASE right (ASER), display a left/right asymmetrical expression pattern of putative chemoreceptor genes that correlates with a diversification of chemosensory specificities(1,2). Here we show that a previously undefined microRNA termed lsy-6 controls this neuronal left/right asymmetry of chemosensory receptor expression. lsy-6 mutants that we retrieved from a genetic screen for defects in neuronal left/right asymmetry display a loss of the ASEL-specific chemoreceptor expression profile with a concomitant gain of the ASER-specific profile. Alsy-6 reporter gene construct is expressed in less than ten neurons including ASEL, but not ASER. lsy-6 exerts its effects on ASEL through repression of cog-1, an Nkx-type homeobox gene, which contains a lsy-6 complementary site in its 30 untranslated region and that has been shown to control ASE-specific chemoreceptor expression profiles(3). lsy-6 is the first microRNA to our knowledge with a role in neuronal patterning, providing new insights into left/right axis formation. ------------------- Key: 6261 Medline: 14530273 Authors: Jonassen T;Davis DE;Larsen PL;Clarke CF Title: Reproductive fitness and quinone content of Caenorhabditis elegans clk-1 mutants fed coenzyme Q isoforms of varying length. Citation: Journal of Biological Chemistry 278: 51735-51742 2003 Type: ARTICLE Genes: clk-1 Abstract: Caenorhabditis elegans clk-1 mutants lack coenzyme Q(9) and accumulate the biosynthetic intermediate demethoxy-Q(9). A dietary source of ubiquinone (Q) is required for larval growth and development of the gonad and germ cells. We considered that uptake of the shorter Q(8) isoform present in the Escherichia coli food may contribute to the Clk phenotypes of slowed development and reduced brood size observed when the animals are fed Q-replete E. coli. To test the effect of isoprene tail length, N2 and clk-1 animals were fed E. coli engineered to produce Q(7), Q(8), Q(9), or Q(10). Wild-type nematodes showed no change in reproductive fitness regardless of the Q(n) isoform fed. clk-1(e2519) fed the Q(9) diet showed increased egg production; however, this diet did not improve reproductive fitness of the clk-1(qm30) animals. Furthermore, animals with the more severe clk-1(qm30) allele become sterile and their progeny inviable when fed Q(7)-containing bacteria. The content of Q(7) in the mitochondria of clk-1 animals was decreased relative to Q(8), suggesting less effective transport of Q(7) to the mitochondria, impaired retention, or decreased stability. Additionally, regardless of E. coli diet, clk-1(qm30) animals contain a dysfunctional dense form of mitochondria. The gonads of clk-1(qm30) worms fed Q(7)-containing food were severely shrunken and disordered. The differential fertility of clk-1 mutant nematodes fed Q isoforms may result from changes in Q localization, altered recognition by Q-binding proteins, and/or potential defects in mitochondrial function resulting from the mutant CLK-1 polypeptide itself. ------------------- Key: 6262 Medline: 14644423 Authors: Lee MH;Han SM;Han JW;Kim YM;Ahnn J;Koo HS Title: Caenorhabditis elegans dna-2 is involved in DNA repair and is essential for germ-line development. Citation: FEBS Letters 555: 250-256 2003 Type: ARTICLE Genes: dna-2 mre-11 Abstract: Caenorhabditis elegans germ cell proliferation and development were severely damaged in second generation dna-2 homozygotes. Even in the first generation, a much higher incidence of aberrant chromosomes in oocytes and resultantly higher embryonic lethality were found vs. wild type, when DNA breaks were induced by gamma-rays or camptothecin. The deficiency of dna-2 in combination with RNA interference on mre-11 gene expression synergistically aggravated germ-line development, especially oocyte formation. These results suggest that C. elegans Dna-2 is involved in a DNA repair pathway paralleling homologous recombination or non-homologous end joining with mre-11 ------------------- Key: 6263 Medline: 14684823 Authors: Berry KL;Bulow HE;Hall DH;Hobert O Title: A C. elegans CLIC-like protein required for intracellular tube formation and maintenance. Citation: Science 302: 2134-2137 2003 Type: ARTICLE Genes: exc-4 Abstract: The Caenorhabditis elegans excretory canal is composed of a single elongated and branched cell that is tunneled by an inner lumen of apical character. Loss of the exc-4 gene causes a cystic enlargement of this intracellular tube. exc-4 encodes a member of the chloride intracellular channel (CLIC) family of proteins. EXC-4 protein localizes to various tubular membranes in distinct cell types, including the lumenal membrane of the excretory tubes. A conserved 55 - amino acid domain enables EXC-4 translocation from the cytosol to the lumenal membrane. The tubular architecture of this membrane requires EXC-4 for both its formation and maintenance. ------------------- Key: 6264 Medline: 14677634 Authors: Sampayo JN;Olsen A;Lithgow GJ Title: Oxidative stress in Caenorhabditis elegans: protective effects of superoxide dismutase/catalase mimetics. Citation: Aging Cell 2: 319-326 2003 Type: REVIEW Genes: Abstract: The lifespan of Caenorhabditis elegans can be extended by the administration of synthetic superoxide dismutase/ catalase mimetics (SCMs) without any effects on development or fertility. Here we demonstrate that the mimetics, Euk-134 and Euk-8, confer resistance to the oxidative stress-inducing agent, paraquat and to thermal stress. The protective effects of the compounds are apparent with treatments either during development or during adulthood and are independent of an insulin/IGF-I-like signalling pathway also known to affect thermal and oxidative stress resistance. Worms exposed to the compounds do not induce a cellular stress response and no detrimental effects are observed. ------------------- Key: 6265 Medline: Authors: McElwee J;Bubb K;Thomas JH Title: Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16. Citation: Aging Cell 2: 341- 2003 Type: CORRECT Genes: Abstract: ------------------- Key: 6266 Medline: 14657363 Authors: Yau DM;Yokoyama N;Goshima Y;Siddiqui ZK;Siddiqui SS;Kozasa Title: Identification and molecular characterization of the Galpha12-Rho guanine nucleotide exchange factor pathway in Caenorhabditis elegans. Citation: Proceedings of the National Academy of Sciences USA 100: 14748-14753 2003 Type: ARTICLE Genes: gpa-12 rrf-3 Abstract: Galpha12/13-mediated pathways have been shown to be involved in various fundamental cellular functions in mammalian cells such as axonal guidance, apoptosis, and chemotaxis. Here, we identified a homologue of Rho-guanine nucleotide exchange factor (GEF) in Caenorhabditis elegans (CeRhoGEF), which functions downstream of gpa-12, the C elegans homologue of Galpha12/13. CeRhoGEF contains a PSD-95/Dlg/ZO-1 domain and a regulator of G protein signaling (RGS) domain upstream of the Dbl hornology-pleckstrin homology region similar to mammalian RhoGEFs with RGS domains, PSD-95/Dlg/ZO-1-RhoGEF and leukemia-associated RhoGEF. It has been shown in mammalian cells that these RhoGEFs interact with activated forms of Galpha12 or Galpha13 through their RGS domains. We demonstrated by coimmunoprecipitation that the RGS domain of CeRhoGEF interacts with GPA-12 in an AIF(4)(-) activation-dependent manner and confirmed that the Dbl homologypleckstrin homology domain of CeRhoGEF was capable of Rhodependent signaling. These results proved conservation of the Galpha12-RhoGEF pathway in C elegans. Expression of DsRed or GFP under the control of the promoter of CeRhoGEF or gpa-12 revealed an overlap of their expression patterns in ventral cord motor neurons and several neurons in the head. RNA-mediated gene interference for CeRhoGEF and gpa-12 resulted in similar phenotypes such as embryonic lethality and sensory and locomotive defects in adults. Thus, the Galpha12/13-RhoGEF pathway is likely ------------------- Key: 6267 Medline: 14768892 Authors: Preclin V;Martin E;Segalat L Title: Target sequences of Tc1, Tc3 and Tc5 transposons of Caenorhabditis elegans. Citation: Genetical Research 82: 85-88 2003 Type: ARTICLE Genes: gpa-2 mut-7 Abstract: We report here the consensus target sequence of transposons Tc1, Tc3 and Tc5 of Caenorhabditis elegans. These sequences were obtained by molecular analysis of 1008 random new insertions which have not been exposed to natural selection. This analysis reveals consensus target sites slightly different from those previously reported, and confirms that the mariner elements Tc1 and Tc3 insert in sites which are not preferentially palindromic. ------------------- Key: 6268 Medline: 14642561 Authors: Jeong YS;Kang Y;Lim KH;Lee MH;Lee J;Koo HS Title: Deficiency of Caenorhabditis elegans RecQ5 homologue reduces life span and increases sensitivity to ionizing Citation: DNA Repair 2: 1309-1319 2003 Type: ARTICLE Genes: him-6 rcq-5 Abstract: Gene expression and RNA interference phenotypes were investigated for a Caenorhabditis elegans homologue (Ce-RCQ-5) of human RecQ5 protein. Expression of the mRNA was observed by in situ hybridization from earliest embryogenesis and gradually decreased during late embryogenesis. Ce-RCQ-5 was immuno-localized in the nuclei of embryos, germ cells, and oocytes and also in the nuclei of various somatic cells of larvae and adults. Despite ubiquitous expression in postembryonic cells, RCQ-5 protein expression was highest in intestinal cells, which was confirmed by tagging the gene expression with green fluorescence protein. When endogenous Ce-rcq-5 gene expression was inhibited by RNA interference, no clear phenotypes were observed during development. However, C. elegans life span was reduced by 37% due to RNA interference of rcq-5 gene, suggesting its possible role in maintenance of genomic stability, as has been ascribed to other RecQ family DNA helicases. In addition, C. elegans became significantly more sensitive to ionizing radiation after inhibition of rcq-5 gene expression, indicating an involvement of C. elegans RCQ-5 in a cellular response to DNA damage, possibly in DNA repair. ------------------- Key: 6269 Medline: 14651925 Authors: Kim C;Forrester WC Title: Functional analysis of the domains of the C. elegans Ror receptor tyrosine kinase CAM-1. Citation: Developmental Biology 264: 376-390 2003 Type: ARTICLE Genes: cam-1 Abstract: cam-1 encodes a Caenorhabditis elegans orphan receptor tyrosine kinase (RTK) of the Ror family that is required for cell migration and to orient cell polarity. Ror RTKs share a common domain structure. The predicted extracellular region contains immunoglobulin (Ig), cysteine-rich (CRD), and kringle (Kri) domains. Intracellularly are tyrosine kinase (Kin) and serine- and threonine (S/T)-rich domains. To investigate the functional requirement for CAM-1 domains in mediating cell migration, we engineered deletions that remove various domains and assessed the ability of these CAM-1 derivatives to rescue cam-1 mutant phenotypes. We find that the Ig, Kri, Kin, and S/T domains are dispensable for cell migration, but the CRD is required. Surprisingly, the entire intracellular region of CAM-1 is not required for proper cell migration. Most notably, a version of CAM-1 from which all domains besides the CRD and transmembrane domains have been deleted is able to rescue the migration of a single cell type, although not those of other cell types. Our results show that CAM-1 does not function exclusively as a canonical RTK and that it may function, at least in part, to regulate the distribution of a secreted ligand-possibly a Writ protein. ------------------- Key: 6270 Medline: 14644192 Authors: Glotzer M Title: Cytokinesis: progress on all fronts. Citation: Current Opinion in Cell Biology 15: 684-690 2003 Type: REVIEW Genes: let-21 par-2 zen-4 Abstract: Cell multiplication requires sequestration of the duplicated and segregated genome into two daughter cells. The mitotic spindle is critical for orchestrating sister chromatid separation and division plane positioning. During anaphase, spindle microtubules become bundled to form the central spindle, which is essential for completion of cytokinesis. Central spindle assembly is mediated by a microtubule-associated protein and a kinesin-RhoGAP complex, both of which are regulated by phosphorylation/dephosphorylation. The central spindle also plays a role in cleavage furrow positioning, which appears to involve activation of RhoA. New results have provided some initial clues as to how furrow positioning is achieved. Particularly notable is the discovery that a protein activated by RhoA, formin, has actin nucleation ------------------- Key: 6271 Medline: 14638320 Authors: Aboobaker A;Blaxter M Title: Hox gene evolution in nematodes: novelty conserved. Citation: Current Opinion in Genetics & Development 13: 593-598 2003 Type: REVIEW Genes: ced-3 ceh-13 egl-5 let-60 lin-3 lin-39 mab-3 mab-5 mes-2 mes-3 mes-6 nob-1 pal-1 php-3 sop-2 Abstract: The conserved homeobox (Hox) gene cluster is neither conserved nor clustered in the nematode Caenorhabditis elegans. Instead, C. elegans has a reduced and dispersed gene complement that is the result the loss of Hox genes in stages throughout its evolutionary history. The roles of Hox genes in patterning the nematode body axis are also divergent, although there are tantalising remnants of ancient regulatory systems. Hox patterning also differs greatly between C. elegans and a second "model" nematode, Pristionchus pacificus. The pattern of Hox gene evolution may be indicative of the move to deterministic developmental modes in nematodes. ------------------- Key: 6272 Medline: 14675154 Authors: Estevez M;Estevez AO;Cowie RH;Gardner KL Title: The voltage-gated calcium channel UNC-2 is involved in stress-mediated regulation of tryptophan hydroxylase. Citation: Journal of Neurochemistry 88: 102-113 2004 Type: ARTICLE Genes: bas-1 daf-1 daf-2 daf-3 daf-4 daf-5 daf-7 daf-8 daf-12 daf-14 dbl-1 sma-2 sma-3 sma-4 sma-6 tph-1 unc-2 unc-43 Abstract: Migraine is an episodic pain disorder whose pathophysiology is related to deficiency of serotonin signaling and abnormal function of the P/Q-type calcium channel, CACNA1A. Because the relationship of the CACNA1A channel to serotonin signaling is unknown and potentially of therapeutic interest we have used genetic analysis of the Caenorhabditis elegans ortholog of this calcium channel, UNC-2, to help identify candidate downstream effectors of the human channel. By genetic dissection of the lethargic mutant phenotype of unc-2, we have established an epistasis pathway showing that UNC-2 function antagonizes a transforming growth factor (TGF)-beta pathway influencing movement rate. This same UNC-2/TGF-beta pathway is required for accumulation of normal serotonin levels and stress-induced modulation of tryptophan hydroxylase (tph) expression in the serotonergic chemosensory ADF neurons, but not the NSM neurons. We also show that transgenic expression of the migraine-associated Ca2+ channel, CACNA1A, in unc-2 animals can functionally substitute for UNC-2 in stress-activated regulation of tph expression. The demonstration that these evolutionarily related channels share a conserved ability to modulate tph expression through their effects on TGF-beta signaling provides the first specific example of how CACNA1A function may influence levels of the critical migraine neurotransmitter ------------------- Key: 6273 Medline: 14641049 Authors: Sampayo JN;Gill MS;Lithgow GJ Title: Oxidative stress and aging - the use of superoxide dismutase/catalase mimetics to extend lifespan. Citation: Biochemical Society Transactions 31: 1305-1307 2003 Type: ARTICLE Genes: age-1 clk-1 daf-2 ins-1 ins-18 isp-1 lrs-2 pdk-1 sir-2.1 unc-31 unc-64 Abstract: To date, more than 40 genes have been identified in the nematode Coenorhabditis elegans, which, when mutated, lead to an increase in lifespan. Of those tested, all confer an increased resistance to oxidative stress. in addition, the lifespan of C elegans can also be extended by the administration of synthetic superoxide dismutase/catalase mimetics. These compounds also appear to confer resistance to oxidative damage, since they protect against paraquat treatment. The protective effects of these compounds are apparent with treatment during either development or adulthood. These findings have demonstrated that pharmacological intervention in the aging process is possible and that these compounds can provide important information about the underlying mechanisms. To date, such interventions have targeted known processes rather than screening compound libraries because of the limitations of assessing lifespan in nematodes. However, we have recently developed a microplate-based assay that allows for a rapid and objective score of nematode survival at rates many times higher than previously possible. This system now provides the opportunity to perform high-throughput screens for compounds that affect nematode survival in the face of acute oxidative stress and will facilitate the identification of novel drugs that extend nematode ------------------- Key: 6274 Medline: Authors: Srinivasan J;Sinz W;Jesse T;Wiggers-Perebolte L;Jansen K;Buntjer J;van der Meulen M;Sommer RJ Title: An integrated physical and genetic map of the nematode Pristionchus pacificus. Citation: Molecular Genetics & Genomics 269: 715-722 2003 Type: ARTICLE Genes: Abstract: The free-living nematode Pristionchus pacificus is one of several species that have recently been developed as a satellite system for comparative functional studies in evolutionary developmental biology. Comparisons of developmental processes between P. pacificus and the well established model organism Caenorhabditis elegans at the cellular and genetic levels provide detailed insight into the molecular changes that shape evolutionary transitions. To facilitate genetic analysis and cloning of mutations in P. pacificus, we previously generated a BAC-based genetic linkage map for this organism. Here, we describe the construction of a physical map of P. pacificus genome based on AFLP fingerprint analysis of 7747 BAC clones. Most of the SSCP markers used to generate the genetic linkage map were derived from BAC ends, so that the physical genome map and the genetic map can be integrated. The contigs that make up the physical map are evenly distributed over the genetic linkage map and no clustering is observed, indicating that the physical map provides a valid representation of the P. pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes. ------------------- Key: 6275 Medline: 14675531 Authors: Davies AG;Pierce-Shimomura JT;Kim H;VanHoven MK;Thiele TR;Bonci A;Bargmann CI;McIntire SL Title: A central role of the BK potassium channel in behavioral responses to ethanol in C. elegans. Citation: Cell 115: 655-666 2003 Type: ARTICLE Genes: dgk-1 goa-1 slo-1 Abstract: The activities of many neuronal proteins are modulated by ethanol, but the fundamental mechanisms underlying behavioral effects of ethanol remain unclear. To identify mechanisms responsible for intoxication, we screened for Caenorhabditis elegans mutants with altered behavioral responses to ethanol. We found that slo-1 mutants, which were previously recognized as having slightly uncoordinated movement, are highly resistant to ethanol in two behavioral assays. Numerous loss-of-function slo-1 alleles emerged from our screens, indicating that slo-1 has a central role in ethanol responses. slo-1 encodes the BK potassium channel. Electrophysiological analysis shows that ethanol activates the channel in vivo, which would inhibit neuronal activity. Moreover, behaviors of slo-1 gain-of-function mutants resemble those of ethanol-intoxicated animals. These results demonstrate that selective activation of BK channels is responsible for acute intoxicating effects of ethanol in C. elegans. BK channel activation may explain a variety of behavioral responses to ethanol in invertebrate and vertebrate systems. ------------------- Key: 6276 Medline: Authors: Herman RK Title: The tale behind the worm. Citation: Science 303: 42- 2004 Type: REVIEW Genes: Abstract: I'm one of the 2000 or so worm people who study the tiny nematode Caenorhabditis elegans. When we are asked by an outsider why we play with worms, our much-practiced answer goes something like this: In the mid-1960s, Sydney Brenner chose C. elegans as a model organism for elucidating animal development and behavior because of the roundworm's cellular simplicity and advantages for genetic studies. The analysis of mutants helps us learn what the nonmutant versions of genes do. We know the location and lineage of every cell in an adult C. elegans as well as the wiring of all the worm's 302 neurons, down to the last synapse. C. elegans was the first multicellular organism to have its DNA completely sequenced (1), and many of its genes resemble those of humans and do similar jobs. The importance of such research was highlighted when Brenner, John Sulston, and Bob Horvitz were awarded the 2002 Nobel Prize in physiology or medicine for their worm work. ------------------- Key: 6277 Medline: Authors: Labouesse M Title: Caenorhabditis elegans. Citation: M S-Medecine Sciences 19: 1171-1172 2003 Type: REVIEW Genes: Abstract: (In French.) ------------------- Key: 6278 Medline: Authors: Pujol N;Ewbank JJ Title: A worm's life. Citation: M S-Medecine Sciences 19: 1209-1217 2003 Type: REVIEW Genes: clk-1 daf-2 daf-16 dbl-1 glp-1 nsy-1 odr-10 pmk-1 sek-1 str-2 Abstract: Despite its relative anatomic simplicity, the nematode Caenorhabditis elegans (C. elegans) is a complex multicellular organism. In this review, we describe studies that have contributed to a better understanding of certain aspects of the worm's physiology. We focus on the cellular and molecular basis of the interaction between C. elegans and its environment, including its sensory capacities, the intrinsic biological clock that governs the speed of its life, and on some of the factors that control its life span. We also outline very recent findings that have demonstrated the existence of an innate immune system in C. elegans. Finally, we highlight a number of novel techniques that are transforming the worm from a largely genetic model system into an attractive organism for functional genomic ------------------- Key: 6279 Medline: Authors: Segalat L;Neri C Title: C. elegans as a model for human inherited degenerative diseases. Citation: M S-Medecine Sciences 19: 1218-1225 2003 Type: REVIEW Genes: dyc-1 dys-1 egl-19 hlh-1 mec-3 mec-7 osm-10 Abstract: C. elegans as a model for human inherited degenerative diseases. The nematode C. elegans is an established model for developmental biology. Since the early 90's, this simple model organism has been increasingly used for studying human disease pathogenesis. C. elegans models based either on the mutagenesis of human disease genes conserved in this nematode or transgenesis with disease genes not conserved in C. elegans show several features that are observed in mammalian models. These observations suggest that the genetic dissection and pharmacological manipulation of disease-like phenotypes in C. elegans will shed light on the cellular mechanisms that are altered in human diseases, and the compounds that may be used as drugs. This review illustrates these aspects by commenting on two inherited degenerative diseases, Duchenne's muscular dystrophy and Huntington's neurodegenerative disease. ------------------- Key: 6280 Medline: Authors: Weimer RM;Jorgensen EM Title: Controversies in synaptic vesicle exocytosis. Citation: Journal of Cell Science 116: 3661-3666 2003 Type: REVIEW Genes: unc-13 unc-18 Abstract: At the heart of synaptic transmission resides the synaptic vesicle cycle- a membrane trafficking pathway in which small membrane-bound vesicles mediate the release of neurotransmitter from presynaptic terminals. The cycle resembles general membrane trafficking and has three phases: vesicle filling, release and recycling. During filling, neurotransmitter is loaded into vesicles via vesicular neurotransmitter transporters. It is then released by exocytosis: vesicles dock with the plasma membrane and undergo a maturation step, termed priming; then, following influx of calcium through voltage-gated channels, a calcium sensor promotes fusion of the vesicle with the plasma membrane. Membrane fusion consumes vesicle membrane and vesicle proteins; thus, these components must be recycled to sustain neurotransmitter release. ------------------- Key: 6281 Medline: 12915588 Authors: Cram EJ;Clark SG;Schwarzbauer JE Title: Talin loss-of-function uncovers roles in cell contractility and migration in C. elegans. Citation: Journal of Cell Science 116: 3871-3878 2003 Type: ARTICLE Genes: pat-2 pat-3 Abstract: Integrin receptors for extracellular matrix transmit mechanical and biochemical information through molecular connections to the actin cytoskeleton and to several intracellular signaling pathways. In Caenorhabditis elegans, integrins are essential for embryonic development, muscle cell adhesion and contraction, and migration of nerve cell axons and gonadal distal tip cells. To identify key components involved in distal tip cell migration, we are using an RNA interference (RNAi)-based genetic screen for deformities in gonad morphogenesis. We have found that talin, a cytoskeletal-associated protein and focal adhesion component, is expressed in the distal tip cell and plays a central role in regulating its migration. Reduction of talin expression caused severe defects in gonad formation because of aberrant distal tip cell migration and also disrupted oocyte maturation and gonad sheath cell structure. Contractile muscle cells showed disorganization of the actin cytoskeleton leading to complete paralysis, a phenotype that was also observed with depletion of pat-2 and pat-3 integrins. These in vivo analyses show that talin is required not only for strong adhesion and cytoskeletal organization by contractile cells, but also for dynamic regulation of integrin signals during cell migration. In addition, induction of distal tip cell migration defects by bacterial RNAi in C. elegans provides an effective screen to identify genes involved in integrin signaling and ------------------- Key: 6282 Medline: 14625390 Authors: Lesa GM;Palfreyman M;Hall DH;Clandinin MT;Rudolph C;Jorgensen EM;Schiavo G Title: Long chain polyunsaturated fatty acids are required for efficient neurotransmission in C. elegans. Citation: Journal of Cell Science 116: 4965-4975 2003 Type: ARTICLE Genes: egl-1 elt-2 fat-3 rab-3 Abstract: The complex lipid constituents of the eukaryotic plasma membrane are precisely controlled in a cell-type-specific manner, suggesting an important, but as yet, unknown cellular function. Neuronal membranes are enriched in long-chain polyunsaturated fatty acids (LC-PUFAs) and alterations in LC-PUFA metabolism cause debilitating neuronal pathologies. However, the physiological role of LC-PUFAs in neurons is unknown. We have characterized the neuronal phenotype of C. elegans mutants depleted of LC-PUFAs. The C. elegans genome encodes a single Delta6-desaturase gene (fat-3), an essential enzyme for LC-PUFA biosynthesis. Animals lacking fat-3 function do not synthesize LC-PUFAs and show movement and egg-laying abnormalities associated with neuronal impairment. Expression of functional fat-3 in neurons, or application of exogenous LC-PUFAs to adult animals rescues these defects. Pharmacological, ultrastructural and electrophysiological analyses demonstrate that fat-3 mutant animals are depleted of synaptic vesicles and release abnormally low levels of neurotransmitter at cholinergic and serotonergic neuromuscular junctions. These data indicate that LC-PUFAs are essential for efficient neurotransmission in C. elegans and may account for the clinical conditions associated with mis-regulation of ------------------- Key: 6283 Medline: Authors: Evans CJ;Aguilera RJ Title: DNase II: genes, enzymes and function. Citation: Gene 322: 1-15 2003 Type: REVIEW Genes: cps-6 crn-1 crn-2 crn-3 crn-4 crn-5 cyp-13 nuc-1 Abstract: Deoxyribonuclease (DNase) II, which was discovered more than 50 years ago, is a mammalian endonuclease that functions optimally at acid pH in the absence of divalent cations. Its lysosomal localization and ubiquitous tissue distribution suggested that this enzyme played a role in the degradation of exogenous DNA encountered by phagocytosis, although the relative importance of such a role was unknown. Subsequent investigations also suggested that DNase II was important for DNA fragmentation and degradation during cell death. Within the last few years, our work and that of others has lead to the cloning of various mammalian DNase II genes as well as the identification and characterization of highly homologous genes in the invertebrates Caenorhabditis elegans and Drosophila melanogaster. Interestingly, studies of the C elegans DNase II homolog NUC-1 were the first to suggest that DNase II enzymes were fundamentally important in engulfment-mediated DNA degradation, particularly that associated with programmed cell death, due to the presence of persistent apoptotic-cell nuclei within phagocytic cells in nuc-1 mutants. Similarly, mutation of the Drosophila DNase II-like gene was found to result in the accumulation of low-molecular-weight DNA throughout the animals. Homozygous mutation (knockout) of the DNase II gene in mice revealed a much more complex and extensive phenotype including perinatal lethality. The lethality of DNase II-knockout mice is likely the result of multiple developmental defects, the most obvious being a loss of definitive erythropoiesis. Closer examination revealed that a defect in engulftnent-mediated DNA degradation is the primary defect in DNase II-null mice. In this review, we have compiled information from studies on DNase II from various organisms to provide a consensus model for the role ------------------- Key: 6284 Medline: 12925583 Authors: Moghal N;Garcia LR;Khan LA;Iwasaki K;Sternberg PW Title: Modulation of EGF receptor-mediated vulva development by the heterotrimeric G-protein G(alpha)q and excitable cells in C. elegans. Citation: Development 130: 4553-4566 2003 Type: ARTICLE Genes: aex-3 bar-1 dys-1 egl-19 egl-30 goa-1 let-23 let-60 lin-3 lin-15 lin-31 myo-3 phm-2 pry-1 sur-1 unc-4 unc-13 unc-18 unc-64 Abstract: The extent to which excitable cells and behavior modulate animal development has not been examined in detail. Here, we demonstrate the existence of a novel pathway for promoting vulval fates in C elegans that involves activation of the heterotrimeric Galphaq protein, EGL-30. EGL-30 acts with muscle-expressed EGL-19 L-type voltage-gated calcium channels to promote vulva development, and acts downstream or parallel to LET-60 (RAS). This pathway is not essential for vulval induction on standard Petri plates, but can be stimulated by expression of activated EGL-30 in neurons, or by an EGL-30-dependent change in behavior that occurs in a liquid environment. Our results indicate that excitable cells and animal behavior can provide modulatory inputs into the effects of growth factor signaling on cell fates, and suggest that communication between these cell populations is important for normal development to occur under certain ------------------- Key: 6285 Medline: 12952898 Authors: Yochem J;Herman RK Title: Investigating C. elegans development through mosaic analysis. Citation: Development 130: 4761-4768 2003 Type: REVIEW Genes: daf-2 glp-1 her-1 let-23 let-60 lin-12 lin-44 ncl-1 sma-3 sur-5 unc-5 unc-6 unc-36 unc-52 vab-8 Abstract: The analysis of genetically mosaic worms, in which some cells carry a wild-type gene and others are homozygous mutant, can reveal where in the animal a gene acts to prevent the appearance of a mutant phenotype. In this primer article, we describe how Caenorhabditis elegans genetic mosaics are generated, identified and analyzed, and we discuss examples in which the analysis of mosaic worms has provided important information about the development of this organism. ------------------- Key: 6286 Medline: 12944426 Authors: Ruvinsky I;Ruvkun G Title: Functional tests of enhancer conservation between distantly related species. Citation: Development 130: 5133-5142 2003 Type: ARTICLE Genes: ace-1 ric-19 sng-1 unc-25 unc-30 unc-47 unc-119 vab-3 Abstract: Expression patterns of orthologous genes are often conserved, even between distantly related organisms, suggesting that once established, developmental programs can be stably maintained over long periods of evolutionary time. Because many orthologous transcription factors are also functionally conserved, one possible model to account for homologous gene expression patterns, is conservation of specific binding sites within cis-regulatory elements of orthologous genes. If this model is correct, a cis-regulatory element from one organism would be expected to function in a distantly related organism. To test this hypothesis, we fused the green fluorescent protein gene to neuronal and muscular enhancer elements from a variety of Drosophila melanogaster genes, and tested whether these would activate expression in the homologous cell types in Caenorhabditis elegans. Regulatory elements from several genes directed appropriate expression in homologous tissue types, suggesting conservation of regulatory sites. However, enhancers of most Drosophila genes tested were not properly recognized in C elegans, implying that over this evolutionary distance enough changes occurred in cis-regulatory sequences and/or transcription factors to prevent proper recognition of heterospecific enhancers. Comparisons of enhancer elements of orthologous genes between C. elegans and C. briggsae revealed extensive conservation, as well as specific instances of functional divergence. Our results indicate that functional changes in cis-regulatory sequences accumulate on timescales much shorter than the divergence of arthropods and nematodes, and that mechanisms other than conservation of individual binding sites within enhancer elements are responsible for the conservation of expression patterns of homologous genes between distantly related species. ------------------- Key: 6288 Medline: 13129846 Authors: Hutter H Title: Extracellular cues and pioneers act together to guide axons in the ventral cord of C. elegans. Citation: Development 130: 5307-5318 2003 Type: ARTICLE Genes: glr-1 lin-11 mab-20 nid-1 odr-2 sax-3 slt-1 unc-6 unc-30 unc-47 unc-129 vab-1 Abstract: The ventral cord is the major longitudinal axon tract in C elegans containing essential components of the motor circuit. Previous studies have shown that axons grow out sequentially and that there is a single pioneer for the right axon tract which is important for the correct outgrowth of follower axons. Here, the dependencies between early and late outgrowing axons in the ventral cord were studied systematically with laser ablation experiments and a detailed analysis of mutants using multi-color GFP markers. Different classes of axon were affected to a different extent when the AVG pioneer neuron was eliminated. In the majority of the animals, axons were able to grow out normally even in the absence of the pioneer, suggesting that its presence is not absolutely essential for the correct outgrowth of follower axons. The transcription factor LIN-11 was found to be essential for the differentiation and pioneering function of the AVG neuron. UNC-30 appears to play a similar role for the PVP pioneer neurons. Later outgrowing axons typically do not simply follow earlier outgrowing ones, but subtle dependencies between certain groups of early and late outgrowing axons do exist. Different groups of axons growing in the same axon bundle apparently use different combinations of guidance cues for their navigation and can ------------------- Key: 6289 Medline: 14534135 Authors: Tsou MFB;Hayashi A;Rose LS Title: LET-99 opposes G(alpha)/GPR signaling to generate asymmetry for spindle positioning in response to PAR and MES-1/SRC-1 signaling. Citation: Development 130: 5717-5730 2003 Type: ARTICLE Genes: gpa-16 gpb-1 goa-1 gpr-1 gpr-2 let-99 mes-1 par-3 spn-1 src-1 Abstract: G-protein signaling plays important roles in asymmetric cell division. In C elegans embryos, homologs of receptor-independent G protein activators, GPR-1 and GPR-2 (GPR-1/2), function together with Galpha (GOA-1 and GPA-16) to generate asymmetric spindle pole elongation during divisions in the P lineage. Although Galpha is uniformly localized at the cell cortex, the cortical localization of GPR-1/2 is asymmetric in dividing P cells. In this report, we show that the asymmetry of GPR-1/2 localization depends on PAR-3 and its downstream intermediate LET-99. Furthermore, in addition to its involvement in spindle elongation, Galpha is required for the intrinsically programmed nuclear rotation event that orients the spindle in the one-cell. LET-99 functions antagonistically to the Galpha/GPR-1/2 signaling pathway, providing an explanation for how Galpha-dependent force is regulated asymmetrically by PAR polarity cues during both nuclear rotation and anaphase spindle elongation. In addition, Galpha and LET-99 are required for spindle orientation during the extrinsically polarized division of EMS cells. In this cell, both GPR-1/2 and LET-99 are asymmetrically localized in response to the MES-1/SRC-1 signaling pathway. Their localization patterns at the EMS/P-2 cell boundary are complementary, suggesting that LET-99 and Galpha/GPR-1/2 signaling function in opposite ways during this cell division as well. These results provide insight into how polarity cues are transmitted into specific spindle positions in both extrinsic and intrinsic pathways of asymmetric cell division. ------------------- Key: 6290 Medline: 14534136 Authors: Ding M;Goncharov A;Jin Y;Chisholm AD Title: C. elegans ankyrin repeat protein VAB-19 is a component of epidermal attachment structures and is essential for epidermal morphogenesis. Citation: Development 130: 5791-5801 2003 Type: ARTICLE Genes: let-805 mup-4 pat-3 sma-1 smg-3 vab-10 vab-19 nDf2 Abstract: Elongation of the epidermis of the nematode Caenorhabditis elegans involves both actomyosin-mediated changes in lateral epidermal cell shape and body muscle attachment to dorsal and ventral epidermal cells via intermediate-filament/hemidesmosome structures. vab-19 mutants are defective in epidermal elongation and muscle attachment to the epidermis. VAB-19 is a member of a conserved family of ankyrin repeat-containing proteins that includes the human tumor suppressor Kank. In epidermal cells, VAB-19::GFP localizes with components of epidermal attachment structures. In vab-19 mutants, epidermal attachment structures form normally but do not remain localized to muscle-adjacent regions of the epidermis. VAB-19 localization requires function of the transmembrane attachment structure component Myotactin. vab-19 mutants also display aberrant actin organization in the epidermis. Loss of function in the spectrin SMA-1 partly bypasses the requirement for VAB-19 in elongation, suggesting that VAB-19 and SMA-1/spectrin might play antagonistic roles in regulation of the actin cytoskeleton. ------------------- Key: 6291 Medline: 14623821 Authors: Vogel C;Teichmann SA;Chothia C Title: The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Citation: Development 130: 6317-6328 2003 Type: ARTICLE Genes: Abstract: Drosophila melanogaster is an arthropod with a much more complex anatomy and physiology than the nematode Caenorhabditis elegans. We investigated one of the protein superfamilies in the two organisms that plays a major role in development and function of cell-cell communication: the immunoglobulin superfamily (IgSF). Using hidden Markov models, we identified 142 IgSF proteins in Drosophila and 80 in C. elegans. Of these, 58 and 22, respectively, have been previously identified by experiments. On the basis of homology and the structural characterisation of the proteins, we can suggest probable types of function for most of the novel proteins. Though overall Drosophila has fewer genes than C. elegans, it has many more IgSF cell-surface and secreted proteins. Half the IgSF proteins in C. elegans and three quarters of those in Drosophila have evolved subsequent to the divergence of the two organisms. These results suggest that the expansion of this protein superfamily is one of the factors that have contributed to the formation of the more complex physiological features that are found in Drosophila. ------------------- Key: 6292 Medline: 12944400 Authors: McCracken S;Longman D;Johnstone IL;Caceres JF;Blencowe BJ Title: An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation. Citation: Journal of Biological Chemistry 278: 44153-44160 2003 Type: ARTICLE Genes: rsr-1 suf-1 Abstract: SRm160 (the SR-related nuclear matrix protein of 160 kDa) functions as a splicing coactivator and 3'-end cleavage-stimulatory factor. It is also a component of the splicing-dependent exon-junction complex (EJC), which has been implicated in coupling of pre-mRNA splicing with mRNA turnover and mRNA export. We have investigated whether the association of SRm160 with the EJC is important for efficient 3'-end cleavage. The EJC components RNPS1, REF, UAP56, and Y14 interact with SRm160. However, when these factors were tethered to transcripts, only SRm160 and RNPS1 stimulated 3'-end cleavage. Whereas SRm160 stimulated cleavage to a similar extent in the presence or absence of an active intron, stimulation of 3'-end cleavage by tethered RNPS1 is dependent on an active intron. Assembly of an EJC adjacent to the cleavage and polyadenylation signal in vitro did not significantly affect cleavage efficiency. These results suggest that SRm160 stimulates cleavage independently of its association with EJC components and that the cleavage-stimulatory activity of RNPS1 may be an indirect consequence of its ability to stimulate splicing. Using RNA interference (RNAi) in Caenorhabditis elegans, we determined whether interactions between SRm160 and the cleavage machinery are important in a whole organism context. Simultaneous RNAi of SRm160 and the cleavage factor CstF-50 (Cleavage stimulation factor 50-kDa subunit) resulted in late embryonic developmental arrest. In contrast, RNAi of CstF-50 in combination with RNPS1 or REFs did not result in an apparent phenotype. Our combined results provide evidence for an evolutionarily conserved interaction between SRm160 and the 3'-end cleavage machinery that functions independently of EJC ------------------- Key: 6293 Medline: 14559182 Authors: Nelson P;Kiriakidou M;Sharma A;Maniataki E;Mourelatos Z Title: The microRNA world: small is mighty. Citation: Trends in Biochemical Sciences 28: 534-540 2003 Type: REVIEW Genes: hbl-1 let-7 lin-4 lin-14 lin-28 Abstract: A new paradigm of RNA-directed gene expression regulation has emerged recently, profound in scope but arresting in the apparent simplicity of its core mechanism. Cells express numerous small ( approximately 22 nucleotide) RNAs that act as specificity determinants to direct destruction or translational repression of their mRNA targets. These small RNAs arise from processing of double-stranded RNA by the Dicer nuclease and incorporate with proteins that belong to the Argonaute family. Small RNAs might also target and silence homologous DNA sequences. The immense potential of small RNAs as controllers of gene networks is just beginning to unfold. ------------------- Key: 6294 Medline: 12966085 Authors: Dowell P;Otto TC;Adi S;Lane MD Title: Convergence of peroxisome proliferator-activated receptor gamma and Foxo1 signaling pathways. Citation: Journal of Biological Chemistry 278: 45485-45491 2003 Type: ARTICLE Genes: daf-12 daf-16 Abstract: The forkhead factor Foxo1 (or FKHR) was identified in a yeast two-hybrid screen as a peroxisome proliferator-activated receptor (PPAR) gamma-interacting protein. Foxo1 antagonized PPARgamma activity and vice versa indicating that these transcription factors functionally interact in a reciprocal antagonistic manner. One mechanism by which Foxo1 antagonizes PPARgamma activity is through disruption of DNA binding as Foxo1 inhibited the DNA binding activity of a PPARgamma/retinoid X receptor alpha heterodimeric complex. The Caenorhabditis elegans nuclear hormone receptor, DAF-12, interacted with the C. elegans forkhead factor, DAF-16, paralleling the interaction between PPARgamma and Foxo1. daf-12 and daf-16 have been implicated in C. elegans insulin-like signaling pathways, and PPARgamma and Foxo1 likewise have been linked to mammalian insulin signaling pathways. These results suggest a convergence of PPARgamma and Foxo1 signaling that may play a role in insulin action and the insulinomimetic properties of PPARgamma ligands. A more general convergence of nuclear hormone receptor and forkhead factor pathways may be important for multiple biological processes and this convergence may be evolutionarily conserved. ------------------- Key: 6295 Medline: 14559923 Authors: Brooks DR;Appleford PJ;Murray L;Isaac RE Title: An essential role in molting and morphogenesis of Caenorhabditis elegans for ACN-1, a novel member of the angiotensin-converting enzyme family that lacks a metallopeptidase active site. Citation: Journal of Biological Chemistry 278: 52340-52346 2003 Type: ARTICLE Genes: acn-1 ltd-1 nhr-23 nhr-25 Abstract: Genome sequence analyses predict many proteins that are structurally related to proteases but lack catalytic residues, thus making functional assignment difficult. We show that one of these proteins (ACN-1), a unique multi-domain angiotensin-converting enzyme (ACE)-like protein from Caenorhabditis elegans, is essential for larval development and adult morphogenesis. Green fluorescent protein-tagged ACN-1 is expressed in hypodermal cells, the developing vulva, and the ray papillae of the male tail. The hypodermal expression of acn-1 appears to be controlled by nhr-23 and nhr-25, two nuclear hormone receptors known to regulate molting in C. elegans. acn-1(RNAi) causes arrest of larval development because of a molting defect, a protruding vulva in adult hermaphrodites, severely disrupted alae, and an incomplete seam syncytium. Adult males also have multiple tail defects. The failure of the larval seam cells to undergo normal cell fusion is the likely reason for the severe disruption of the adult alae. We propose that alteration of the ancestral ACE during evolution, by loss of the metallopeptidase active site and the addition of new protein modules, has provided opportunities for novel molecular interactions important for post-embryonic ------------------- Key: 6296 Medline: 14668369 Authors: Geng W;Cosman P;Baek JH;Berry CC;Schafer WR Title: Quantitative classification and natural clustering of Caenorhabditis elegans behavioral phenotypes. Citation: Genetics 165: 1117-1126 2003 Type: ARTICLE Genes: egl-19 goa-1 nic-1 unc-2 unc-29 unc-36 unc-38 Abstract: Genetic analysis of nervous system function relies on the rigorous description of behavioral phenotypes. However, standard methods for classifying the behavioral patterns of mutant Caenorhabditis elegans rely on human observation and are therefore subjective and imprecise. Here we describe the application of machine learning to quantitatively define and classify the behavioral patterns of C. elegans nervous system mutants. We have used an automated tracking and image processing system to obtain measurements of a wide range of morphological and behavioral features from recordings of representative mutant types. Using principal component analysis, we represented the behavioral patterns of eight mutant types as data clouds distributed in multidimensional feature space. Cluster analysis using the k-means algorithm made it possible to quantitatively assess the relative similarities between different behavioral phenotypes and to identify natural phenotypic clusters among the data. Since the patterns of phenotypic similarity identified in this study closely paralleled the functional similarities of the mutant gene products, the complex phenotypic signatures obtained from these image data appeared to represent an effective diagnostic of the mutants' underlying molecular defects. ------------------- Key: 6297 Medline: 14668370 Authors: Rizzon C;Martin E;Marais G;Duret L;Segalat L;Biemont C Title: Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans. Citation: Genetics 165: 1127-1135 2003 Type: ARTICLE Genes: mut-7 Abstract: To identify the factors (selective or mutational) that affect the distribution of transposable elements (TEs) within a genome, it is necessary to compare the pattern of newly arising element insertions to the pattern of element insertions that have been fixed in a population. To do this, we analyzed the distribution of recent mutant insertions of the Tc1, Tc3, and Tc5 elements in a mut-7 background of the nematode Caenorhabditis elegans and compared it to the distribution of element insertions (presumably fixed) within the sequenced genome. Tc1 elements preferentially insert in regions with high recombination rates, whereas Tc3 and Tc5 do not. Although Tc1 and Tc3 both insert in TA dinucleotides, there is no clear relationship between the frequency of insertions and the TA dinucleotide density. There is a strong selection against TE insertions within coding regions: the probability that a TE will be fixed is at least 31 times lower in coding regions than in noncoding regions. Contrary to the prediction of theoretical models, We found that the selective pressure against TE insertions does not increase with the recombination rate. These findings indicate that the distribution of these three transposon families in the genome of C. elegans is determined essentially by just two factors: the pattern of insertions, which is a characteristic of each family, and the selection against ------------------- Key: 6298 Medline: 14668410 Authors: Cinar HN;Richards KL;Oommen KS;Newman AP Title: The EGL-13 SOX domain transcription factor affects the uterine pi cell lineages in Caenorhabditis elegans. Citation: Genetics 165: 1623-1628 2003 Type: ARTICLE Genes: cog-2 egl-13 lin-11 lin-12 Abstract: We isolated egl-13 mutants in which the pi cells of the Caenorhabditis elegans uterus initially appeared to develop normally but then underwent an extra round of cell division. The data suggest that egl-13 is required for maintenance of the pi cell fate. ------------------- Key: 6299 Medline: 14703012 Authors: Karabinos A;Bussing I;Schulze E;Wang J;Weber K;Schnabel R Title: Functional analysis of the single calmodulin gene in the nematode Caenorhabditis elegans by RNA interference and 4-D microscopy. Citation: European Journal of Cell Biology 82: 557-563 2003 Type: ARTICLE Genes: cal-1 cal-2 cal-3 cal-4 cmd-1 nmy-1 Abstract: Calmodulin (CaM), a small calcium-binding protein, is the key mediator of numerous calcium-induced changes in cellular activity. Its ligands include enzymes, cytoskeletal proteins and ion channels, identified in large part by biochemical and cell biological approaches. Thus far it has been difficult to assess the function of CaM genetically, because of the maternal supply in Drosophila and the presence of at least three nonallelic genes in vertebrates. Here we use the unique possibility offered by the C. elegans model system to inactivate the single CaM gene (cmd-1) through RNA interference (RNAi). We show that the RNAi microinjection approach results in a severe embryonic lethal phenotype. Embryos show disturbed morphogenesis, aberrant cell migration patterns, a striking hyperproliferation of cells and multiple defects in apoptosis. Finally, we show that RNAi delivery by the feeding protocol does not allow the efficient silencing of the CaM gene obtained by microinjection. General differences between the two delivery methods are discussed. ------------------- Key: 6300 Medline: 14680656 Authors: Hill JK;Gillespie PG Title: Seeing touch: moving closer to the worm mechanotransduction complex. Citation: Current Biology 13: R967-R969 2003 Type: REVIEW Genes: mec-4 mec-10 Abstract: In touch receptor cells of the nematode, two channel subunits of the DEG/ENaC family have long been thought to carry out mechanotransduction. New work shows that these channel subunits are responsible for events that occur within 50 milliseconds of transduction, and may be the transduction channel subunits themselves. ------------------- Key: 6301 Medline: 14662656 Authors: Grad LI;Lemire BD Title: Mitochondrial complex I mutations in Caenorhabditis elegans produce cytochrome c oxidase deficiency, oxidative stress and vitamin-responsive lactic acidosis. Citation: Human Molecular Genetics 13: 303-314 2004 Type: ARTICLE Genes: nuo-1 Abstract: Mitochondrial dysfunction, with an estimated incidence of 1 in 10 000 live births, is among the most common genetically determined conditions. Missense mutations in the human NDUFV1 gene, which encodes the 51 kDa active site subunit of the NADH-ubiquinone oxidoreductase or complex I, can lead to severe neurological disorders. Owing to the rare and often sporadic nature of mitochondrial disorders, the mechanisms of pathogenesis of most mutations remain poorly understood. We have generated transgenic strains of Caenorhabditis elegans that express disease-causing mutations in the nuo-1 gene, the C. elegans homolog of the NDUFV1 gene. The transgenic strains demonstrate hallmark features of complex I dysfunction such as lactic acidosis and decreased NADH-dependent mitochondrial respiration. They are also hypersensitive to exogenous oxidative stress, suggesting that cellular defense mechanisms against reactive oxygen species are already taxed by an endogenous stress. The lactic acidosis induced by the NDUFV1 mutations could be partially corrected with the vitamins riboflavin and thiamine or with sodium dichloroacetate, an activator of the pyruvate dehydrogenase complex, resulting in significant increases in animal fitness. Surprisingly, cytochrome c oxidase activity and protein levels were reduced, establishing a connection between complexes I and IV. Our results indicate that complex I mutations exert their pathogenic effects in multiple ways: by impeding the metabolism of NADH, by increasing the production of reactive oxygen species, and by interfering with the function or assembly of other mitochondrial respiratory chain components. ------------------- Key: 6302 Medline: 14734103 Authors: Millet ACM;Ewbank JJ Title: Immunity in Caenorhabditis elegans. Citation: Current Opinion in Immunology 16: 4-9 2004 Type: REVIEW Genes: abf-2 age-1 akt-1 akt-2 daf-2 daf-4 daf-16 dbl-1 lon-1 mab-21 mef-2 nsy-1 pdk-1 pmk-1 sek-1 skn-1 sma-2 sma-3 sma-4 sma-6 unc-43 Abstract: Until very recently it was not known whether the invertebrate Caenorhabditis elegans was capable of mounting a specific immune response to protect itself from pathogens. It has only just become clear that this simple nematode in fact possesses a complex innate immune system, involving multiple signalling pathways and an armoury of antimicrobial proteins and peptides. Genetic and microarray approaches are now revealing the molecular cross-talk that exists between the different signalling cascades. ------------------- Key: 6303 Medline: 14701877 Authors: Karp X;Greenwald I Title: Post-transcriptional regulation of the E/Daughterless ortholog HLH-2, negative feedback, and birth order bias during the AC/VU decision in C. elegans. Citation: Genes & Development 17: 3100-3111 2003 Type: ARTICLE Genes: hlh-2 lag-2 lin-12 Abstract: The anchor cell/ventral uterine precursor cell (AC/VU) decision in Caenorhabditis elegans is a canonical example of lin-12/Notch-mediated lateral specification. Two initially equivalent cells interact via the receptor LIN-12 and its ligand LAG-2, so that one becomes the AC and the other a VU. During this interaction, feedback loops amplify a small difference in lin-12 activity, limiting lin-12 transcription to the presumptive VU and lag-2 transcription to the presumptive AC. Here, we find that hlh-2 appears to be required for the VU fate and directly activates lag-2 transcription in the presumptive AC. HLH-2 appears to accumulate selectively in the presumptive AC prior to differential transcription of lin-12 or lag-2, and is therefore the earliest detectable difference between the two cells undergoing the AC/VU decision. The restricted accumulation of HLH-2 to the presumptive AC reflects post-transcriptional down-regulation of HLH-2 in the presumptive VU. Our observations suggest that hlh-2 is regulated as part of the negative feedback that down-regulates lag-2 transcription in the presumptive VU. Finally, we show that the AC/VU decision in an individual hermaphrodite is biased by the relative birth order of the two cells, so that the first-born cell is more likely to become the VU. We propose models to suggest how birth order, HLH-2 accumulation, and transcription of lag-2 may be linked during the AC/VU decision. ------------------- Key: 6304 Medline: Authors: Askjaer P;Galy V;Hannak E;Mattaj IW Title: Ran GTPase cycle and importins alpha and beta are essential for spindle formation and nuclear envelope assembly in living Caenorhabditis elegans embryos. Citation: Molecular Biology of the Cell 15: 3- 2004 Type: CORRECT Genes: npp-9 npp-10 Abstract: In the MATERIALS AND METHODS section and in Table 1 of the article "Ran GTPase Cycle and Importin alpha and beta Are Essential for Spindle Formation and Nuclear Envelope Assemble in Living Caenorhabditis elegans Embryos", by P. Askjaer, V. Galy, E. Hannak, and I.W. Mattaj, (Mol. Biol. Cell [2002] 13, 4355-4370), the C. elegans gene F59A2.1 encoding a homologue of vertebrate RanBP2 was incorrectly named npp-10. Instead, it should read npp-9. The authors apologize for this error. ------------------- Key: 6305 Medline: 14565976 Authors: Lu C;Srayko M;Mains PE Title: The Caenorhabditis elegans microtubule-severing complex MEI-1/MEI-2 katanin interacts differently with two superficially redundant beta-tubulin isotypes. Citation: Molecular Biology of the Cell 15: 142-150 2004 Type: Genes: mei-1 mei-2 tbb-1 tbb-2 sDf130 Abstract: The microtubule-severing protein complex katanin is required for a variety of important microtubule-base morphological changes in both animals and plants. Caenorhabditis elegans katanin is encoded by the mei-1 and mei-2 genes and is required for oocyte meiotic spindle formation and must be inactivated before the first mitotic cleavage. We identified a mutation, sb26, in the tbb-2 beta-tubulin gene that partially inhibits MEI-1/MEI-2 activity: sb26 rescues lethality caused by ectopic MEI-1/MEI-2 expression during mitosis, and sb26 increases meiotic defects in a genetic background where MEI-1/MEI-2 activity is lower than normal. sb26 does not interfere with MEI-1/MEI-2 microtubule localization, suggesting that this mutation likely interferes with severing. Tubulin deletion alleles and RNA-mediated interference revealed that TBB-2 and the other germline enriched beta-tubulin isotype, TBB-1, are redundant for embryonic viability. However, limiting MEI-1/MEI-2 activity in these experiments revealed that MEI-1/MEI-2 preferentially interacts with TBB-2-containing microtubules. Our results demonstrate that these two superficially redundant beta-tubulin isotypes have functionally distinct roles in vivo. ------------------- Key: 6306 Medline: 14565969 Authors: Dang H;Li Z;Skolnik EY;Fares H Title: Disease-related myotubularins functions in endocytic traffic in Caenorhabditis elegans. Citation: Molecular Biology of the Cell 15: 189-196 2004 Type: ARTICLE Genes: arf-6 cup-6 cup-10 mtm-6 mtm-9 Abstract: MTM1, MTMR2, and SBF2 belong to a family of proteins called the myotubularins. X-linked myotubular myopathy, a severe congenital disorder characterized by hypotonia and generalized muscle weakness in newborn males, is caused by mutations in MTM1 (Laporte et al., 1996). Charcot-Marie-Tooth types 4131 and 4132 are severe demyelinating neuropathies caused by mutations in MTMR2 (Bolino et al., 2000) and SBF2/MTMR13 (Senderek et al., 2003), respectively. Although several myotubularins are known to regulate phosphoinositide-phosphate levels in cells, little is known about the actual cellular process that is defective in patients with these diseases. Mutations in worm MTM-6 and MTM-9, myotubularins belonging to two subgroups, disorganize phosphoinositide 3-phosphate localization and block endocytosis in the coelomocytes of Caenorhabditis elegans. We demonstrate that MTM-6 and MTM-9 function as part of a complex to regulate an endocytic pathway that involves the Arf6 GTPase, and we define protein domains required for MTM-6 activity. ------------------- Key: 6307 Medline: 14702046 Authors: Bean CJ;Schaner CE;Kelly WG Title: Meiotic pairing and imprinted X chromatin assembly in Caenorhabditis elegans. Citation: Nature Genetics 36: 100-105 2004 Type: ARTICLE Genes: her-1 him-3 him-8 tra-2 sDp1 sDp2 sDp3 Abstract: The genetic imprinting of individual loci or whole chromosomes, as in imprinted X-chromosome inactivation in mammals(1,2), is established and reset during gametogenesis; defects in this process in the parent can result in disease in the offspring(3). We describe a sperm-specific chromatin-based imprinting of the X chromosome in the nematode Caenorhabditis elegans that is restricted to histone H3 modifications. The epigenetic imprint is established during spermatogenesis and its stability in the offspring is affected by the presence of a pairing partner during meiosis in the parental germ line. We observed that DNA lacking a pairing partner during meiosis, the normal situation for the X chromosome in males, is targeted for methylation of histone H3 at Lys9 (H3-Lys9) and can be silenced. Targeting unpaired DNA for silencing during meiosis, a potential hallmark of genome defense, could therefore have a conserved role in imprinted X-chromosome inactivation and, ultimately, in sex ------------------- Key: 6308 Medline: 14681585 Authors: Newbury S;Woollard A Title: The 5'-3' exoribonuclease xrn-1 is essential for ventral epithelial enclosure during C. elegans embryogenesis. Citation: RNA 10: 59-65 2004 Type: ARTICLE Genes: dcr-1 xrn-1 Abstract: Ribonucleases have been studied in yeast and bacteria, but their biological significance to multicellular organisms is virtually unknown. However, there is increasing evidence that specific, timed transcript degradation is critical for regulation of many cellular processes, including early development and RNA interference. in this report we have investigated the effects of the 5'-3' exoribonuclease xrn-1 on the development of the nematode worm Caenorhabditis elegans. Silencing of xrn-1 expression using RNA interference results in embryos that fail to complete ventral enclosure, where the outer layer of cells normally closes over the mesoderm in a purse-string movement. Our data suggest that xrn-1 is involved in a critical aspect of epithelial movement and reveal an unexpected link between RNA stability and morphogenesis. Because xrn-1 is highly conserved in all eukaryotes, it is possible that it plays a role in similar morphological processes such as dorsal or thorax closure in Drosophila and wound healing in humans. In contrast to work in human tissue culture cells, where the 3'-5' pathway has been shown to be the most important for degradation of mRNAs. Our work shows that the 5'-3' degradation pathway is crucially important at a critical stage of development in C elegans. We have also investigated whether xrn-1 can influence the response of C. elegans to RNA interference. Our data indicate that xrn-1 plays a facilitating, but not crucial role in this process. ------------------- Key: 6309 Medline: 14688791 Authors: Nishiwaki K;Kubota Y;Chigira Y;Roy SK;Suzuki M;Schvarzstein M;Jigami Y;Hisamoto N;Matsumoto K Title: An NDPase links ADAM protease glycosylation with organ morphogenesis in C. elegans. Citation: Nature Cell Biology 6: 31-37 2004 Type: ARTICLE Genes: dpy-7 mec-7 mig-17 mig-23 unc-54 Abstract: In the nematode Caenorhabditis elegans, the gonad acquires two U-shaped arms through the directed migration of its distal tip cells (DTCs), which are located at the tip of the growing gonad arms(1). A member of the ADAM (a disintegrin and metalloprotease) family, MIG-17, regulates directional migration of DTCs: MIG-17 is synthesized and secreted from the muscle cells of the body wall, and diffuses to the gonad where it is required for DTC migration(2). The mig-23 mutation causes defective migration of DTCs and interacts genetically with mig-17. Here, we report that mig-23 encodes a membrane-bound nucleoside diphosphatase (NDPase) required for glycosylation and proper localization of MIG-17. Our findings indicate that an NDPase affects organ ------------------- Key: 6310 Medline: 14697201 Authors: Malone CJ;Misner L;Le Bot N;Tsai MC;Campbell JM;Ahringer J;White JG Title: The C. elegans Hook protein, ZYG-12, mediates the essential attachment between the centrosome and nucleus. Citation: Cell 115: 825-836 2003 Type: ARTICLE Genes: dhc-1 dli-1 spd-5 sun-1 tba-1 tba-2 zyg-9 zyg-12 Abstract: The centrosome and nucleus are intimately associated in most animal cells, yet the significance of this interaction is unknown. Mutations in the zyg-12 gene of Caenorhabditis elegans perturb the attachment of the centrosome to the nucleus, giving rise to aberrant spindles and ultimately, DNA segregation defects and lethality. These phenotypes indicate that the attachment is essential. ZYG-12 is a member of the Hook family of cytoskeletal linker proteins and localizes to both the nuclear envelope (via SUN-1) and centrosomes. ZYG-12 is able to bind the dynein subunit DLI-1 in a two-hybrid assay and is required for dynein localization to the nuclear envelope. Loss of dynein function causes a low percentage of defective centrosome/nuclei interactions in both Drosophila and Caenorhabditis elegans. We propose that dynein and ZYG-12 move the centrosomes toward the nucleus, followed by a ZYG-12/SUN-1-dependent anchorage. ------------------- Key: 6311 Medline: 14697358 Authors: Pang KM;Ishidate T;Nakamura K;Shirayama M;Trzepacz C;Schubert CM;Priess JR;Mello CC Title: The minibrain kinase homolog, mbk-2, is required for spindle positioning and asymmetric cell division in early C. elegans embryos. Citation: Developmental Biology 265: 127-139 2004 Type: ARTICLE Genes: mbk-2 mei-1 mel-26 mex-5 mex-6 par-1 par-2 par-3 pie-1 Abstract: In the newly fertilized Caenorhabditis elegans zygote, cytoplasmic determinants become localized asymmetrically along the anterior-posterior (A - P) axis of the embryo. The mitotic apparatus then orients so as to cleave the embryo into anterior and posterior blastomeres that differ in both size and developmental potential. Here we describe a role for MBK-2, a member of the Dyrk family of protein kinases, in asymmetric cell division in C. elegans. In mbk-2 mutants, the initial mitotic spindle is misplaced and cytoplasmic factors, including the germline-specific protein PIE-1, are mislocalized. Our findings support a model in which MBK-2 down-regulates the katanin-related protein MEI-1 to control spindle positioning and acts through distinct, as yet unknown factors, to control the localization of cytoplasmic determinants. These findings in conjunction with work from Schizosaccharomyces pombe indicate a possible conserved role for Dyrk family kinases in the regulation of spindle placement during cell ------------------- Key: 6312 Medline: 14704165 Authors: Colosimo ME;Tran S;Sengupta P Title: The divergent orphan nuclear receptor ODR-7 regulates olfactory neuron gene expression via multiple mechanisms in Caenorhabditis elegans. Citation: Genetics 165: 1779-1791 2003 Type: ARTICLE Genes: nhr-74 nsy-1 odr-1 odr-7 odr-10 str-2 Abstract: Nuclear receptors regulate numerous critical biological processes. The C. elegans genome is predicted to encode similar to270 nuclear receptors of which >250 are unique to nematodes. ODR-7 is the only member of this large divergent family whose functions have been defined genetically. ODR-7 is expressed in the AWA olfactory neurons and specifies AWA sensory identity by promoting the expression of AWA-specific signaling genes and repressing the expression of an AWC-specific olfactory receptor gene. To elucidate the molecular mechanisms of action of a divergent nuclear receptor, we have identified residues and domains required for different aspects of ODR-7 function in vivo. ODR-7 utilizes an unexpected diversity of mechanisms to regulate the expression of different sets of target genes. Moreover, these mechanisms are distinct in normal and heterologous cellular contexts. The odr-7ortholog in the closely related nematode C. briggsae can fully substitute for all ODR-7-mediated functions, indicating conservation of function across 25-120 million years of divergence. ------------------- Key: 6313 Medline: 14704166 Authors: Katju V;Lynch M Title: The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Citation: Genetics 165: 1793-1803 2003 Type: ARTICLE Genes: Abstract: The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with less than or equal to10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms. ------------------- Key: 6314 Medline: 14704167 Authors: Bastiani CA;Gharib S;Simon MI;Sternberg PW Title: Caenorhabditis elegans G(alpha)(q) regulates egg-laying behavior via a PLC(beta)-independent and serotonin-dependent signaling pathway and likely functions both in the nervous system and in muscle. Citation: Genetics 165: 1805-1822 2003 Type: ARTICLE Genes: cha-1 egl-1 egl-8 egl-30 itr-1 tpa-1 unc-13 Abstract: egl-30encodes the single C. elegans ortholog of vertebrate Got,, family members. We analyzed the expression pattern of EGL-30 and found that it is broadly expressed, with highest expression in the nervous system and in pharyngeal muscle. We isolated dominant, gain-of-function alleles of egl-30 as intragenic revertants of an egl-30 reduction-of-function mutation. Using these gain-of function mutants and existing reduction-of-function mutants, we examined the site and mode of action of EGL-30. On the basis of pharmacological analysis, it has been determined that egl-30 functions both in the nervous system and in the vulval muscles for egg-laying behavior. Genetic epistasis over mutations that eliminate detectable levels of serotonin reveals that egl-30 requires serotonin to regulate egg laying. Furthermore, pharmacological response assays strongly suggest that EGL-30 may directly couple to a serotonin receptor to mediate egg laying. We also examined genetic interactions with mutations in the gene that encodes the single C. elegans homolog of PLCbeta and mutations in genes that encode signaling molecules downstream of PLCbeta. We conclude that PLCbeta functions in parallel with egl-30 with respect to egg laying or is not the major effector of EGL-30. In contrast, PLCbeta-mediated signaling is likely downstream of EGL-30 with respect to pharyngeal-pumping behavior. Our data indicate that there are multiple signaling pathways downstream of EGL-30 and that different pathways could predominate with respect to the regulation of different behaviors. ------------------- Key: 6315 Medline: 14688212 Authors: Rostaing P;Weimer RM;Jorgensen EM;Triller A;Bessereau JL Title: Preservation of immunoreactivity and fine structure of adult C. elegans tissues using high-pressure freezing. Citation: Journal of Histochemistry & Cytochemistry 52: 1-12 2004 Type: ARTICLE Genes: acr-5 ajm-1 gap-43 lin-15 unc-17 vab-10 Abstract: The location of a protein labeled by immunogold techniques can be resolved under an electron beam to within nanometers of its epitope, a resolution that makes immunoelectron microscopy a valuable tool for studies of cell biology. However, tissues in the nematode Caenorhabditis elegans are difficult to preserve for immunoelectron microscopic studies. The animal's cuticle slows the diffusion of solutions into the animal and thus makes it difficult to preserve both immunoreactivity and cell morphology. Here we describe a protocol that circumvents these problems. Specifically, we instantly immobilized tissue in vitreous ice by freezing living adult animals under high pressure. Frozen specimens were then chemically fixed, dehydrated, and embedded at low temperatures. As a result, chemical diffusion across the cuticle could occur over an extended period without morphological deterioration. We show that this method is capable of preserving both cell morphology, including fine structures, and immunoreactivity. Therefore, it provides a means to characterize the localization of endogenous proteins and exogenous proteins, such as the green fluorescent protein (GFP), with respect to subcellular compartments in C elegans tissues by using postembedding immunogold labeling. ------------------- Key: 6316 Medline: 14740010 Authors: Lochnit G;Geyer R Title: Evidence for the presence of the Kennedy and Bremer-Greenberg pathways in Caenorhabditis elegans. Citation: Acta Biochimica Polonica 50: 1239-1243 2003 Type: ARTICLE Genes: Abstract: Nematodes were found to synthesize phosphorylcholine-containing molecules not present in higher organisms, i.e. phosphorylcholine-substituted glycosphingolipids and (glyco)proteins. Investigations on the biosynthesis of these structures provided first biochemical evidence for the presence of the Kennedy and Bremer-Greenberg pathways in the model organism Caenorhabditis elegans. ------------------- Key: 6317 Medline: 14646232 Authors: Takanami T;Zhang YZ;Aoki H;Abe T;Yoshida S;Takahashi H;Horiuchi S;Higashitani A Title: Efficient repair of DNA damage induced by heavy ion particles in meiotic prophase I nuclei of Caenorhabditis elegans. Citation: Journal of Radiation Research 44: 271-276 2003 Type: ARTICLE Genes: atl-1 ced-3 rad-51 rdh-1 Abstract: The effects of heavy ion particle irradiation on meiosis and reproductive development in the nematode Caenorhabditis elegans were studied. Meiotic pachytene nuclei are significantly resistant to particle irradiation by the heavy ions carbon and argon, as well as to X-rays, but not UV, whereas diplotene to diakinesis stage oocytes and early embryonic cells are not. Chromosomal abnormalities appear in mitotic cells and in maturing oocytes irradiated with heavy ion particles during the diplotene to the early diakinesis stages, but not in oocytes irradiated during the pachytene stage. The pachytene nuclei of ced-3 mutants, which are defective in apoptosis, are similarly resistant to ionizing radiation, but pachytene nuclei depleted for Ce-atl-1 (ataxia-telangiectasia like 1) or Ce-rdh-1/rad-51 are more sensitive. Pachytene nuclei thus appear to effectively repair heavy ion-induced DNA damage by the meiotic homologous recombination system. ------------------- Key: 6318 Medline: 14704673 Authors: Podbilewicz B Title: Sweet control of cell migration, cytokinesis and organogenesis. Citation: Nature Cell Biology 6: 9-11 2004 Type: REVIEW Genes: mig-17 mig-23 sqv-5 Abstract: Why are proteins glycosylated? On the basis of new studies, I propose two models to clarify the specific functions of glycosylation in worms. The first explains how intra- and inter-cellular trafficking of an N-glycosylated disintegrin-metalloprotease guides somatic gonadal cells through their migratory route, determining the shape of an organ. The second explains how rigid coats of secreted chondroitin proteoglycans bend membranes to drive cytokinesis and epithelial invagination. ------------------- Key: 6319 Medline: 14697357 Authors: Dichtel-Danjoy ML;Felix MA Title: The two steps of vulval induction in Oscheius tipulea CEW1 recruit common regulators including a MEK kinase. Citation: Developmental Biology 265: 113-126 2004 Type: ARTICLE Genes: Abstract: The cell interactions that specify the spatial pattern of vulval precursor cell (VPC) fates differ between the nematodes Oscheius tipulae CEW1 and Caenorhabditis elegans. In the former, the centered pattern of fates is obtained by two successive inductions from the gonadal anchor cell, whereas in the latter, a single inductive step by the anchor cell (EGF-Ras-MAP kinase pathway) can act as a morphogen and is reinforced by lateral signaling between the vulval precursors (Notch pathway). We performed a genetic screen for vulva mutants in O. tipulae CEW1. Here we present the mutants that specifically affect the vulval induction mechanisms. Phenotypic and epistatic analyses of these mutants show that both vulval induction steps share common components, one of which appears to be MEK kinase(s). Moreover, the inductive pathway (including MEK kinase) influences the competence of the vulval precursor cells and more strikingly their division pattern as well, irrespective of their vulval fate. Finally, a comparison of vulval mutant phenotypes obtained in C. elegans and O. tipulae CEW1 highlights the evolution of vulval induction mechanisms between the two species. ------------------- Key: 6320 Medline: 14616061 Authors: Schneider SQ;Bowerman B Title: Cell polarity and the cytoskeleton in the Caenorhabditis elegans zygote. Citation: Annual Review of Genetics 37: 221-249 2003 Type: REVIEW Genes: cdc-42 cyk-1 cul-3 efn-2 gld-1 glp-1 goa-1 gpa-16 gpb-1 gpc-1 gpr-1 gpr-2 ipp-5 let-23 let-99 lin-3 lin-5 lip-1 mei-1 mei-2 mex-1 mex-3 mex-5 mex-6 mlc-4 nmy-2pal-1 par-1 par-2 par-3 par-4 par-5 par-6 pfn-1 pie-1 pkc-3 plk-1 pod-1 pos-1 ric-8 spe-11 vab-1 zen-4 zif-1 Abstract: The anterior-posterior axis of the Caenorhabditis elegans zygote forms shortly after fertilization when the sperm pronucleus and its associated centrosomal asters provide a cue that establishes the anterior-posterior (AP) body axis. In response to this cue, the microfilament cytoskeleton polarizes the distribution of a group of widely conserved, cortically localized regulators called the PAR proteins, which are required for the first mitotic division to be asymmetric. These asymmetries include a posterior displacement of the first mitotic spindle and the differential segregation of cell-fate determinants to the anterior and posterior daughters produced by the first cleavage of the zygote. Here we review recent advances in our understanding of the mechanisms that polarize the one-cell zygote to generate an AP axis of asymmetry. ------------------- Key: 6321 Medline: 14688121 Authors: Tawill S;Le Goff L;Ali F;Blaxter M;Allen JE Title: Both free-living and parasitic nematodes induce a characteristic Th2 response that is dependent on the presence of intact glycans. Citation: Infection and Immunity 72: 398-407 2004 Type: ARTICLE Genes: Abstract: Infection with parasitic nematodes is characterized by the induction of a profound type 2 immune response. We have studied the role of glycans in the induction of the skewed type 2 response by antigens of the parasitic nematode Brugia malayi as well as the free-living nematode Caenorhabditis elegans. Lymph node cells from BALB/c mice immunized with soluble extracts of the two nematodes showed distinct antigen-specific proliferation and cytokine production; however, both nematodes induced antigen-specific-interleukin 4 (IL-4) production, demonstrating that the induction of a biased type 2 response is not unique to parasitic nematodes. Sodium periodate-treated soluble extracts of both nematodes consistently induced significantly less IL-4 production than the respective mock-treated extracts, indicating that glycans play a critical role in the induction of the Th2 immune response by these nematodes. The glycan-dependent induction of the Th2-potentiating cytokine IL-4 occurs by 72 h postinoculation. Our data suggest that glycan determinants common to nematodes act as ligands, displaying distinct molecular patterns that trigger the immune system to launch a biased Th2 immune response upon exposure to these organisms or their products. Further, the similarity of our findings to those for Schistosoma mansoni egg antigen is striking considering the enormous phylogenetic distance between nematodes and trematodes. These data thus have important implications for how the mammalian host responds to widely divergent metazoan invaders and suggest that the powerful C. elegans model system can be used to ------------------- Key: 6322 Medline: 14738755 Authors: Felix MA Title: Genomes: a helpful cousin for our favourite worm. Citation: Current Biology 14: R75-R77 2004 Type: REVIEW Genes: lin-48 Abstract: The recently published genome of the nematdoe Caenorhabditis briggsae provides a drastic improvement in structural annotation of the C. elegans genome, as well as a promising source of evolutionary comparisons. ------------------- Key: 6323 Medline: 14738731 Authors: Tijsterman M;May RC;Simmer F;Okihara KL;Plasterk RHA Title: Genes required for systemic RNA interference in Caenorhabditis elegans. Citation: Current Biology 14: 111-116 2004 Type: ARTICLE Genes: cav-1 cav-2 dyn-1 ehs-1 par-1 par-6 pos-1 rab-5 rme-1 rme-8 rsd-2 rsd-3 rsd-4 rsd-6 rsd-8 unc-11 unc-15 unc-22 Abstract: RNA interference (RNAi) in the nematode worm, Caenorhabditis elegans, occurs systemically. Double-stranded RNA (dsRNA) provided in the diet can be absorbed from the gut lumen and distributed throughout the body, triggering RNAi in tissues that are not exposed to the initial dsRNA trigger [1]. This is in marked contrast to other animals, in which RNAi does not spread from targeted tissues to neighboring cells [2]. Here, we report the characterization of mutants defective in the systemic aspect of RNAi, but not in the core RNAi process itself. Analysis of these mutants suggests that dsRNA uptake is a specific process involving several unique proteins. ------------------- Key: 6324 Medline: 14696039 Authors: Jones AK;Sattelle DB Title: Functional genomics of the nicotinic acetylcholine receptor gene family of the nematode, Caenorhabditis elegans. Citation: BioEssays 26: 39-49 2003 Type: REVIEW Genes: acr-2 acr-3 acr-4 acr-5 acr-6 acr-7 acr-8 acr-9 acr-10 acr-11 acr-12 acr-13 acr-14 acr-15 acr-16 acr-17 acr-18 acr-19 acr-20 acr-21 acr-23 deg-3 des-2 lev-1 lev-9 lev-10 lev-11 ric-3 tpa-1 unc-22 unc-29 unc-38 unc-50 unc-63 Abstract: Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that bring about a diversity of fast synaptic actions. Analysis of the Caenorhabditis elegans genome has revealed one of the most-extensive and diverse nAChR gene families known, consisting of at least 27 subunits. Striking variation with possible functional implications has been observed in normally conserved motifs at the acetylcholine-binding site and in the channel-lining region. Some nAChR subunits are particular to neurons whilst others are present in both neurons and muscles. The localization of subunits in non-synaptic regions suggests novel roles for nAChRs. Genetic and heterologous expression studies have identified a subset of nAChR subunits that are important drug targets while the study of mutants has identified genes functionally-linked to nAChRs. Future studies using C. elegans offer the prospect of increasing our understanding of the functional diversity of a complex nAChR gene family as well as addressing the role of nAChRs and associated proteins in human disorders. ------------------- Key: 6325 Medline: Authors: Alcedo J;Kenyon C Title: Regulation of C. elegans longevity by specific gustatory and olfactory neurons. Citation: Neuron 41: 45-55 2003 Type: ARTICLE Genes: daf-2 daf-16 fem-1 fer-15 odr-1 odr-2 odr-3 odr-7 odr-10 osm-3 rrf-3 srd-1 str-2 Abstract: The life span of C. elegans is extended by mutations that inhibit the function of sensory neurons. In this study, we show that specific subsets of sensory neurons influence longevity. We find that certain gustatory neurons inhibit longevity, whereas others promote longevity, most likely by influencing insulin/IGF-1 signaling. Olfactory neurons also influence life span, and they act in a distinct pathway that involves the reproductive system. In addition, we find that a putative chemosensory G protein-coupled receptor that is expressed in some of these sensory neurons inhibits longevity. Together our findings imply that the life span of C. elegans is regulated by environmental cues and that these cues are perceived and integrated in a complex and sophisticated fashion by specific chemosensory neurons. ------------------- Key: 6326 Medline: 14730154 Authors: Kawano T;Takuwa K;Ishiguro M;Nakajima T;Kimura Y Title: Cloning and characterization of a Caenorhabditis elegans cDNA encoding a new insulin/IGF-like peptide. Citation: Bioscience Biotechnology and Biochemistry 67: 2678-2682 Type: ARTICLE Genes: Abstract: A Caenorhabditis elegans cDNA encoding a new insulin/IGF-like peptide was cloned and examined. The predicted peptide shows significant sequence similarity with the peptide Ceinsulin-1 reported previously and contains a characteristic insertion consisting of three residues in the putative B domain as with the Ceinsulin-1. The gene expression pattern during development is almost identical to that of Ceinsulin-1. The predicted tertiary structure of the peptide is quite similar to that of Ceinsulin-1, and their predicted receptor-recognition surfaces also closely match. These facts suggest that both peptides could recognize the same receptor. ------------------- Key: 6327 Medline: Authors: Chen JJ;Caswell-Chen EP Title: Why Caenorhabditis elegans adults sacrifice their bodies to progeny. Citation: Nematology 5: 641-645 2003 Type: ARTICLE Genes: Abstract: We present a novel interpretation regarding the ecology and evolution of matricidal hatching ('bagging') in Caenorhabditis elegans. Subjecting young and mature adult C elegans to stress induced matricidal hatching. The process of egg retention followed by internal hatching under starvation was reversible, depending on whether adults were returned to food before internal juveniles caused irreversible harm to the adult. We surface sterilised adult C elegans and then starved them to test the hypothesis that matricidal hatching promotes progeny survival by enhancing to some degree the transition to the dauer stage. When the surface sterilisation stress time was short, the parent C elegans enclosed many progeny that competed for resources so that apparently only a few progeny obtained sufficient nutrition to support transition to the dauer stage. Longer sterilisation stress and starvation resulted in fewer, larger progeny with a higher proportion reaching the dauer stage, suggesting a direct correlation between the phenomena. In stressful environments, the production of even a single, stress-resistant, long-lived dauer, in lieu of progeny that cannot achieve the dauer, is a fitness advantage. The results are consistent with the hypothesis. We infer that intra-uterine hatch is a part of the C elegans life cycle, and complements androdioecy and the dauer stage to enhance progeny survival and dispersal under stress. This is a possible explanation of why a seemingly detrimental behaviour, matricidal hatching, has been perpetuated in C elegans through evolutionary time. ------------------- Key: 6328 Medline: 14681444 Authors: Gunsalus KC;Yueh WC;MacMenamin P;Piano F Title: RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Citation: Nucleic Acids Research 32: D406-D410 2004 Type: ARTICLE Genes: Abstract: RNA interference (RNAi) is being used in large-scale genomic studies as a rapid way to obtain in vivo functional information associated with specific genes. How best to archive and mine the complex data derived from these studies provides a series of challenges associated with both the methods used to elicit the RNAi response and the functional data gathered. RNAiDB (RNAi Database; http://www. rnai.org) has been created for the archival, distribution and analysis of phenotypic data from large-scale RNAi analyses in Caenorhabditis elegans. The database contains a compendium of publicly available data and provides information on experimental methods and phenotypic results, including raw data in the form of images and streaming time-lapse movies. Phenotypic summaries together with graphical displays of RNAi to gene mappings allow quick intuitive comparison of results from different RNAi assays and visualization of the gene product(s) potentially inhibited by each RNAi experiment based on multiple sequence analysis methods. RNAiDB can be searched using combinatorial queries and using the novel tool PhenoBlast, which ranks genes according to their overall phenotypic similarity. RNAiDB could serve as a model database for distributing and navigating in vivo functional information from large-scale systematic ------------------- Key: 6329 Medline: 14681445 Authors: Harris TW;Chen N;Cunningham F;Tello-Ruiz M;Antoshechkin I;Bastiani C;Bieri T;Blasiar D;Bradnam K;Chan J;Chen CK;Chen WJ;Davis P;Kenny E;Kishore R;Lawson D;Lee R;Muller HM;Nakamura C;Ozersky P;Petchers Title: WormBase: a multi-species resource for nematode biology and genomics. Citation: Nucleic Acids Research 32: D411-D417 2004 Type: ARTICLE Genes: Abstract: WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system. ------------------- Key: 6330 Medline: 14681448 Authors: Wylie T;Martin JC;Dante M;Mitreva MD;Clifton SW;Chinwalla A;Waterston RH;Wilson RK;McCarter JP Title: Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Citation: Nucleic Acids Research 32: D423-D426 2004 Type: ARTICLE Genes: Abstract: Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington University's Genome Sequencing Center (GSC), St Louis. A sister project at the University of Edinburgh and the Sanger Institute is also underway. More than 295,000 ESTs have been generated from >30 nematodes other than Caenorhabditis elegans including key parasites of humans, animals and plants. Nematode.net currently provides NemaGene EST cluster consensus sequence, enhanced online BLAST search tools, functional classifications of cluster sequences and comprehensive information concerning the ongoing generation of nematode genome data. The long-term goal of nematode.net is to provide the scientific community with the highest quality sequence information and tools for studying these diverse species. ------------------- Key: 6331 Medline: 14681447 Authors: Srinivasan J;Otto GW;Kahlow U;Geisler R;Sommer RJ Title: AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus. Citation: Nucleic Acids Research 32: D421-D422 2004 Type: ARTICLE Genes: Abstract: Pristionchus pacificus is a free-living nematode of the Diplogastridae family and was recently developed as a satellite system in evolutionary developmental biology. AppaDB, a P.pacificus database, was created (http://appadb.eb.tuebingen. mpg.de) to integrate the genomic data of P.pacificus, comprising the physical map, genetic linkage map, EST and BAC end sequence and hybridization data. This developing database serves as a repository to search and find any information regarding physical contigs or genetic markers required for mapping of mutants. Additionally, it provides a platform for the Caenorhabditis elegans community to compare nematode genetic data in an evolutionary perspective. ------------------- Key: 6332 Medline: Authors: Li S;Armstrong CM;Bertin N;Ge H;Milstein S;Boxem M;Vidalain PO;Han JDJ;Chesneau A;Hoa G;Goldberg DS;Li N;Martinez M;Rual JF;Lamesch P;Xu L;Tewari M;Wong SL;Zhang LV;Berriz GF;Jacotot L;Vaglio P;Reboul Title: A map of the interactome network of the metazoan C. Citation: Science 303: 540-543 2004 Type: ARTICLE Genes: Abstract: To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with a subset of metazoan-specific proteins, more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens. Independent coaffinity purification assays experimentally validated the overall quality of this Y2H data set. Together with already described Y2H interactions and interologs predicted in silico, the current version of the Worm Interactome (WI5) map contains similar to5500 interactions. Topological and biological features of this interactome network, as well as its integration with phenome and transcriptome data sets, lead to numerous biological hypotheses. ------------------- Key: 6333 Medline: 15002776 Authors: Conant GC;Wagner A Title: Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans. Citation: Proceedings of the Royal Society of London B 271: 89-96 Type: ARTICLE Genes: Abstract: We examine robustness to mutations in the nematode worm Caenorhabditis elegans and the role of single-copy and duplicate genes in it. We do so by integrating complete genome sequence and microarray gene expression data with results from a genome-scale study using RNA interference (RNAi) to temporarily eliminate the functions of more than 16 000 worm genes. We found that 89% of single-copy and 96% of duplicate genes show no detectable phenotypic effect in an RNAi knock-down experiment. We find that mutational robustness is greatest for closely related gene duplicates, large gene families and similarly expressed genes. We discuss the different causes of mutational robustness in single-copy and duplicate genes, as well as its evolutionary origin. ------------------- Key: 6335 Medline: Authors: Antebi A Title: Long life: a matter of taste (and smell). Citation: Neuron 41: 1-6 2004 Type: REVIEW Genes: daf-2 daf-16 Abstract: Insulin/IGF signaling has emerged as a central regulator of metazoan aging. In C. elegans, insulin-like peptides are expressed predominately in neurons. Alcedo and Kenyon demonstrate that removal of specific gustatory and olfactory neurons result in longer life, suggesting that metazoan longevity is influenced by sensory perception. ------------------- Key: 6336 Medline: 12949121 Authors: Lee KZ;Sommer RJ Title: Operon structure and trans-splicing in the nematode Pristionchus pacificus. Citation: Molecular Biology and Evolution 20: 2097-2103 2003 Type: ARTICLE Genes: Abstract: In the nematode Caenorhabditis elegans, up to 15% of the genes are organized in operons. Polycistronic precursor RNAs are processed by trans-splicing at the 5' ends of genes by adding a specific trans-spliced leader. Ten different spliced leaders are known in C. elegans that differ in sequence and abundance. The SL1 leader is most abundant and is spliced to the 5' ends of monocistronic genes and to upstream genes in operons. Trans-splicing is common among nematodes and was observed in the genera Panagrellus, Ascaris, Haemonchus, Anisakis, and Brugia. However, little is known about operons in nonrhabditid nematodes. Dolichorhabditis CEW1, another rhabditid nematode that is now called Oscheius CEW1, contains operons and SL2 trans-splicing. We have studied the presence of operons and trans-splicing in Pristionchus pacificus, a species of the Diplogastridae that has recently been developed as a satellite organism in evolutionary developmental biology. We provide evidence that P. pacificus contains operons and that downstream genes are trans-spliced to SL2. Surprisingly, the one operon analyzed so far in P. pacificus is not conserved in C. elegans, ------------------- Key: 6337 Medline: 14647240 Authors: Ameisen JC Title: Looking for death at the core of life in the light of evolution. Citation: Cell Death and Differentiation 11: 4-10 2004 Type: REVIEW Genes: Abstract: 'Nothing makes sense in biology, but in the light of evolution' wrote Theodosius Dobzhansky, one of the founders of the New Synthesis that led to the unification of evolutionary theory and genetics in the midst of the 20th century. During the last 3 years, the Nobel Committee has provided strong support to this view by highlighting the importance of seminal discoveries identifying in various, early diverging model organisms, ancestral evolutionary conserved molecular mechanisms of crucial importance for our own survival and fitness. ------------------- Key: 6338 Medline: 14685167 Authors: Knudson AG Title: Of sea urchins and worms: development and cancer. Citation: Cell Death and Differentiation 11: 11-12 2004 Type: REVIEW Genes: Abstract: The award of the 2002 Nobel Prize to Brenner, Sulston, and Horvitz was one of the most satisfying I can recall, recognizing as it did the long sought meaningful conjunction of developmental biology with cancer research. Cancer is the ultimate derangement of growth and differentiation, affecting as it does the placenta, the embryo, the fetus, the infant, the child, the adolescent, and the adult of any age. Little wonder then that developmental biologists (embryologists in bygone days) have contributed so much to our understanding of cancer's origin. Indeed, the first coherent view of cancer was painted by the great embryologist Theodor Boveri in his heuristic volume of 1914 on the origin of cancer. Having observed the developmental aberrations of sea urchin embryos that can follow upon abnormalities of centrosome number and of the segregation of chromosomes, he associated causally the already known phenomenon of centrosome abnormalities of cancer with the latter's histopathology. He further posited that such pathology could be attributed to a single chromosomally aberrant cell. ------------------- Key: 6339 Medline: 14685168 Authors: Stergiou L;Hengartner MO Title: Death and more: DNA damage response pathways in the nematode C. elegans. Citation: Cell Death and Differentiation 11: 21-28 2004 Type: REVIEW Genes: atl-1 atm-1 ced-3 ced-4 ced-9 cep-1 chk-1 chk-2 clk-2 egl-1 hpr-7 hpr-17 hsr-9 hus-1 mre-11 mrt-2 rad-5 rad-51 spo-11 Abstract: Genotoxic stress is a threat to our cells' genome integrity. Failure to repair DNA lesions properly after the induction of cell proliferation arrest can lead to mutations or large-scale genomic instability. Because such changes may have tumorigenic potential, damaged cells are often eliminated via apoptosis. Loss of this apoptotic response is actually one of the hallmarks of cancer. Towards the effort to elucidate the DNA damage-induced signaling steps leading to these biological events, an easily accessible model system is required, where the acquired knowledge can reveal the mechanisms underlying more complex organisms. Accumulating evidence coming from studies in Caenorhabditis elegans point to its usefulness as such. In the worm's germline, DNA damage can induce both cell cycle arrest and apoptosis, two responses that are spatially separated. The latter is a tightly controlled process that is genetically indistinguishable from developmental programmed cell death. Upstream of the central death machinery, components of the DNA damage signaling cascade lie and act either as sensors of the lesion or as transducers of the initial signal detected. This review summarizes the findings of several studies that specify the elements of the DNA damage-induced responses, as components of the cell cycle control machinery, the repairing process or the apoptotic outcome. The validity of C. elegans as a tool to further dissect the complex signaling network of these responses and the high potential for it to reveal important links to cancer and other ------------------- Key: 6340 Medline: Authors: Boyce M;Degterev A;Yuan J Title: Caspases: an ancient cellular sword of Damocles. Citation: Cell Death and Differentiation 11: 29-37 2004 Type: REVIEW Genes: ced-3 ced-4 csp-1 csp-2 csp-3 Abstract: Caspases are a family of cysteine proteases homologous to the Caenorhabditis elegans programmed cell death gene product CED-3. Caspases and their distant relatives, meta- and paracaspases, have been found in phylogenetically distant nonmetazoan groups, including plants, fungi and prokaryotes. This review summarizes the current information on the mechanisms and functions of non-mammalian caspases and their relatives in apoptotic and nonapoptotic processes, and explores the possible evolutionary origin of the caspase family. ------------------- Key: 6341 Medline: 14647239 Authors: Putcha GV;Johnson EM Title: "Men are but worms:" neuronal cell death in C. elegans and vertebrates. Citation: Cell Death and Differentiation 11: 38-48 2004 Type: REVIEW Genes: ced-3 ced-4 ced-9 ces-1 egl-1 tra-1 Abstract: Awarding the 2002 Nobel Prize in Physiology or Medicine to Sydney Brenner, H Robert Horvitz, and John E Sulston for 'their discoveries concerning the genetic regulation of organ development and programmed cell death (PCD)' highlights the significant contribution that the study of experimental organisms, such as the nematode Caenorhabditis elegans, has made to our understanding of human physiology and pathophysiology. Their studies of lineage determination in worms established the 'central dogma' of apoptosis: The BH3-only protein EGL-1 is induced in cells destined to die, interacts with the BCL-2-like inhibitor CED-9, displacing the adaptor CED-4, which then promotes activation of the caspase CED-3. The vast majority of cells undergoing PCD during development in C. elegans, as in vertebrates, are neurons. Accordingly, the genetic regulation of apoptosis is strikingly similar in nematode and vertebrate neurons. This review summarizes these similarities - and the important differences - in the molecular mechanisms responsible for neuronal PCD in C. elegans and vertebrates, and examines the implications that our understanding of physiological neuronal apoptosis may have for the diagnosis and treatment of acute and chronic human neurodegenerative ------------------- Key: 6342 Medline: 14711411 Authors: Boulton SJ;Martin JS;Polanowska J;Hill DE;Gartner A;Vidal M Title: BRCA1/BARD1 orthologs required for DNA repair in Caenorhabditis elegans. Citation: Current Biology 14: 33-39 2004 Type: ARTICLE Genes: brc-1 brd-1 rad-51 smt-1 tac-1 ubc-9 Abstract: Inherited germline mutations in the tumor suppressor gene BRCA1 predispose individuals to early onset breast and ovarian cancer [1]. BRCA1 together with its structurally related partner BARD1 is required for homologous recombination and DNA double-strand break repair, but how they perform these functions remains elusive [2, 3]. As part of a comprehensive search for DNA repair genes in C. elegans, we identified a BARD1 ortholog. In protein interaction screens, Ce-BRD-1 was found to interact with components of the sumoylation pathway, the TACC domain protein TAC-1, and most importantly, a homolog of mammalian BRCA1. We show that animals depleted for either Ce-brc-1 or Ce-brd-1 display similar abnormalities, including a high incidence of males, elevated levels of p53-dependent germ cell death before and after irradiation, and impaired progeny survival and chromosome fragmentation after irradiation. Furthermore, depletion of ubc-9 and tac-1 leads to radiation sensitivity and a high incidence of males, respectively, potentially linking these genes to the C. elegans BRCA1 pathway. Our findings support a shared role for Ce-BRC-1 and Ce-BRD-1 in C. elegans DNA repair processes, and this role will permit studies of the BRCA1 pathway in an organism amenable to rapid genetic and biochemical analysis. ------------------- Key: 6343 Medline: 14711416 Authors: Satterlee JS;Ryu WS;Sengupta P Title: The CMK-1 CaMKI and the TAX-4 cyclic nucleotide-gated channel regulate thermosensory neuron gene expression and function in C. elegans. Citation: Current Biology 14: 62-68 2004 Type: ARTICLE Genes: ckk-1 cmk-1 crh-1 gcy-8 nhr-38 tax-2 tax-4 ttx-1 ttx-3 Abstract: The cultivation temperature (T-c) modulates the thermosensory responses exhibited by C. elegans on thermal gradients [1-5]. The AFD sensory neurons are essential for thermosensory behaviors [2], but the molecular mechanisms by which temperature is sensed and the memory of the T-c is encoded are unknown. Here, we show that the CMK-1 Ca2+/calmodulin-dependent protein kinase I (CaMKI) and the TAX-4 cyclic nucleotide-gated channel regulate gene expression, morphology, and functions of the AFD thermosensory neurons. Mutations in cmk-1 and tax-4 result in temperature-dependent defects in AFD-specific gene expression, and TAX-4 functions are required during larval stages to maintain gene expression in the adult. CMK-1 and TAX-4 act cell autonomously to regulate AFD-mediated thermosensory behaviors. The molecular requirements for CMK-1 activity in the AFD neurons appear to be distinct from those previously described [6, 7]. We propose that the activation of distinct programs of AFD-specific gene expression at different temperatures by CMK-1 and TAX-4 enables C. elegans to sense and/or encode a memory for the T-c. ------------------- Key: 6345 Medline: Authors: Abbott AL Title: Heterochronic genes. Citation: Current Biology 13: R824-R825 2003 Type: REVIEW Genes: daf-12 hbl-1 let-7 lin-4 lin-14 lin-28 lin-29 lin-41 lin-42 lin-46 lin-57 lin-58 Abstract: ------------------- Key: 6346 Medline: 14627718 Authors: Liang J;Lints R;Foehr ML;Tokarz R;Yu L;Emmons SW;Liu J;Savage-Dunn C Title: The Caenorhabditis elegans schnurri homolog sma-9 mediates stage- and cell type-specific responses to DBL-1 BMP-related signaling. Citation: Development 130: 6453-6464 2003 Type: ARTICLE Genes: cat-2 daf-4 dbl-1 lon-1 lon-3 sma-2 sma-3 sma-4 sma-6 sma-9 Abstract: In Caenorhabditis elegans, the DBL-1 pathway, a BMP/TGFbeta-related signaling cascade, regulates body size and male tail development. We have cloned a new gene, sma-9, that encodes the C elegans homolog of Schnurri, a large zinc finger transcription factor that regulates dpp target genes in Drosophila. Genetic interactions, the sma-9 loss-of-function phenotype, and the expression pattern suggest that sma-9 acts as a downstream component and is required in the DBL-1 signaling pathway, and thus provide the first evidence of a conserved role for Schnurri proteins in BMP signaling. Analysis of sma-9 mutant phenotypes demonstrates that SMA-9 activity is temporally and spatially restricted relative to known DBL-1 pathway components. In contrast with Drosophila schnurri, the presence of multiple alternatively spliced sma-9 transcripts suggests protein isoforms with potentially different cell sublocalization and molecular functions. We propose that SMA-9 isoforms function as transcriptional cofactors that confer specific responses to DBL-1 pathway ------------------- Key: 6347 Medline: 14752152 Authors: Sternberg PW Title: A pattern of precision. Citation: Science 303: 637-638 2004 Type: REVIEW Genes: ark-1 dpy-23 egl-17 lin-12 lip-1 lst-3 lst-4 Abstract: The amazing precision with which different cell types find their correct locations in developing tissues has fascinated biologists for decades. Models of cell fate patterning during development emphasize the contrast between spatial gradients of developmental signals that act at long range and cell-to-cell signaling events that act locally. Development of the vulva in the nematode Caenorhabditis elegans provides an elegant model system for examining the patterning of cell fate in an animal. There is strong evidence that two different intercellular signals contribute to the relatively simple induction of cell fate among vulval precursor cells (VPCs): a long-range spatial gradient of epidermal growth factor (EGF) mediated by the EGF receptor (1,2) and a cell-to-cell lateral signal mediated by the Notch-like receptor LIN-12 (3-5). It is well established that the combined action of the EGF receptor and LIN-12 receptor signaling pathways generate the pattern of VPCs in the developing vulva (6); however, the molecular details of this cooperative effect have remained elusive. On page 663 of this issue, Yoo et al. (7) provide the missing molecular connection. They report that VPCs activated by a low lever of EGF are blocked from adopting a particular cell fate by a LIN-12 lateral signal ------------------- Key: 6348 Medline: 14752159 Authors: Yoo AS;Bais C;Greenwald I Title: Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development. Citation: Science 303: 663-666 2004 Type: ARTICLE Genes: ark-1 dpy-23 egl-17 gap-1 lag-1 let-23 lin-12 lip-1 lst-1 lst-2 lst-3 lst-4 mpk-1 unc-101 vha-7 Abstract: The Caenorhabditis elegans vulva is an important paradigm for cell-cell interactions in animal development. The fates of six vulval precursor cells are patterned through the action of the epidermal growth factor receptor - mitogen-activated protein kinase (EGFR-MAPK) inductive signaling pathway, which specifies the 1degrees fate, and the LIN-12/Notch lateral signaling pathway, which specifies the 2degrees fate. Here, we provide evidence that the inductive signal is spatially graded and initially activates the EGFR-MAPK pathway in the prospective 2degrees cells. Subsequently, this effect is counteracted by the expression of multiple new negative regulators of the EGFR-MAPK pathway, under direct transcriptional control of the LIN-12-mediated lateral signal. ------------------- Key: 6349 Medline: 14749834 Authors: Zheng Y;Mellem JE;Brockie PJ;Madsen DM;Maricq AV Title: SOL-1 is a CUB-domain protein required for GLR-1 glutamate receptor function in C. elegans. Citation: Nature 427: 451-457 2004 Type: ARTICLE Genes: glr-1 nmr-1 sol-1 Abstract: Ionotropic glutamate receptors (iGluRs) mediate most excitatory synaptic signalling between neurons. Binding of the neurotransmitter glutamate causes a conformational change in these receptors that gates open a transmembrane pore through which ions can pass. The gating of iGluRs is crucially dependent on a conserved amino acid that was first identified in the 'lurcher' ataxic mouse(1). Through a screen for modifiers of iGluR function in a transgenic strain of Caenorhabditis elegans expressing a GLR-1 subunit containing the lurcher mutation, we identify suppressor of lurcher (sol-1). This gene encodes a transmembrane protein that is predicted to contain four extracellular beta-barrel-forming domains known as CUB domains(2,3). SOL-1 and GLR-1 are colocalized at the cell surface and can be coimmunoprecipitated. By recording from neurons expressing GLR-1, we show that SOL-1 is an accessory protein that is selectively required for glutamate-gated currents. We propose that SOL-1 participates in the gating of non-NMDA (N-methyl-D-aspartate) iGluRs, thereby providing a previously unknown mechanism of regulation for this important class of neurotransmitter receptor. ------------------- Key: 6350 Medline: 14739645 Authors: Monleon D;Chiang YW;Aramini JM:Swapna GVT;Macapagal D;Gunsalus KC;Kim S;Szyperski T;Montelione GT Title: Backbone 1H, 15N and 13C assignments for the 21 kaD Caenorhabditis elegans homologue of 'brain-specific' protein. Citation: Journal of Biomolecular NMR 28: 91-92 2004 Type: ARTICLE Genes: Abstract: The Northeast Structural Genomics Consortium (NESG) is a pilot project designed to evaluate the feasibility and value of structural genomics. The 21 kDa Caenorhabditis elegans protein coded by gene CE32E8.3 (TrEMBL protein P91127, referred to here as WR33) is one of several hundred targets identified for structural analysis by the Northeast Structural Genomics Consortium (www.nesg.org). WR33 belongs to a large protein domain family with homologues in several eukaryotic genomes, including those of Homo sapiens (TrEMBL proteins Q9Y326, O94811, and Q9Y6H0), Mus musculis (TrEMBL protein Q9CRB6), and Drosophila melanogaster (TrEMBL protein Q(VV43). The 25 kDa Bos Taurus (bovine) homologue from this family (Q27957), with 38% sequence identity with WR33 over 175 residues, is characterized as 'brain specific protein P25' (Shiratsuchi et al., 1995) and is expressed in oligodendrocytes and neutrophils of bovine brain tissue. However, none of the members of this strongly conserved protein domain family has a characterized biological function. ------------------- Key: 6351 Medline: 14723706 Authors: Nagamatsu Y;Ohshima Y Title: Mechanisms for the control of body size by a G-kinase and a downstream TGF beta signal pathway in Caenorhabditis elegans. Citation: Genes to Cells 9: 39-47 2004 Type: ARTICLE Genes: dbl-1 egl-4 lon-1 sma-1 sma-2 sma-4 sma-6 Abstract: We recently showed that egl-4 mutants in Caenorhabditis elegans have a much larger body size and that the egl-4 gene encodes cyclic GMP-dependent protein kinases (G-kinases). Cell sizes, but not cell numbers, in the major organs are increased in the mutants. Genetic interaction studies suggest that EGL-4 represses the DBL-1/TGFbeta pathway that is known to control body size. To understand the mechanisms of body size control in C. elegans, we analysed sma-2, sma-4 and sma-6 small mutants in the DBL-1 pathway. The volumes of major organs were precisely determined with the method developed by us. They are significantly decreased as compared to those of the wild-type while cell numbers are not, indicating that cell size is decreased. DNA contents in the nuclei of major organs are not significantly changed in the small mutants and in an egl-4 large mutant. Total protein contents are much decreased in the small mutants and slightly increased in the egl-4 mutant. Based on these results, we propose that decreased cell and body size of the small mutants in the DBL-1/TGFbeta pathway is mainly due to decreased levels of protein expression, and that increase in fluid content is a major reason for the increase in cell and body size in ------------------- Key: 6352 Medline: 14634695 Authors: Quintin S;Mains PE;Zinke A;Hyman AA Title: The mbk-2 kinase is required for inactivation of MEI-1/katanin in the one-cell Caenorhabditis elegans Citation: EMBO Reports 4: 1175-1181 2003 Type: ARTICLE Genes: mbk-2 mei-1 mel-26 tbb-2 zyg-9 Abstract: The Caenorhabditis elegans early embryo is widely used to study the regulation of microtubule-related processes. In a screen for mutants affecting the first cell division, we isolated a temperature-sensitive mutation affecting pronuclear migration and spindle positioning, phenotypes typically linked to microtubule or centrosome defects. In the mutant, microtubules are shorter and chromosome segregation is impaired, while centrosome organization appears normal. The mutation corresponds to a strong loss of function in mbk-2, a conserved serine/threonine kinase. The microtubule-related defects are due to the postmeiotic persistence of MEI-1, a homologue of the microtubule-severing protein katanin. In addition, P-granule distribution is abnormal in mbk-2 mutants, consistent with genetic evidence that mbk-2 has other functions and with the requirement of mbk-2 activity at the one-cell stage. We propose that mbk-2 potentiates the degradation of MEI-1 and other proteins, possibly via ------------------- Key: 6353 Medline: 14648222 Authors: Buckley MS;Chau J;Hoppe PE;Coulter DE Title: odd-skipped homologs function during gut development in C. elegans. Citation: Development Genes & Evolution 214: 10-18 2004 Type: ARTICLE Genes: odd-1 odd-2 Abstract: Genes in the odd-skipped (odd) family encode a discrete subset of C2H2 zinc finger proteins that are widely distributed among metazoan phyla. Although the initial member (odd) was identified as a Drosophila pair-rule gene, various homologs are expressed within each of the three germ layers in complex patterns that suggest roles in many pathways beyond segmentation. To further investigate the evolutionary history and extant functions of genes in this family, we have initiated a characterization of two homologs, odd-1 and odd-2, identified in the genome of the nematode, Caenorhabditis elegans. Sequence comparisons with homologs from insects (Drosophila and Anopheles) and mammals suggest that two paralogs were present within an ancestral metazoan; additional insect paralogs and both extant mammalian genes likely resulted from gene duplications that occurred after the split between the arthropods and chordates. Analyses of gene function using RNAi indicate that odd-1 and odd-2 play essential and distinct roles during gut development. Specific expression of both genes in the developing intestine and other cells in the vicinity of the gut was shown using GFP-reporters. These results indicate primary functions for both genes that are most like those of the Drosophila paralogs bowel and drumstick, and support a model in which gut specification represents the ancestral role for genes in ------------------- Key: 6354 Medline: 14627726 Authors: Frank CA;Baum FP;Garriga G Title: HLH-14 is a C. elegans Achate-Scute protein that promotes neurogenesis through asymmetric cell division. Citation: Development 130: 6507-6518 2004 Type: ARTICLE Genes: ced-3 ham-1 hlh-2 hlh-14 nlp-1 sra-6 srb-6 unc-86 ccDf5 maDf4 Abstract: Achaete-Scute basic helix-loop-helix (bHLH) proteins promote neurogenesis during metazoan development. In this study, we characterize a C elegans Achaete-Scute homolog, HLH-14. We find that a number of neuroblasts express HLH-14 in the C elegans embryo, including the PVQ/HSN/PHB neuroblast, a cell that generates the PVQ interneuron, the HSN motoneuron and the PHB; sensory neuron. hlh-14 mutants lack all three of these neurons. The fact that HLH-14 promotes all three classes of neuron indicates that C elegans proneural bHLH factors may act less specifically than their fly and mammalian homologs. Furthermore, neural loss in hlh-14 mutants results from a defect in an asymmetric cell division: the PVQ/HSN/PHB neuroblast inappropriately assumes characteristics of its sister cell, the hyp7/T blast cell. We argue that bHLH proteins, which control various aspects of metazoan development, can control cell fate choices in C. elegans by regulating asymmetric cell divisions. Finally, a reduction in the function of hlh-2, which encodes the C elegans E/Daughterless bHLH homolog, results in similar neuron loss as hlh-14 mutants and enhances the effects of partially reducing hlh-14 function. We propose that HLH-14 and HLH-2 act together to specify neuroblast lineages and promote ------------------- Key: 6355 Medline: 14660541 Authors: Yonker SA;Meyer BJ Title: Recruitment of C. elegans dosage compensation proteins for gene-specific versus chromosome-wide repression. Citation: Development 130: 6519-6532 2003 Type: ARTICLE Genes: dpy-21 dpy-26 dpy-27 dpy-28 her-1 mix-1 sdc-1 sdc-2 sdc-3 xol-1 Abstract: In C elegans, an X-chromosome-wide regulatory process compensates for the difference in X-linked gene dose between males (XO) and hermaphrodites (XX) by equalizing levels of X-chromosome transcripts between the sexes. To achieve dosage compensation, a large protein complex is targeted to the X chromosomes of hermaphrodites to reduce their expression by half. This repression complex is also targeted to a single autosomal gene, her-1. By silencing this male-specific gene, the complex induces hermaphrodite sexual development. Our analysis of the atypical dosage compensation gene dpy-21 revealed the first molecular differences in the complex that achieves gene-specific versus chromosome-wide repression. dpy-21 mutations, shown here to be null, cause elevated X-linked gene expression in XX animals, but unlike mutations in other dosage compensation genes, they do not cause extensive XX-specific lethality or disrupt the stability or targeting of the dosage compensation complex to X. Nonetheless, DPY-21 is a member of the dosage compensation complex and localizes to X chromosomes in a hermaphrodite-specific manner. However, DPY-21 is the first member of the dosage compensation complex that does not also associate with her-1. In addition to a difference in the composition of the complex at her-1 versus X, we also found differences in the targeting of the complex to these sites. Within the complex, SDC-2 plays the lead role in recognizing X-chromosome targets, while SDC-3 plays the lead in ------------------- Key: 6356 Medline: Authors: Braeckman BP;Houthoofd K;Vanfleteren J Title: Energy metabolism, anti-oxidant defense and aging in Caenorhabditis elegans. Citation: Model Systems in Aging 3: 99-144 2004 Type: REVIEW Genes: aap-1 age-1 akt-1 akt-2 atp-1 cco-1 clk-1 clk-2 clk-3 ctl-1 ctl-1 cyc-1 daf-2 daf-4 daf-7 daf-12 daf-16 daf-18 daf-23 eat-2 fer-15 gas-1 glp-4 gro-1 ins-1 ins-9 ins-18 ins-22 isp-1 ist-1 mev-5 nuo-1 old-1 pdk-1 rad-5 sir-2.1 sod-3 tkr-1 unc-31 unc-64 Abstract: Food restrictions and impaired gene function by mutation or RNAi treatment can extend the lifespan of Caenorhabditis elegans considerably. In contrast to the widespread belief, the antiaging action of these interventions is not due to a reduction of the rate of metabolism. Calorie restriction causes several alterations that are similar to those observed for the Ins/IGF mutants, but acts independently of this pathway. Life extension is associated with coordinated increases in superoxide dismutase and catalase activities in calorie-restricted worms and in mutants in the Ins/IGF transduction pathway. Mutation in any one of the clk genes does not result in a clear metabolic downregulation or upregulation of antioxidant enzymes. Lifespan extension in these mutants might by linked to their slow developmental rate during juvenile life, analogous to the effects caused by silencing of several genes with a mitochondrial function by RNAi treatment, and suggesting a regulatory system that makes various rates of juvenile life to persist during adulthood. The outcome would be slowing of a number of processes ------------------- Key: 6357 Medline: 14706351 Authors: Gravel C;Stergiou L;Gagnon SN;Desnoyers S Title: The C. elegans gene pme-5: molecular cloning and role in the DNA-damage response of a tankyrase orthologue. Citation: DNA Repair 3: 171-182 2004 Type: ARTICLE Genes: hus-1 pme-5 Abstract: Tankyrases are recently identified proteins characterized by ankyrin repeats and a poly(ADP-ribose) polymerase (PARP) signature motif. In vertebrates, tankyrases mediate protein-protein interactions via the ankyrin domain. Many partners have been identified that could function in telomere maintenance, signal transduction in vesicular transport, and cell death. To further our knowledge of tankyrases and to study their function in development, we sought and found a tankyrase-related gene in Caenorhabditis elegans that we named pine-5 (poly(ADP-ribose) metabolism enzyme-5). The protein encoded includes a large ankyrin domain and a catalytic PARP domain containing the well-conserved PARP signature sequence and the regulatory region. Unlike other tankyrases, PME-5 lacks a sterile-alpha module (SAM), but has a coiled coil domain which may mediate oligomerization. We also found that pnie-5 mRNA is alternatively spliced at the fifth exon, producing a long (PME-5L) and a short (PME-5S) transcript. Both isoforms are constitutively expressed during the life cycle of C. elegans. We also show DNA damage increases expression of pine-5, a response that requires the DNA damage checkpoint gene hus-1. Moreover, DNA damage-induced germ cell apoptosis was slightly increased in pme-5(RNAi) hermaphrodites. Altogether, these data indicate that pme-5 is part of a DNA damage response pathway which leads to apoptosis in C. elegans. ------------------- Key: 6358 Medline: 14747334 Authors: Burkeen AK;Maday SL;Rybicka KK;Sulcove JA;Ward J;Huang MM;Barstead R;Franzini-Armstrong C;Allen TStC Title: Disruption of Caenorhabditis elegans muscle structure and function caused by mutation of troponin I. Citation: Biophysical Journal 86: 991-1001 2004 Type: ARTICLE Genes: unc-27 Abstract: Caenorhabditis elegans strains mutant for the unc-27 gene show abnormal locomotion and muscle structure. Experiments revealed that unc-27 is one of four C. elegans troponin I genes and that three mutant alleles truncate the protein: recessive and presumed null allele e155 terminates after nine codons; semidominant su142sd eliminates the inhibitory and C-terminal regions; and semidominant su195sd abbreviates the extreme C-terminus. Assays of in vivo muscular performance at high and low loads indicated that su142sd is most deleterious, with e155 least and su195sd intermediate. Microscopy revealed in mutant muscle a prevalent disorder of dense body positioning and a less well defined sarcomeric structure, with small islands of thin. laments interspersed within the overlap region of A bands and even within the H zone. The mutants' rigid paralysis and sarcomeric disarray are consistent with unregulated contraction of the sarcomeres, in which small portions of each myofibril shorten irregularly and independently of one another, thereby distorting the disposition of. laments. The exacerbated deficits of su142sd worms are compatible with involvement in vivo of the N-terminal portion of troponin I in enhancing force production, and the severe impairment associated with su195sd highlights importance of the extreme C-terminus in ------------------- Key: 6359 Medline: 14698813 Authors: Johnson TE Title: Advantages and disadvantages of Caenorhabditis elegans for aging research. Citation: Experimental Gerontology 38: 1329-1332 2003 Type: REVIEW Genes: age-1 daf-16 fer-15 old-1 Abstract: 'The Worm' Caenorhabditis elegans has become the organism of choice for research in to the genetic basis of longevity and aging. There are several dozen laboratories exploring aging in this nematode species and several thousand investigators use this species to address their question of interest. Although the number of papers reporting advances in C. elegans aging is significantly less than the number published on aging in the mouse or in the fruit fly, the worm papers arguably are preeminent. For example, the Feb. 28, 2003, annual aging issue of Science carried four review; in three of these, C. elegans played a prominent role (Longo and Finch, 2003; Tatar et al., 2003; Hekimi and Guarente, 2003). The reasons for this are manifold but prominent among them are the facile genetics that has led to the identification of a hundred or more genes that prolong life over that of the wild type. The Award of the Nobel Prize to Drs Brenner, Sulston and Horvitz (Marx, 2002) has secured a place for the worm, along side of its more classical brethren: Drosophila and mice. ------------------- Key: 6360 Medline: 14695939 Authors: Rodriguez-Aguilera JC;Asencio C;Ruiz-Ferrer M;Vela J;Navas Title: Caenorhabditis elegans ubiquinone biosynthesis genes. Citation: Biofactors 18: 237-244 2003 Type: ARTICLE Genes: clk-1 coq-1 coq-2 coq03 coq-4 coq-5 coq-6 coq-7 coq-8 Abstract: Ubiquinone (coenzyme Q, Q) is an essential lipid electron carrier in the mitochondria respiratory chain, and also functions as antioxidant and participates as a cofactor of mitochondrial uncoupling proteins. Caenorhabditis elegans synthesize Q9, but both dietary Q8 and endogenous Q9 biosynthesis determine Q balance. Thus, it is of current interest to know the regulatory mechanisms of Q9 biosynthesis in this nematode. Here we review results that leaded to identification of genes involved in Q9 biosynthesis in this nematode using the RNA interference technology. C. elegans coq genes were silenced and depletion of Q content was observed, indicating that the genes related here participate in Q9 biosynthesis. Silenced populations showed an extension of adult life span, probably by the decrease of endogenous oxidative stress produced in mitochondria. We also report the heterologous complementation of C. elegans coq-5 and coq-7 genes in their homologue yeast coq null mutants, leading to restore its ability to growth in non-fermentable sugars. These complemented yeast strains accumulated Q6 but also the intermediate demethoxy-Q6. These findings support the conservative functional homology of these genes. ------------------- Key: 6361 Medline: 14698617 Authors: Myllyharju J;Kivirikko KI Title: Collagens, modifying enzymes and their mutations in humans, flies and worms. Citation: Trends in Genetics 20: 33-43 2004 Type: REVIEW Genes: bli-1 bli-2 bli-4 cle-1 dpy-2 dpy-3 dpy-5 dpy-7 dpy-8 dpy-10 dpy-11 dpy-13 dpy-18 emb-9 let-2 let-268 lon-3 pdi-2 pdi-3 phy-1 phy-2 phy-3 rol-6 sqt-1 sqt-3 Abstract: Collagens and proteins with collagen-like domains form large superfamilies in various species, and the numbers of known family members are increasing constantly. Vertebrates have at least 27 collagen types with 42 distinct polypeptide chains, >20 additional proteins with collagen-like domains and similar to20 isoenzymes of various collagen-modifying enzymes. Caenorhabditis elegans has similar to175 cuticle collagen polypeptides and two basement membrane collagens. Drosophila melanogaster has far fewer collagens than many other species but has similar to20 polypeptides similar to the catalytic subunits of prolyl 4-hydroxylase, the key enzyme of collagen synthesis. More than 1300 mutations have so far been characterized in 23 of the 42 human collagen genes in various diseases, and many mouse models and C. elegans mutants are also available to analyse the collagen gene family and their modifying ------------------- Key: 6362 Medline: Authors: Weiner A Title: Soaking up RNAi. Citation: Molecular Cell 12: 535-536 2003 Type: REVIEW Genes: sid-1 Abstract: RNA interference (RNAi) describes the ability of double-stranded RNA (dsRNA) to inhibit homologous gene expression at the RNA or DNA level. In a recent paper, Feinberg and Hunter report that a single transmembrane dsRNA transport protein may enable RNAi to spread systemically from one cell to another. ------------------- Key: 6363 Medline: 12872228 Authors: Masselon C;Pasa-Tolic L;Lee SW;Li L;Anderson GA;Harkewicz R;Smith RD Title: Identification of tryptic peptides from large databases using multiplexed tandem mass spectrometry: simulations and experimental results. Citation: Proteomics 3: 1279-1286 2003 Type: ARTICLE Genes: Abstract: Multiplexed tandem mass spectrometry (MS/MS) has recently been demonstrated as a means to increase the throughput of peptide identification in liquid chromatography (LC) MS/MS experiments. In this approach, a set of parent species is dissociated simultaneously and measured in a single spectrum (in the same manner that a single parent ion is conventionally studied), providing a gain in sensitivity and throughput proportional to the number of species that can be simultaneously addressed. In the present work, simulations performed using the Caenorhabditis elegans predicted proteins database show that multiplexed MS/MS data allow the identification of tryptic peptides from mixtures of up to ten peptides from a single dataset with only three "y" or "b" fragments per peptide and a mass accuracy of 2.5 to 5 ppm. At this level of database and data complexity, 98% of the 500 peptides considered in the simulation were correctly identified. This compares favorably with the rates obtained for classical MS/MS at more modest mass measurement accuracy. LC multiplexed Fourier transform-ion cyclotron resonance MS/MS data obtained from a 66 kDa protein (bovine serum albumin) tryptic digest sample are presented to illustrate the approach, and confirm that peptides can be effectively identified from the C. elegans database to which the ------------------- Key: 6364 Medline: 14747830 Authors: Sengupta P Title: Taking sides in the nervous system with miRNA. Citation: Nature Neuroscience 7: 100-102 2004 Type: REVIEW Genes: ceh-36 cog-1 gcy-5 gcy-5 gcy-7 lin-49 lsy-6 unc-37 Abstract: At first glance, the nervous systems of vertebrates and invertebrates seem bilaterally symmetrical, but on closer inspection left-right asymmetries become apparent. Humans, for example, show gross anatomical differences between right and left temporal lobes, and visual and language faculties are asymmetrically distributed between the two hemispheres. How these asymmetries arise during development remains something of a mystery (for review, see ref.1). In the nematode Caenorhabditis elegans, the AWC and ASE chemosensory neuron pairs are bilaterally symmetrical based on anatomical considerations, but nevertheless display asymmetrical gene expression patterns. A recent study in nature by Johnston and Hobert identifies a microRNA (miRNA) as a crucial mediator of this asymmetry in the ASE neurons. ------------------- Key: 6365 Medline: 14730301 Authors: McCarroll SA;Murphy CT;Zou S;Pletcher SD;Chin CS;Jan YN;Kenyon C;Bargmann CI;Li H Title: Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Citation: Nature Genetics 36: 197-204 2004 Type: ARTICLE Genes: Abstract: We developed a method for systematically comparing gene expression patterns across organisms using genome-wide comparative analysis of DNA microarray experiments. We identified analogous gene expression programs comprising shared patterns of regulation across orthologous genes. Biological features of these patterns could be identified as highly conserved subpatterns that correspond to Gene Ontology categories. Here, we demonstrate these methods by analyzing a specific biological process, aging, and show that similar analysis can be applied to a range of biological processes. We found that two highly diverged animals, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, implement a shared adult-onset expression program of genes involved in mitochondrial metabolism, DNA repair, catabolism, peptidolysis and cellular transport. Most of these changes were implemented early in adulthood. Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and mRNA degradation. ------------------- Key: 6366 Medline: 14698436 Authors: Couthier A;Smith J;McGarr P;Craig B;Gilleard JS Title: Ectopic expression of a Haemonchus contortus GATA transcription factor in Caenorhabditis elegans reveals conserved function in spite of extensive sequence divergence. Citation: Molecular & Biochemical Parasitology 133: 241-253 2004 Type: ARTICLE Genes: elt-1 elt-2 elt-3 elt-4 elt-5 elt-6 elt-7 end-1 end-3 ibf-2 med-1 med-2 Abstract: Comparative analysis between Caenorhabditis elegans and other nematode species offers a powerful approach to study gene function. C. elegans also has great potential as a surrogate expression system to study the function of genes from parasitic nematode species where transgenic methodologies are unavailable. However there is little information on the extent to which the biology of C. elegans is conserved with other nematode species and very few parasitic nematode genes have yet been functionally expressed in C. elegans. We have identified and characterised a homologue of the C elegans GATA transcription factor elt-2, a central regulator of endoderm development, from the parasitic nematode Haemonchus contortus. The H. contortus ELT-2 polypeptide is present in endoderm nuclei throughout embryonic and post-embryonic development, except for in the infective L3 stage, and our experiments reveal that the development of the H. contortus endodermal lineage is strikingly similar to that of C elegans. Sequence conservation between the H. contortus and C elegans ELT-2 polypeptides broadly reflects function since the major region of sequence identity corresponds to the DNA binding domain. However, the overall level of sequence identity is remarkably low with the only other major region of identity corresponding to an unusual zinc finger domain. In spite of this, ectopic expression of the H. contortus elt-2 gene in transgenic C elegans is sufficient to activate a programme of endodermal differentiation demonstrating that function is highly conserved. This approach of ectopic expression using an inducible promoter provides an effective way in which to use C elegans for the in vivo functional analysis of ------------------- Key: 6367 Medline: 14706697 Authors: Kawano T;Kataoka N;Dreyfuss G;Sakamoto H Title: Ce-Y14 and MAG-1, components of exon-exon junction complex, are required for embyrogenesis and germline sexual switching in Caenorhabditis elegans. Citation: Mechanisms of Development 121: 27-35 2004 Type: ARTICLE Genes: mag-1 nxf-1 Abstract: Y14 is a component of the splicing-dependent exon-exon junction complex (EJC) and is involved in the mRNA quality control system called nonsense-mediated mRNA decay. It has recently been shown that together with another EJC component, Mago, the Drosophila homologue DmY14/Tsunagi is required for proper localization of oskar mRNA during oogenesis, a process critical for posterior formation in Drosophila development. Here we show that the nematode Caenorhabditis elegans Ce-Y14 and MAG-1 (Mago homologue) are required for late embryogenesis and proper germline sexual differentiation. Like in other organisms, Ce-Y14 preferentially binds to spliced mRNA and specifically interacts with MAG-1. Consistent with the evolutionarily conserved interaction between Y14 and Mago homologues, suppression of Ce-Y14 by RNAi resulted in the same phenotypes as those caused by RNAi of mag-1 lethality during late embryogenesis and masculinization of the adult hermaphrodite germline. Our results demonstrate that the evolutionarily conserved interaction between two EJC components, Ce-Y14 and MAG-1, has critical developmental roles in C. elegans. ------------------- Key: 6368 Medline: 14982397 Authors: Jonker MJ;Sweijen RAJC;Kammenga JE Title: Toxicity of simple mixtures to the nematode Caenorhabditis elegans in relation to soil sorption. Citation: Environmental Toxicology & Chemistry 23: 480-488 2004 Type: ARTICLE Genes: Abstract: Single and combined toxicity of copper-zinc, copper-cadmium, cadmium-lead, copper-carbendazim, and copper-carbendazimiprodione to the nematode Caenorhabditis elegans in soil was studied. The one-week population increase was estimated as the toxicity endpoint. The aim was to study the relationship between mixture interactions in the soil and the combined toxic effect. Soil sorption was quantified using the Freundlich adsorption constant. Joint toxicity patterns were quantified by comparing mixture effects to the effect of individual constituents and were related to total metal concentrations in the soil, water-soluble concentrations, and 0.01 M CaCl2-extractable concentrations. The metal with the highest adsorption constant influenced the sorption of metal with the lowest adsorption constant when both were combined, indicating interaction. Consequently, both the composition of the mixture as well as the relative toxicity of individual mixture constituents differed between total, water-soluble, and CaCl2-extractable concentrations, which was taken into account in the data quantification procedure that was applied. Both the additive and the independent model were generally inadequate to describe the effects of metal mixtures. Compared to the additive model, synergism was observed at dose levels higher than the median effect isobole. A general relationship between mixture interactions in the soil and the combined toxicity was not ------------------- Key: 6369 Medline: 14660440 Authors: Hansen D;Wilson-Berry L;Dang T;Schedl T Title: Control of the proliferation versus meiotic development decision in the C. elegans germline through regulation of GLD-1 protein accumulation. Citation: Development 131: 93-104 2004 Type: ARTICLE Genes: fbf-1 fbf-2 fog-3 gld-1 gld-2 glp-1 lag-1 lag-2 let-241 nos-3 Abstract: Maintenance of the stem cell population in the C elegans germline requires GLP-1/Notch signaling. We show that this signaling inhibits the accumulation of the RNA binding protein GLD-1. In a genetic screen to identify other genes involved in regulating GLD-1 activity, we identified mutations in the nos-3 gene, the protein product of which is similar to the Drosophila translational regulator Nanos. Our data demonstrate that nos-3 promotes GLD-1 accumulation redundantly with gld-2, and that nos-3 functions genetically downstream or parallel to fbf, an inhibitor of GLD-1 translation. We show that the GLD-1 accumulation pattern is important in controlling the proliferation versus meiotic development decision, with low GLD-1 levels allowing proliferation and increased levels promoting ------------------- Key: 6370 Medline: 14660442 Authors: Hwang BJ;Sternberg PW Title: A cell-specific enhancer that specifies lin-3 expression in the C. elegans anchor cell for vulval development. Citation: Development 131: 143-151 2004 Type: ARTICLE Genes: hlh-2 let-23 lin-3 nhr-25 Abstract: During C. elegans vulval development, the anchor cell (AC) in the somatic gonad expresses lin-3, activating the EGF receptor signaling pathway in vulval precursor cells (VPCs) and thereby inducing and patterning VPCs. Previous studies with lin-3 mutants and transgene expression have revealed that the level of LIN-3 in the AC must be precisely regulated for proper vulval development. To understand how lin-3 expression is achieved in the AC, we identified a 59 bp lin-3 enhancer sufficient to activate lin-3 transcription solely in the AC. The enhancer contains two E-box elements, and one FTZ-F1 nuclear hormone receptor (NHR) binding site that is mutated in a vulvaless mutant, lin-3(e1417). Mutagenesis studies show that both E-boxes and the NHR binding site are necessary to express lin-3 in the AC. In vitro DNA-binding studies and in vivo functional assays indicate that distinct trans-acting factors, including the E-protein/Daughterless homolog HLH-2 and unidentified nuclear hormone receptor(s), are necessary for lin-3 transcription in the AC and thus are involved in vulval development. ------------------- Key: 6371 Medline: 14738749 Authors: van den Heuvel S Title: Protein degradatin: CUL-3 and BTB - partners in Citation: Current Biology 14: R59-R61 2004 Type: REVIEW Genes: cul-3 cul-4 mei-1 mei-2 mel-26 Abstract: In early C. elegrans embryos, the transition from meiosis to mitosis requires degradation of the MEI-1 protein. A novel class of SCF-like ubiquitin ligases has been identified that mediates this process. These ligases contain the CUL-3 scaffold at their core and use a BTB-domain protein in substrate recognition. ------------------- Key: 6372 Medline: 14761308 Authors: Lee J;Nam S;Hwang SB;Hong M;Kwon JY;Jeong KS;Im SH;Shim J;Park MC Title: Functional genomic approaches using the nematode Caenorhabditis elegans as a model system. Citation: Journal of Biochemistry and Molecular Biology 37: 107-113 2004 Type: REVIEW Genes: rrf-3 Abstract: Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cells lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology. ------------------- Key: 6373 Medline: 14744438 Authors: Bartel DP Title: MicroRNAs: genomics, biogenesis, mechanism, and function. Citation: Cell 116: 281-297 2004 Type: REVIEW Genes: cog-1 hbl-1 let-7 lin-4 lin-14 lin-28 lsy-6 Abstract: MicroRNAs (miRNAs) are endogenous similar to22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs; for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes. ------------------- Key: 6374 Medline: 14706236 Authors: Ishii N;Senoo-Matsuda N;Miyake K;Yasuda K;Ishii T;Hartman PS;Furukawa S Title: Coenzyme Q10 can prolong life C. elegans lifespan by lowering oxidative stress. Citation: Mechanisms of Ageing & Development 125: 41-46 2004 Type: ARTICLE Genes: mev-1 Abstract: The mev-1 gene encodes cytochrome b, a large subunit of the Complex II enzyme succinate-CoQ oxidoreductase. The mev-1(kn1) mutants are hypersensitive to oxidative stress and age precociously, probably because of elevated superoxide anion production in mitochondria. Coenzyme Q (CoQ) is essential for the mitochondrial respiratory chain. Here, we show that CoQ(10) and Vitamin E extended the life span of wild-type Caenorhabditis elegans. Conversely, only CoQ10 recovered the life shortening effects seen in mev-1. We also show that CoQ(10) but not Vitamin E reduced superoxide anion levels in wild type and mev-1. Another previously described phenotype of mev-1 animals is the presence of supernumerary apoptotic cells. We now demonstrate that CoQ(10) (but not Vitamin E) suppressed these supernumerary apoptoses. Collectively these data suggest that exogenously supplied CoQ(10) can play a significant anti-aging function. It may do so either by acting as an antioxidant to dismutate the free radical superoxide anion or by reducing the uncoupling of reactions during election transport that could otherwise result in superoxide anion production. The latter activity has not been ascribed to CoQ(10); however, it is known that conditions that uncouple electron transport reactions can lead to elevated superoxide anion production. ------------------- Key: 6375 Medline: 14762140 Authors: Hills T;Brockie PJ;Maricq AV Title: Dopamine and glutamate control area-restricted search behavior in Caenorhabditis elegans. Citation: Journal of Neuroscience 24: 1217-1225 2004 Type: ARTICLE Genes: cat-2 ced-1 dat-1 eat-4 glr-1 glr-2 Abstract: Area-restricted search (ARS) is a foraging strategy used by many animals to locate resources. The behavior is characterized by a time-dependent reduction in turning frequency after the last resource encounter. This maximizes the time spent in areas in which resources are abundant and extends the search to a larger area when resources become scarce. We demonstrate that dopaminergic and glutamatergic signaling contribute to the neural circuit controlling ARS in the nematode Caenorhabditis elegans. Ablation of dopaminergic neurons eliminated ARS behavior, as did application of the dopamine receptor antagonist raclopride. Furthermore, ARS was affected by mutations in the glutamate receptor subunits GLR-1 and GLR-2 and the EAT-4 glutamate vesicular transporter. Interestingly, preincubation on dopamine restored the behavior in worms with defective dopaminergic signaling, but not in glr-1, glr-2, or eat-4 mutants. This suggests that dopaminergic and glutamatergic signaling function in the same pathway to regulate turn frequency. Both GLR-1 and GLR-2 are expressed in the locomotory control circuit that modulates the direction of locomotion in response to sensory stimuli and the duration of forward movement during foraging. We propose a mechanism for ARS in C. elegans in which dopamine, released in response to food, modulates glutamatergic signaling in the locomotory control circuit, thus resulting in an increased turn frequency. ------------------- Key: 6376 Medline: 14729570 Authors: Vella MC;Choi EY;Lin SY;Reinert K;Slack FJ Title: The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. Citation: Genes & Development 18: 132-137 2004 Type: ARTICLE Genes: let-7 lin-4 lin-41 Abstract: Caenorhabditis elegans let-7, a founding member of the microRNA family, is predicted to bind to six sites in the 3'UTR of the mRNA of its target gene, lin-41, to down-regulate LIN-41. Here, we demonstrate that wild-type let-7 microRNA binds in vitro to RNA from the lin-41 3'UTR. This interaction is dependent on two conserved let-7 complementary sites (LCSs). A 27-nucleotide sequence between the LCSs is also necessary for down-regulation in vivo. LCS mutations compensatory to the lesion in let-7(n2853) can partially restore lin-41 3'UTR function in a let-7(n2853) background, providing the first experimental evidence for an animal miRNA binding directly to its validated target in vivo. ------------------- Key: 6377 Medline: 14668486 Authors: Morley JF;Morimoto RI Title: Regulation of longevity in Caenorhabditis elegans by heat shock factor and molecular chaperones. Citation: Molecular Biology of the Cell 15: 657-664 2004 Type: ARTICLE Genes: age-1 daf-2 daf-16 daf-21 hsf-1 hsp-1 hsp-16 old-1 sip-1 Abstract: The correlation between longevity and stress resistance observed in long-lived mutant animals suggests that the ability to sense and respond to environmental challenges could be important for the regulation of life span. We therefore examined the role of heat shock factor (HSF-1), a master transcriptional regulator of stress-inducible gene expression and protein folding homeostasis, in the regulation of longevity. Down-regulation of hsf-1 by RNA interference suppressed longevity of mutants in an insulin-like signaling (ILS) pathway that functions in the nervous system of Caenorhabditis elegans to influence aging. hsf-1 was also required for temperature-induced dauer larvae formation in an ILS mutant. Using tissue-specific expression of wild-type or dominant negative HSF-1, we demonstrated that HSF-1 acts in multiple tissues to regulate longevity. Down-regulation of individual molecular chaperones, transcriptional targets of HSF-1, also decreased longevity of long-lived mutant but not wild-type animals. However, suppression by individual chaperones was to a lesser extent, suggesting an important role for networks of chaperones. The interaction of ILS with HSF-1 could represent an important molecular strategy to couple the regulation of longevity with an ancient genetic switch that governs the ability of cells to sense ------------------- Key: 6378 Medline: Authors: Bolm M;Jansen WTM;Schnabel R;Shhatwal GS Title: Hydrogen peroxide-mediated killing of Caenorhabditis elegans: a common feature of different Streptococcal species. Citation: Infection and Immunity 72: 1192-1194 2004 Type: ARTICLE Genes: Abstract: Recently, we reported that Streptococcus pyogenes kills Caenorhabditis elegans by the use of hydrogen peroxide (H2O2). Here we show that diverse streptococcal species cause death of C. elegans larvae in proportion to the level of H2O2 produced. H2O2 may mask the effects of other pathogenicity factors of catalase-negative bacteria in the C. elegans infection model. ------------------- Key: 6379 Medline: 14630920 Authors: Hashmi S;Zhang J;Oksov Y;Lustigman S Title: The Caenorhabditis elegans cathepsin Z-like cysteine protease, Ce-CPZ-1, has a multifunctional role during the worms' development. Citation: Journal of Biological Chemistry 279: 6035-6045 2004 Type: ARTICLE Genes: cpz-1 cpz-2 Abstract: We have analyzed the expression and function of Ce-cpz-1, a Caenorhabditis elegans cathepsin Z-like cysteine protease gene, during development of the worm. The cpz-1 gene is expressed in various hypodermal cells of all developmental stages and is specifically expressed in the gonads and the pharynx of adult worms. Disruption of cpz-1 function by RNA interference or cpz-1(ok497) deletion mutant suggests that cpz-1 has a role in the molting pathways. The presence of the native CPZ-1 protein in the hypodermis/cuticle of larval and adult stages and along the length of the pharynx of adult worms, as well as the cyclic expression of the transcript during larval development, supports such function. We hypothesize that the CPZ-1 enzyme functions directly as a proteolytic enzyme degrading cuticular proteins before ecdysis and/or indirectly by processing other proteins such as proenzymes and/or other proteins that have an essential role during molting. Notably, an impressive level of the CPZ-1 native protein is present in both the new and the old cuticles during larval molting, in particular in the regions that are degraded prior to shedding and ecdysis. The similar localization of the related Onchocerca volvulus cathepsin Z protein suggests that the function of CPZ-1 during molting might be conserved in other nematodes. Based on the cpz-1 RNA interference and cpz-1 (ok497) deletion mutant phenotypes, it appears that cpz-1 have additional roles during morphogenesis. Deletion of cpz-1 coding sequence or inhibition of cpz-1 function by RNA interference also caused morphological defects in the head or tail region of larvae, improperly developed gonad in adult worms and embryonic lethality. The CPZ-1 native protein in these affected regions may have a role in the cuticular and the basement membrane extracellular matrix assembly process. The present findings have defined a critical role for ------------------- Key: 6380 Medline: 14702387 Authors: Ellis GC;Phillips JB;O'Rourke S;Lyczak R;Bowerman B Title: Maternally expressed and partially redundant beta-tubulins in Caenorhabditis elegans are autoregulated. Citation: Journal of Cell Science 117: 457-464 2004 Type: ARTICLE Genes: tbb-2 nDf15 sDf121 sDf130 sDp3 Abstract: The mitotic spindle, which partitions replicated chromosomes to daughter cells during cell division, is composed of microtubule assemblies of alpha/beta-tubulin heterodimers. Positioning of the mitotic spindle influences the size and location of daughter cells, and can be important for the proper partitioning of developmental determinants. We describe two semi-dominant mis-sense mutations in tbb-2, one of two C. elegans beta-tubulin genes that are maternally expressed and together are required for microtubule-dependent processes in the early embryo. These mutations result in a posteriorly displaced and mis-oriented mitotic spindle during the first cell division. In contrast, a probable tbb-2 null allele is recessive, and when homozygous results in less severe spindle positioning defects and only partially penetrant embryonic lethality. Two of the tbb-2 mutations result in reduced levels of TBB-2 protein, and increased levels of a second maternally expressed beta-tubulin, TBB-1. However, levels of TBB-1 are not increased in a tbb-2 mutant with an allele that does not result in reduced levels of TBB-2 protein. We conclude that feedback regulation influences maternal beta-tubulin expression in C. elegans, but cannot fully restore normal microtubule function in the absence of one beta-tubulin isoform. ------------------- Key: 6381 Medline: 14750151 Authors: Miyahara K;Suzuki N;Ishihara T;Tsuchiya E;Katsura I Title: TBX2/TBX3 transcriptional factor homologue controls olfactory adaptation in Caenorhabditis elegans. Citation: Journal of Neurobiology 58: 392-402 2004 Type: ARTICLE Genes: sdf-13 tbx-2 Abstract: Although transcriptional factors are known to play important roles in synaptic plasticity, their role in olfactory adaptation has not been studied well. Here we report that Ce-TBX-2, the TBX2/TBX3 transcriptional factor homologue of the nematode Caenorhabditis elegans, is involved in olfactory adaptation. Two missense hypomorphic mutations in this gene confer abnormality in adaptation, but not chemotaxis, to all the odorants sensed by AWC olfactory neurons. The Ce-tbx-2 gene is expressed in AWB, AWC, ASJ, and many pharyngeal neurons, but expression in AWC neurons is sufficient for normal adaptation. Unexpectedly, the protein product is localized mostly in cytoplasm. The AWC neurons in the mutants retain their characteristic morphology and many marker gene expressions, suggesting that the mutants are abnormal in neural functions rather than neuronal differentiation. The results of this study imply that some of the mammalian T-box family proteins, which play central roles in embryonic development, may also control functions like neural ------------------- Key: 6382 Medline: 14961122 Authors: Kennedy S;Wang D;Ruvkun G Title: A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Citation: Nature 427: 645-649 2004 Type: ARTICLE Genes: dpy-13 eri-1 hmr-1 lin-1 myo-2 mut-16 rde-1 rde-4 rrf-1 rrf-3 sid-1 unc-13 unc-17 unc-22 unc-25 unc-47 Abstract: In many organisms, introducing double-stranded RNA (dsRNA) causes the degradation of messenger RNA that is homologous to the trigger dsRNA-a process known as RNA interference. The dsRNA is cleaved into short interfering RNAs (siRNAs), which hybridize to homologous mRNAs and induce their degradation(1). dsRNAs vary in their ability to trigger RNA interference: many mRNA-targeting dsRNAs show weak phenotypes, and nearly all mRNAs of the Caenorhabditis elegans nervous system are refractory to RNA interference(2-4). C. elegans eri-1 was identified in a genetic screen for mutants with enhanced sensitivity to dsRNAs. Here we show that eri-1 encodes an evolutionarily conserved protein with domains homologous to nucleic-acid-binding and exonuclease proteins. After exposure to dsRNA or siRNAs, animals with eri-1 mutations accumulate more siRNAs than do wild-type animals. C. elegans ERI-1 and its human orthologue degrade siRNAs in vitro. In the nematode worm, ERI-1 is predominantly cytoplasmic and is expressed most highly in the gonad and a subset of neurons, suggesting that ERI-1 siRNase activity suppresses RNA interference more intensely in these tissues. Thus, ERI-1 is a negative regulator that may normally function to limit the duration, cell-type specificity or endogenous functions of RNA interference. ------------------- Key: 6383 Medline: Authors: Danial NN;Korsmeyer SJ Title: Cell death: critical control points. Citation: Cell 116: 205-219 2004 Type: REVIEW Genes: ced-1 ced-2 ced-3 ced-4 ced-5 ced-6 ced-7 ced-9 ced-12 egl-1 icd-1 nuc-1 Abstract: Programmed cell death is a distinct genetic and biochemical pathway essential to metazoans. An intact death pathway is required for successful embryonic development and the maintenance of normal tissue homeostasis. Apoptosis has proven to be tightly interwoven with other essential cell pathways. The identification of critical control points in the cell death pathway has yielded fundamental insights for basic biology, as well as provided rational targets for new therapeutics. ------------------- Key: 6384 Medline: 14976312 Authors: Csankovszki G;McDonel P;Meyer BJ Title: Recruitment and spreading of the C. elegans dosage compensation complex along X chromosomes. Citation: Science 303: 1182-1185 2004 Type: ARTICLE Genes: dpy-27 let-2 lin-14 lin-15 lon-2 myo-2 unc-1 unc-2 unc-6 unc-9 unc-20 uvt-4 mnDp1 mnDp10 mnDp25 mnDp30 mnDp57 mnDp66 stDp2 yDp4 yDp7 yDp11 yDp13 yDp14 Abstract: To achieve X-chromosome dosage compensation, organisms must distinguish X chromosomes from autosomes. We identified multiple, cis-acting regions that recruit the Caenorhabditis elegans dosage compensation complex (DCC) through a search for regions of X that bind the complex when detached from X. The DCC normally assembles along the entire X chromosome, but not all detached regions recruit the complex, despite having genes known to be dosage compensated on the native X. Thus, the DCC binds first to recruitment sites, then spreads to neighboring X regions to accomplish chromosome-wide gene repression. From a large chromosomal domain, we defined a 793-base pair fragment that functions in vivo as an X-recognition element to ------------------- Key: 6385 Medline: 14638695 Authors: Grimsley CM;Kinchen JM;Tosello-Trampont AC;Brugnera E;Haney LB;Lu M;Chen Q;Klingele D;Hengartner MO;Ravichandran KS Title: Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration. Citation: Journal of Biological Chemistry 279: 6087-6097 2004 Type: ARTICLE Genes: ced-5 Abstract: Cell migration is essential throughout embryonic and adult life. In numerous cell systems, the small GTPase Rac is required for lamellipodia formation at the leading edge and movement ability. However, the molecular mechanisms leading to Rac activation during migration are still unclear. Recently, a mammalian superfamily of proteins related to the prototype member Dock180 has been identified with homologues in Drosophila and Caenorhabditis elegans. Here, we addressed the role of Dock180 and ELMO1 proteins, which function as a complex to mediate Rac activation, in mammalian cell migration. Using mutants of Dock180 and ELMO1 in a Transwell assay as well as transgenic rescue of a C. elegans mutant lacking CED-5 (Dock180 homologue), we identified specific regions of Dock180 and ELMO1 required for migration in vitro and in a whole animal model. In both systems, the Dock180.ELMO1 complex formation and the ability to activate Rac were required. We also found that ELMO1 regulated multiple Dock180 superfamily members to promote migration. Interestingly, deletion mutants of ELMO1 missing their first 531 or first 330 amino acids that can still bind and cooperate with Dock180 in Rac activation failed to promote migration, which correlated with the inability to localize to lamellipodia. This finding suggests that Rac activation by the ELMO.Dock180 complex at discrete intracellular locations mediated by the N-terminal 330 amino acids of ELMO1 rather than generalized Rac activation plays a role in cell migration. ------------------- Key: 6386 Medline: 14762059 Authors: Mitreva M;McCarter JP;Martin J;Dante M;Wylie T;Chiapelli B;Pape D;Clifton SW;Nutman TB;Waterston RH Title: Comparative genomics of gene expression in the parasitice and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Citation: Genome Research 14: 209-220 2004 Type: ARTICLE Genes: Abstract: Although developmental timing of gene expression is used to infer potential gene function, Studies have yet to correlate this information between species. We analyzed 10,921 ESTs in 3311 clusters from first- and infective third-stage larva (L1, L3i) of the parasitic nematode Strongyloides stercoralis and compared the results to Caenorhabditis elegans, a species that has an L3i-like dauer stage. In the comparison of S. stercoralis clusters with stage-specific expression to C elegans homologs expressed in either dauer or nondauer stages, matches between S. stercoralis L1 and C elegans nondauer-expressed genes dominated, suggesting conservation in the repertoire of genes expressed during growth in nutrient-rich conditions. For example, S. stercoralis collagen transcripts were abundant in L1 but not L3i, a pattern consistent with C elegans collagens. Although a greater proportion of S. stercoralis L3i than L1 genes have homologs among the C elegans dauer-specific transcripts, we did not uncover evidence of a robust conserved L3i/dauer 'expression signature.' Strikingly, in comparisons of S. stercoralis clusters to C elegans homologs with RNAi knockouts, those with significant L1-specific expression were more than twice as likely as L3i-specific clusters to match genes with phenotypes. We also provide functional ------------------- Key: 6387 Medline: 14755799 Authors: Moore R;Boyd L Title: Analysis of RING finger genes required for embryogenesis in C. elegans. Citation: Genesis 38: 1-12 2004 Type: ARTICLE Genes: act-1 act-2 act-3 act-4 act-5 arc-1 col-2 col-8 col-9 col-10 col-12 col-13 col-17 col-18 col-19 col-35 col-36 col-39 gpd-1 gpd-2 glp-4 lin-41 par-1 par-2 par-3 par-6 rnf-5 rpm-1 sli-1 sqt-1 tam-1 trf-1 vit-1 vit-2 vit-3 vit-5 Abstract: The RING finger motif exists in E3 ligases of the ubiquitination pathway. These ubiquitin ligases bind to target proteins, leading to their modification by covalent addition of ubiquitin peptides. Current databases contain hundreds of proteins with RING finger motifs. This study investigates the role of RING finger genes in embryogenesis of the nematode, Caenorhabditis elegans. We expand the previous list of RING finger-containing genes and show that there are 103 RING finger-containing genes in the C. elegans genome. DNA microarrays of these 103 genes were probed with various RNA samples to identify 16 RING finger genes whose expression is enriched in the germline. RNA interference (RNAi) analysis was then used to determine the developmental role of these genes. One RING finger gene, C32D5.10, showed a dramatic larval arrest upon RNAi. Three RING finger genes exhibited embryonic lethality after RNAi. These three genes include par-Z and two small RING finger proteins: F35G12.9 (an ortholog of APC11) and ZK287.5 (an ortholog of rbx1). Embryos from RNAi of the APC11 and rbx1 orthologs were arrested in the cell cycle, confirming the role of these particular RING finger proteins in regulation of the cell cycle. ------------------- Key: 6388 Medline: 14685271 Authors: Yoder JH;Chong H;Guan K;Han M Title: Modulation of KSR activity in Caenorhabditis elegans by Zn ions, PAR-1 kinase and PP2A phosphatase. Citation: EMBO Journal 23: 111-119 2004 Type: ARTICLE Genes: ksr-1 let-60 lin-1 lin-15 lin-31 lin-45 mek-2 mpk-1 par-1 rol-4 sur-6 sur-7 sur-8 Abstract: Vulval differentiation in Caenorhabditis elegans is controlled by a conserved signal transduction pathway mediated by Ras and a kinase cascade that includes Raf, Mek and MAPK. Activation of this cascade is positively regulated by a number of proteins such as KSR ( kinase suppressor of Ras), SUR-8/SOC-2, SUR-6/PP2A-B and CDF-1. We describe the functional characterization of sur-7 and several genes that regulate signaling downstream of ras. We identified sur-7 by isolating a mutation that suppresses an activated ras allele, and showed that SUR-7 is a divergent member of the cation diffusion facilitator family of heavy metal ion transporters that is probably localized to the endoplosmic recticulum membrane and regulates cellular Zn2+ concentrations. Genetic double mutant analyses suggest that the SUR-7-mediated effect is not a general toxic response. Instead, Zn2+ ions target a specific step of the pathway, probably regulation of the scaffolding protein KSR. Biochemical analysis in mammalian cells indicates that high Zn2+ concentration causes a dramatic increase of KSR phosphorylation. Genetic analysis also indicates that PP2A phosphatase and PAR-1 kinase act downstream of Raf to positively and negatively regulate KSR activity, respectively. ------------------- Key: 6389 Medline: 14739932 Authors: Sanyal S;Wintle RF;Kindt KS;Nuttley WM;Arvan R;Fitzmaurice P;Bigras E;Merz DC;Hebert TE;van der Kooy D;Schafer WR;Culotti JG;Van Tol HHM Title: Dopamine modulates the plasticity of mechanosensory responses in Caenorhabditis elegans. Citation: EMBO Journal 23: 473-482 2004 Type: ARTICLE Genes: cat-2 dop-1 dop-11 him-5 Abstract: Dopamine-modulated behaviors, including information processing and reward, are subject to behavioral plasticity. Disruption of these behaviors is thought to support drug addictions and psychoses. The plasticity of dopamine-mediated behaviors, for example, habituation and sensitization, are not well understood at the molecular level. We show that in the nematode Caenorhabditis elegans, a D1-like dopamine receptor gene (dop-1) modulates the plasticity of mechanosensory behaviors in which dopamine had not been implicated previously. A mutant of dop-1 displayed faster habituation to nonlocalized mechanical stimulation. This phenotype was rescued by the introduction of a wild-type copy of the gene. The dop-1 gene is expressed in mechanosensory neurons, particularly the ALM and PLM neurons. Selective expression of the dop-1 gene in mechanosensory neurons using the mec-7 promoter rescues the mechanosensory deficit in dop-1 mutant animals. The tyrosine hydroxylase-deficient C. elegans mutant (cat-2) also displays these specific behavioral deficits. These observations provide genetic evidence that dopamine signaling modulates behavioral plasticity in C. elegans. ------------------- Key: 6390 Medline: 14668411 Authors: Reinke V;San Gil I;Ward S;Kazmer K Title: Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans. Citation: Development 131: 311-323 2004 Type: ARTICLE Genes: egl-13 fem-1 fem-3 glp-4 flp-3 flp-6 flp-8 flp-9 her-1 him-5 lin-2 lov-1 mab-3 nlp-1 nlp-2 nlp-3 nlp-12 nlp-14 nlp-25 nlp-31 pkd-2 sir-2.2 Abstract: We performed a genome-wide analysis of gene expression in C. elegans to identify germline- and sex-regulated genes. Using mutants that cause defects in germ cell proliferation or gametogenesis, we identified sets of genes with germline-enriched expression in either hermaphrodites or males, or in both sexes. Additionally, we compared gene expression profiles between males and hermaphrodites lacking germline tissue to define genes with sex-biased expression in terminally differentiated somatic tissues. Cross-referencing hermaphrodite germline and somatic gene sets with in situ hybridization data demonstrates that the vast majority of these genes have appropriate spatial expression patterns. Additionally, we examined gene expression at multiple times during wild-type germline development to define temporal expression profiles for these genes. Sex- and germline-regulated genes have a non-random distribution in the genome, with especially strong biases for and against the X chromosome. Comparison with data from large-scale RNAi screens demonstrates that genes expressed in the oogenic germline display visible phenotypes more frequently than expected. ------------------- Key: 6391 Medline: 14681186 Authors: da Graca LS;Zimmerman KK;Mitchell MC;Kozhan-Gorodetska M;Sekiewicz K;Morales Y;Patterson GI Title: DAF-5 is a Ski oncoprotein homolg that functions in a neuronal TGF beta pathway to regulate C. elegans dauer development. Citation: Development 131: 435-446 2004 Type: ARTICLE Genes: cki-1 daf-1 daf-3 daf-4 daf-5 daf-7 daf-8 daf-14 dpy-7 dpy-30 ges-1 myo-2 myo-3 rnr-1 sma-2 unc-14 unc-119 Abstract: An unconventional TGFbeta superfamily pathway plays a crucial role in the decision between dauer diapause and reproductive growth. We have studied the daf-5 gene, which, along with the daf-3 Smad gene, is antagonized by upstream receptors and receptor-regulated Smads. We show that DAF-5 is a novel member of the Sno/Ski superfamily that binds to DAF-3 Smad, suggesting that DAF-5, like Sno/Ski, is a regulator of transcription in a TGFbeta superfamily signaling pathway. However, we present evidence that DAF-5 is an unconventional Sno/Ski protein, because DAF-5 acts as a co-factor, rather than an antagonist, of a Smad protein. We show that expressing DAF-5 in the nervous system rescues a daf-5 mutant, whereas muscle or hypodermal expression does not. Previous work suggested that DAF-5 and DAF-3 function in pharyngeal muscle to regulate gene expression, but our analysis of regulation of a pharynx specific promoter suggests otherwise. We present a model in which DAF-5 and DAF-3 control the production or release of a hormone from the nervous system by either regulating the expression of biosynthetic genes or by altering the connectivity or the differentiated state of neurons. ------------------- Key: 6392 Medline: 15055763 Authors: Jang SH;Park Y;Park SC;Kim PI;Lee DG;Hahm KS Title: Antinematocidal activity and the mechanism of the antimicrobial peptide, HP (2-20), against Caenorhabditis elegans. Citation: Biotechnology Letters 26: 287-291 2004 Type: ARTICLE Genes: Abstract: The peptide HP (2-20), derived from the N-terminal sequence of Helicobacter pylori ribosomal protein L1 (RPL1), has a nematicidal activity against eggs and worms of Caenorhabditis elegans. Eggs treated with HP (2-20) (69%) has a higher fluorescence intensity with propidium iodide staining, which was similar to that of melittin (82%) but higher than untreated cells (5.7%). Confocal microscopy showed that the peptides were located in the shell of the eggs and the inner and outer surfaces of the worms. HP (2-20) therefore may exert its antinematodal activity by disrupting the structure of the egg's shell and the cell membrane via pore formation or by direct interaction with the lipid bilayers in a detergent-like manner. ------------------- Key: 6393 Medline: 14758362 Authors: Wang X;Chamberlin HM Title: Evolutionary innovation of the excretory system in Caenorhabditis elegans. Citation: Nature Genetics 36: 231-232 2004 Type: ARTICLE Genes: lin-48 Abstract: The evolution of complexity relies on changes that result in new gene functions. Here we show that the unique morphological and functional features of the excretory duct cell in C. elegans result from the gain of expression of a single gene. Our results show that innovation can be achieved by altered expression of a transcription factor without coevolution of all target genes. ------------------- Key: 6394 Medline: 15095973 Authors: Koga M;Ohshima Y Title: The C. elegans ceh-36 gene encodes a putative homemodomain transcription factor involved in chemosensory functins of ASE and AWC neurons. Citation: Journal of Molecular Biology 336: 579-587 2004 Type: ARTICLE Genes: ceh-36 che-1 gcy-5 gcy-6 gcy-7 tax-2 Abstract: Chemotaxis to water-soluble chemicals such as sodium ion is an important behavior of Caenorhabditis elegans for seeking food, and ASE chemosensory neurons have a major role in this behavior. We isolated mutants defective in chemotaxis to sodium acetate. We show here that among them ks86 had a mutation in the ceh-36 gene. ceh-36 :: gfp reporter constructs were expressed in ASE and AWC neurons. In a mutant of the che-1 gene, which encodes another transcription factor and is required for specification of ASE neurons, expression of the ceh-36 :: gfp reporter in ASE is lost. This indicates that the ceh-36 gene functions downstream of the che-1 gene in ASE. In the ceh-36(ks86) mutant, expression of the tax-2 gene encoding a cyclic nucleotide-gated channel was reduced in ASE and AWC. This affords an explanation for defects of the ceh-36 mutant in the chemotaxis mediated by ASE and AWC. When a ceh-36 cDNA was expressed in an adult ceh-36 mutant by a heat shock promoter, chemotaxis to sodium acetate was recovered. These results suggest that ceh-36 is required for functions, and not for development, of ASE. ------------------- Key: 6395 Medline: Authors: Simmer F;Moorman C;van der Linden AM;Kuijk E;van den Berghe PVE;Kamath FS;Fraser AG;Ahringer J;Plasterk RHA Title: Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. Citation: PLoS Biology 1: 77-84 2003 Type: ARTICLE Genes: bli-3 bli-5 dpy-4 dpy-6 dpy-9 egl-30 gpc-2 hlh-2 mes-3 mex-3 rol-3 rrf-3 unc-73 unc-87 unc-108 Abstract: RNA-mediated interference (RNAi) is a method to inhibit gene function by introduction of double-stranded RNA (dsRNA). Recently, an RNAi library was constructed that consists of bacterial clones expressing dsRNA, corresponding to nearly 90% of the 19,427 predicted genes of C. elegans. Feeding of this RNAi library to the standard wild-type laboratory strain Bristol N2 detected phenotypes for approximately 10% of the corresponding genes. To increase the number of genes for which a loss-of-function phenotype can be detected, we undertook a genome-wide RNAi screen using the rrf-3 mutant strain, which we found to be hypersensitive to RNAi. Feeding of the RNAi library to rrf-3 mutants resulted in additional loss-of -function phenotypes for 393 genes, increasing the number of genes with a phenotype by 23%. These additional phenotypes are distributed over different phenotypic classes. We also studied interexerimental variability in RNAi results and found persistent levels of false negatives. In addition, we used the RNAi phenotypes obtained with the genome-wide screens to systematically clone seven existing genetic mutants with visible phenotypes. The genome-wide RNAi screen using rrf-3 significantly increased the functional data on the C. elegans genome. The resulting dataset will be valuable in conjunction wit other functional genomics approaches, as ------------------- Key: 6396 Medline: Authors: Stein LD;Bao Z;Blasiar D;Blumenthal T;Brent MR;Chen N;Chinwalla A;Clarke L;Clee C;Coghlan A;Coulson A;D'Eustachio P;Fitch DHA;Fulton LA;Fulton RE;Griffiths-Jones S;Harris TW;Hillier LW;Kamath R;Kuwaba Title: The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. Citation: PLoS Biology 1: 166-192 2003 Type: ARTICLE Genes: Abstract: The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4 % of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will ------------------- Key: 6397 Medline: 14732394 Authors: Melkman T;Sengupta P Title: The worm's sense of smell. Development of functional diversity in the chemosensory system of Caenorhabditis elegans. Citation: Developmental Biology 265: 302-319 2004 Type: REVIEW Genes: apx-1 ceh-14 ceh-36 ceh-37 che-1 cnd-1 daf-19 gcy-5 gcy-6 gcy-7 glp-1 ham-1 hlh-2 hlh-3 lag-2 lim-4 lin-11 lin-12 lin-32 lit-1 mom-2 odr-1 odr-3 odr-7 odr-10 osm-1 osm-3 osm-6 pop-1 srd-1 str-2 ttx-1 unc-3 unc-42 unc-130 wrm-1 Abstract: Animals sense their chemical environment using multiple chemosensory neuron types, each of which exhibits characteristic response properties. The chemosensory neurons of the nematode Caenorhabditis elegans provide an excellent system in which to explore the developmental mechanisms giving rise to this functional diversity. In this review, we discuss the principles underlying the patterning, generation, differentiation, and diversification of chemosensory neuron subtypes in C. elegans. Current knowledge of the molecular mechanisms underlying each of these individual steps is derived from work in different model organisms. It is essential to describe the complete developmental pathways in each organism to determine whether functional diversification in chemosensory systems is achieved via conserved or novel mechanisms. Such a complete description may be possible in ------------------- Key: 6398 Medline: 14732404 Authors: Crowe E;Candido EPM Title: Characterization of C. elegans RING finger protein 1, a binding partner of ubiquitin-conjugating enzyme 1. Citation: Developmental Biology 265: 446-459 2004 Type: ARTICLE Genes: rfp-1 rrf-3 ubc-1 ubc-2 ubc-12 Abstract: In a yeast two-hybrid screen, RING finger protein 1 (RFP-1) and UBR1 were identified as potential binding partners of C. elegans UBC1, a ubiquitin-conjugating enzyme with a high degree of identity to S. cerevisiae UBC2/RAD6. The interaction of RFP-1 and UBC-1 was confirmed by co-immunoprecipitation experiments. Yeast interaction trap experiments mapped the region of interaction to the basic N-terminal 313 residues of RFP-1. The acidic carboxy-terminal extension of UBC-1 was not required for the interaction with RFP-1. Western blot analysis and indirect immunohistochemical staining show that RFP-1 is present in embryos, larvae, and adults, where it is found in intestinal, nerve ring, pharyngeal, gonadal, and oocyte cell nuclei. Double-stranded RNA interference experiments against rfp-1 indicate that this gene is required for L1 development, vulval development, and for egg laying. By contrast, RNA interference against ubc-1 gave no obvious phenotype, suggesting that ubc-1 is nonessential or is functionally redundant. ------------------- Key: 6399 Medline: 14732406 Authors: Landmann F;Quintin S;Labouesse M Title: Multiple regulatory elements with spatially and temporally distinct activities control the expression of the epithelial differentiation gene lin-26 in C. elegans. Citation: Developmental Biology 265: 478-490 2004 Type: ARTICLE Genes: ceh-13 elt-1 elt-3 elt-5 elt-6 lin-26 lir-1 lir-2 nhr-23 nhr-25 nob-1 pha-4 Abstract: Epithelial differentiation is a very early event during development of most species. The nematode Caenorhabditis elegans, with its well-defined and invariant lineage, offers the possibility to link cell lineage, cell fate specification and gene regulation during epithelial differentiation. Here, we focus on the regulation of the gene lin-26, which is required for proper differentiation of epithelial cells in the ectoderm and mesoderm (somatic gonad). lin-26 expression starts in early embryos and remains on throughout development, in many cell types originating from different sublineages. Using GFP reporters and mutant rescue assays, we performed a molecular dissection of the lin-26 promoter and could identify almost all elements required to establish its complex spatial and temporal expression. Most of these elements act redundantly, or synergistically once combined, to drive expression in cells related by function. We also show that lin-26 promoter elements mediate activation in the epidermis (hypodermis) by the GATA factor ELT-1, or repression in the foregut (pharynx) by the FoxA protein PHA-4. Taken together, our data indicate that lin-26 regulation is achieved to a large extent through ------------------- Key: 6400 Medline: 14729475 Authors: Segbert C;Johnson K;Theres C;van Furden D;Bossinger O Title: Molecular and functional analysis of apical junction formation in the gut epithelium of Caenorhabditis elegans. Citation: Developmental Biology 266: 17-26 2004 Type: ARTICLE Genes: ajm-1 crb-1 dlg-1 erm-1 hmp-1 hmp-2 hmr-1 let-413 Abstract: The Caenorhabditis elegans intestine is a simple and accessible model system to analyze the mechanism of junction assembly. In comparison to Drosophila and vertebrates, the C. elegans apical junction is remarkable because a single electron-dense structure is implicated in complex processes such as epithelial tightness, vectorial transport and cell adhesion. Here we present evidence in support of a heterogeneous molecular assembly of junctional proteins found in Drosophila and vertebrate epithelia associated with different junctions or regions of the plasma membrane. In addition, we show that molecularly diverse complexes participate in different aspects of epithelial maturation in the C. elegans intestine. DLG-1 (Discs large) acts synergistically with the catenin-cadherin complex (HMP-1-HMP-2-HMR-1) and the Ezrin-Radixin-Moesin homolog (ERM-1) to ensure tissue integrity of the intestinal tube. The correct localization of DLG-1 itself depends on AJM-1, a coiled-coil protein. Double depletion of HMP-1 (a-catenin) and LET-413 (C. elegans homolog of Drosophila Scribble) suggests that the catenin-cadherin complex is epistatic to LET-413, while additional depletion of subapically expressed CRB-1 (Crumbs) emphasizes a role of CRB-1 concerning apical -------------------