C. elegans : an invaluable model organism for the proteomics studies of the cholesterol-mediated signaling pathway

References

• Riddle D, Albert P. C. elegans II. Riddle D, Blumenthal T, Meyer B, Priess J (Eds). Cold Spring Harbor Laboratory Press, NY, USA, 739–768 (1997).
   Google Scholar
• Lai CH, Chou CY, Ch’ang LY, Liu CS, Lin W. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. Genome Res.10(5), 703–713 (2000).
   PubMed Web of Science ®Google Scholar
• van Helden J. Prediction of transcriptional regulation by analysis of the non-coding genome. Curr. Genomics4, 217–224 (2003).
   Google Scholar
• The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science282(5396), 2012–2018 (1998).
   PubMed Web of Science ®Google Scholar
• Brett D, Pospisil H, Valcarcel J, Reich J, Bork P. Alternative splicing and genome complexity. Nat. Genet.30, 29–30 (2002).
   PubMed Web of Science ®Google Scholar
• Reboul J, Vaglio P, Rual JF et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet.34(1), 35–41 (2003).
   PubMed Web of Science ®Google Scholar
• Huang RY, Boulton SJ, Vidal M et al. High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins. Biochem. Biophys. Res. Commun.307(4), 928–934 (2003).
   PubMedGoogle Scholar
• Luan CH, Qiu S, Finley JB et al. High-throughput expression of C. elegans proteins. Genome Res.14(10B), 2102–2110 (2004).
   PubMed Web of Science ®Google Scholar
• Lamesch P, Milstein S, Hao T et al. C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res.14(10B), 2064–2069 (2004).
   PubMed Web of Science ®Google Scholar
• Chen N, Lawson D, Bradnam K et al. WormBase as an integrated platform for the C. elegans ORFeome. Genome Res.14(10B), 2155–2161 (2004).
   PubMed Web of Science ®Google Scholar
• Vanfleteren JR, De Vreese A. Analysis of the proteins of aging Caenorhabditis elegans by high resolution two-dimensional gel electrophoresis. Electrophoresis15(2), 289–296 (1994).
   PubMedGoogle Scholar
• Bini L, Heid H, Liberatori S et al. Two-dimensional gel electrophoresis of Caenorhabditis elegans homogenates and identification of protein spots by microsequencing. Electrophoresis18, 557–562 (1997).
   PubMed Web of Science ®Google Scholar
• Kaji H, Tsuji T, Mawuenyega KG et al. Profiling of Caenorhabditis elegans proteins using two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis21(9), 1755–1765 (2000).
   PubMed Web of Science ®Google Scholar
• Schrimpf SP, Langen H, Gomes AV et al. A two-dimensional protein map of Caenorhabditis elegans. Electrophoresis22(6), 1224–1232 (2001).
   PubMedGoogle Scholar
• Madi A, Mikkat S, Ringel B et al. Mass spectrometric proteome analysis for profiling temperature-dependent changes of protein expression in wild-type Caenorhabditis elegans. Proteomics3(8), 1526–1534 (2003).
   PubMedGoogle Scholar
• Bantscheff M, Ringel B, Madi A et al. Proteomics4(8), 2283–2295 (2004).
   PubMedGoogle Scholar
• Mawuenyega KG, Kaji H, Yamuchi Y et al. Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography-tandem mass spectrometry. J. Proteome Res.2(1), 23–35 (2003).
   PubMed Web of Science ®Google Scholar
• Krijgsveld J, Ketting RF, Mahmoudi T et al. Metabolic labeling of C. elegans and D. melanogaster for quantitative Proteomics Nat. Biotechnol.21(8), 927–931 (2003)
   PubMed Web of Science ®Google Scholar
• Tabuse Y, Nabetani T, Tsugita A. Proteomic analysis of protein expression profiles during Caenorhabditis elegans development using two-dimensional difference gel electrophoresis Proteomics5(11), 2876–2891 (2005).
   PubMed Web of Science ®Google Scholar
• Masuda M, Saimaru H, Takamura N et al. An improved method for proteomics studies in C. elegans by fluorogenic derivatization, HPLC isolation, enzymatic digestion and liquid chromatography – tandem mass spectrometric identification. Biomed. Chromatogr.19(7), 556–560 (2005).
   PubMedGoogle Scholar
• Mann M, Jensen ON. Proteomic analysis of post-translational modifications. Nat. Biotechnol.21(3), 255–261 (2003).
   PubMed Web of Science ®Google Scholar
• Kalume DE, Molina H, Pandey A. Tackling the phosphoproteome: tools and strategies. Curr. Opin. Chem. Biol.7(1), 64–69 (2003).
   PubMedGoogle Scholar
• Jensen ON. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr. Opin. Chem. Biol.8(1), 33–41 (2004).
   PubMed Web of Science ®Google Scholar
• Wang X, Inoue S, Gu J et al. Dysregulation of TGF-beta1 receptor activation leads to abnormal lung development and emphysema-like phenotype in core fucose-deficient mice. Proc. Natl Acad. Sci. USA102(44), 15791–15796 (2005).
   PubMed Web of Science ®Google Scholar
• Hirabayashi J, Arata Y, Kasai K. Glycome project: concept, strategy and preliminary application to Caenorhabditis elegans. Proteomics1(2), 295–303 (2001).
   PubMedGoogle Scholar
• Fan X, She YM, Bagshaw RD, et al. Identification of the hydrophobic glycoproteins of Caenorhabditis elegans. Glycobiology15(10), 952–964 (2005).
   PubMed Web of Science ®Google Scholar
• Schachter H. Protein glycosylation lessons from Caenorhabditis elegans. Curr. Opin. Struct. Biol.14(5), 607–616 (2004).
   PubMed Web of Science ®Google Scholar
• Fan X, She YM, Bagshaw RD et al. A method for proteomic identification of membrane-bound proteins containing Asn-linked oligosaccharides. Anal. Biochem.332(1), 178–186 (2004).
   PubMed Web of Science ®Google Scholar
• Kaji H, Isobe T. Protein database of Caenorhabditis elegans. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci.787(1), 91–99 (2003).
   PubMedGoogle Scholar
• Taniguchi N, Nakamura K, Narimatsu H et al. Human Disease Glycomics/Proteome Initiative Workshop and the 4th HUPO Annual Congress. Proteomics6(1), 12–13 (2006).
   Google Scholar
• Gygi SP, Rist B, Aebersold R. Measuring gene expression by quantitative proteome analysis. Curr. Opin. Biotechnol.11(4), 396–401 (2000).
   PubMed Web of Science ®Google Scholar
• Cutler P. Protein arrays: the current state-of-the-art. Proteomics3(1), 3–18 (2003).
   PubMed Web of Science ®Google Scholar
• Li S, Armstrong CM, Bertin N, et al. A map of the interactome network of the metazoan C. elegans. Science303(5657), 540–543 (2004).
   PubMed Web of Science ®Google Scholar
• Walhout AJ, Reboul J, Shtanko O et al. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol.12(22), 1952–1958 (2002).
   PubMed Web of Science ®Google Scholar
• Walhout AJ, Boulton SJ, Vidal M. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast17(2), 88–94 (2000).
   PubMedGoogle Scholar
• Fields S. High-throughput two-hybrid analysis. The promise and the peril. FEBS J.272(21), 5391–5393 (2005).
   PubMed Web of Science ®Google Scholar
• Duchaine TF, Wohlschlegel JA, Kennedy S et al. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell124(2), 343–354 (2006).
   PubMedGoogle Scholar
• Skop AR, Liu H, Yates J III et al. Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms. Science305(5680), 61–66 (2004).
   PubMed Web of Science ®Google Scholar
• Gilleard JS, Woods DJ, Dow JA. Model-organism genomics in veterinary parasite drug-discovery. Trends Parasitol.21(7), 302–305 (2005).
   PubMed Web of Science ®Google Scholar
• Olsen A, Vantipalli MC, Lithgow GJ. Using Caenorhabditis elegansas a model for aging and age-related diseases. Ann. NY Acad. Sci.1067, 120–128 (2006).
   PubMed Web of Science ®Google Scholar
• Kwok TC, Ricker N, Fraser R et al. A small-molecule screen in C. elegans yields a new calcium channel antagonist. Nature441(7089), 91–95 (2006).
   PubMed Web of Science ®Google Scholar
• Lochnit G, Bongaarts R, Geyer R. Searching new targets for anthelminthic strategies: interference with glycosphingolipid biosynthesis and phosphorylcholine metabolism affects development of Caenorhabditis elegans.Int. J. Parasitol.35(8), 911–923 (2005).
   PubMed Web of Science ®Google Scholar
• Gaud A, Simon JM, Witzel T et al. Prednisone reduces muscle degeneration in dystrophin-deficient Caenorhabditis elegans. Neuromuscul. Disord.14(6), 365–370 (2004).
   PubMed Web of Science ®Google Scholar
• Jain KK. RNAi and siRNA in target validation. Drug. Discov. Today9(7), 307–309 (2004).
   PubMedGoogle Scholar
• Williams PL, Dusenbery DB. Screening test for neurotoxins using Caenorhabditis elegans. Prog. Clin. Biol. Res.253, 163–170 (1987).
   PubMedGoogle Scholar
• Kimura KD, Tissenbaum HA, Liu Y et al. daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. Science277(5328), 942–946 (1997).
   PubMed Web of Science ®Google Scholar
• Patterson GI, Padgett RW. TGF beta-related pathways. Roles in Caenorhabditis elegans development. Trends Genet.16(1), 27–33 (2000).
   PubMed Web of Science ®Google Scholar
• Jia K, Albert PS, Riddle DL. DAF-9, a cytochrome P450 regulating C. elegans larval development and adult longevity. Development129(1), 221–231 (2002).
   PubMed Web of Science ®Google Scholar
• Gerisch B, Antebi A. Hormonal signals produced by DAF-9/cytochrome P450 regulate C. elegans dauer diapause in response to environmental cues. Development131(8), 1765–1776 (2004).
   PubMed Web of Science ®Google Scholar
• Kurzchalia TV, Ward S. Why do worms need cholesterol? Nat. Cell Biol.5(8), 684–688 (2003).
   PubMed Web of Science ®Google Scholar
• Bae S, Seong J, Paik YK. Cholesterol biosynthesis from lanosterol: molecular cloning, chromosomal localization, functional expression and liver-specific gene regulation of rat sterol delta8-isomerase, a cholesterogenic enzyme with multiple functions. Biochem. J.353, 689–699 (2001).
   PubMedGoogle Scholar
• Braverman N, Lin P, Moebius FF et al. Mutations in the gene encoding 3 beta-hydroxysteroid-delta 8, delta 7-isomerase cause X-linked dominant Conradi-Hunermann syndrome. Nat. Genet.22, 291–294 (1999).
   PubMed Web of Science ®Google Scholar
• Chitwood DJ. Biochemistry and function of nematode steroids. Crit. Rev. Biochem. Mol. Biol.34, 273–284 (1999).
   PubMed Web of Science ®Google Scholar
• Lee EY, Shim YH, Chitwood DJ et al. Cholesterol-producing transgenic Caenorhabditis elegans lives longer due to newly acquired enhanced stress resistance. Biochem. Biophys. Res. Commun.328(4), 929–936 (2005).
   PubMedGoogle Scholar
• Simons K, Ikonen E. Functional rafts in cell membranes. Nature387(6633), 569–572 (1997).
   PubMed Web of Science ®Google Scholar
• Yochem J, Tuck S, Greenwald I, Han M. A gp330/megalin-related protein is required in the major epidermis of Caenorhabditis elegans for completion of molting. Development126(3), 597–606 (1999).
   PubMedGoogle Scholar
• Scheel J, Srinivasan J, Honnert U et al. Involvement of caveolin-1 in meiotic cell-cycle progression in Caenorhabditis elegans.Nat. Cell Biol.1(2), 127–129 (1999).
   PubMed Web of Science ®Google Scholar
• Church DL, Guan KL, Lambie EJ. Three genes of the MAP kinase cascade, mek-2, mpk-1/sur-1 and let-60 ras, are required for meiotic cell cycle progression in Caenorhabditis elegans. Development121, 2525–2535 (1995).
   PubMed Web of Science ®Google Scholar
• Matyash M, Matyash V, Nolte C et al. Requirement of functional ryanodine receptor type 3 for astrocyte migration. FASEB J.16(1), 84–86 (2002).
   PubMedGoogle Scholar
• Schedin P, Jonas P, Wood WB Function of the her-1 gene is required for maintenance of male differentiation in adult tissues of C. elegans. Dev. Genet.15(3), 231–239 (1994).
   PubMedGoogle Scholar
• Thiele C, Hannah MJ, Fahrenholz F et al. Cholesterol binds to synaptophysin and is required for biogenesis of synaptic vesicles. Nat. Cell Biol.2(1), 42–49 (2000).
   PubMed Web of Science ®Google Scholar
• Motola DL, Cummins CL, Rottiers V et al. Identification of ligands for DAF-12 that govern dauer formation and reproduction in C. elegans. Cell124(6), 1209–1223 (2006).
   PubMed Web of Science ®Google Scholar
• Michaux G, Gansmuller A, Hindelang C et al. CHE-14, a protein with a sterol-sensing domain, is required for apical sorting in C. elegans ectodermal epithelial cells. Curr. Biol.10(18), 1098–1107 (2000).
   PubMedGoogle Scholar
• Choi BK, Chitwood DJ, Paik YK. Proteomic changes during disturbance of cholesterol metabolism by azacoprostane treatment in Caenorhabditis elegans. Mol. Cell. Proteomics2(10), 1086–1095 (2003).
   PubMedGoogle Scholar
• Chitwood DJ, Lusby WR, Lozano R, Thompson MJ, Svoboda JA. Novel nuclear methylation of sterols by the nematode Caenorhabditis elegans. Steroids42, 311–319 (1983).
   PubMedGoogle Scholar
• Jeong PY, Jung M, Yim YH et al. Chemical structure and biological activity of the Caenorhabditis elegans dauer-inducing pheromone. Nature433(7025), 541–545 (2005).
   PubMed Web of Science ®Google Scholar
• Shim YH, Chun JH, Lee EY et al. Role of cholesterol in germ-line development of Caenorhabditis elegans. Mol. Reprod. Dev.61(3), 358–366 (2002).
   PubMedGoogle Scholar
• Sternberg PW, Schmid SL. Caveolin, cholesterol and Ras signaling. Nat. Cell Biol.1(2), E35–E37 (1999).
   PubMedGoogle Scholar
• Kuwabara PE, Lee MH, Schedl T et al. C. elegans patched gene, ptc-1, functions in germ-line cytokinesis. Genes Dev.14(15), 1933–1944 (2000).
   PubMedGoogle Scholar
• Shibata Y, Branicky R, Landaverde IO et al. Redox regulation of germline and vulval development in Caenorhabditis elegans. Science302(5651), 1779–1782 (2003).
   PubMedGoogle Scholar
• Reinke V, Smith HE, Nance J et al. A global profile of germline gene expression in C. elegans. Mol. Cell.6(3), 605–616 (2000).
   PubMed Web of Science ®Google Scholar
• Steiner S, Gatlin CL, Lennon JJ et al. Proteomics to display lovastatin-induced protein and pathway regulation in rat liver. Electrophoresis21(11), 2129–2137 (2000).
   PubMed Web of Science ®Google Scholar
• Steiner S, Gatlin CL, Lennon JJ, et al. Cholesterol biosynthesis regulation and protein changes in rat liver following treatment with fluvastatin. Toxicol. Lett.120(1–3), 369–377 (2001).
   PubMed Web of Science ®Google Scholar
• Park JY, Seong JK, Paik YK. Proteomic analysis of diet-induced hypercholesterolemic mice. Proteomics4(2), 514–523 (2004).
   PubMed Web of Science ®Google Scholar
• Fenyo D. Identifying the proteome: software tools. Curr. Opin. Biotechnol.11(4), 391–395 (2000).
   PubMed Web of Science ®Google Scholar
• Costanzo MC, Hogan JD, Cusick ME et al. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res.28(1), 73–76 (2000).
   PubMedGoogle Scholar
• Costanzo MC, Crawford ME, Hirschman JE et al. PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res.29(1), 75–79 (2001).
   PubMedGoogle Scholar
• Kersey P, Bower L, Morris L et al. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res.33(Database issue), D297–D302 (2005).
   Google Scholar
• Wu CH, Apweiler R, Bairoch A et al. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res.34(Database issue), D187–D191 (2006).
   PubMed Web of Science ®Google Scholar
• Mulder NJ, Apweiler R, Attwood TK et al. InterPro, progress and status in 2005. Nucleic Acids Res.33(Database issue), D201–D205 (2005).
   Web of Science ®Google Scholar
• Kriventseva EV, Servant F, Apweiler R. Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. Nucleic Acids Res.31(1), 388–389 (2003).
   PubMedGoogle Scholar
• Camon E, Magrane M, Barrell D et al. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res.32(Database issue), D262–D266 (2004).
   PubMed Web of Science ®Google Scholar
• Valencia A. Automatic annotation of protein function. Curr. Opin. Struct. Biol.15(3), 267–274 (2005).
   PubMedGoogle Scholar
• Kent WJ. BLAT – the BLAST-like alignment tool. Genome Res.12(4), 656–664 (2002).
   PubMed Web of Science ®Google Scholar
• Hoersch S, Leroy C, Brown NP et al. The GeneQuiz web server: protein functional analysis through the Web. Trends Biochem. Sci.25(1), 33–35 (2000).
   PubMedGoogle Scholar
• Huang Y, Li Y. Prediction of protein subcellular locations using fuzzy k-NN method. Bioinformatics20(1), 21–28 (2004).
   PubMed Web of Science ®Google Scholar
• von Heijne G. A new method for predicting signal sequence cleavage sites. Nucleic Acids Res.14(11), 4683–4690 (1986).
   PubMed Web of Science ®Google Scholar
• Tsur D, Tanner S, Bafna ZE et al. Identification of post-translational modifications by blind search of mass spectra. Nat. Biotechnol.23(12), 1562–1567 (2005).
   PubMed Web of Science ®Google Scholar
• Han Y, Ma B, Zhang K. SPIDER: software for protein identification from sequence tags with de novo sequencing error. J. Bioinform. Comput. Biol.3(3), 697–716 (2005).
   PubMedGoogle Scholar
• Searle BC, Dasari S, Turner M et al. High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results. Anal. Chem.76(8), 2220–2230 (2004).
   PubMedGoogle Scholar
• Julenius K, Molgaard A, Gupta R et al. Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology15(2), 153–164 (2005).
   PubMed Web of Science ®Google Scholar
• Xenarios I, Salwinski L, Duan XJ et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res.30(1), 303–305 (2002).
   PubMed Web of Science ®Google Scholar
• Zanzoni A, Montecchi-Palazzi L, Quondam M et al. MINT: a Molecular INTeraction database. FEBS Lett.513(1), 135–140 (2002).
   PubMed Web of Science ®Google Scholar
• Bader GD, Betel D, Hogue CW. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res.31(1), 248–250 (2003).
   PubMed Web of Science ®Google Scholar
• Oltvai ZN, Barabasi AL. Systems biology. Life’s complexity pyramid. Science298(5594), 763–764 (2002).
   PubMed Web of Science ®Google Scholar
• Titz B, Schlesner M, Uetz P. What do we learn from high-throughput protein interaction data? Expert Rev. Proteomics1(1), 111–121 (2004).
   PubMed Web of Science ®Google Scholar
• Yu H, Luscombe NM, Lu HX et al. Annotation transfer between genomes: protein–protein interologs and protein–DNA regulogs. Genome Res.14(6), 1107–1118 (2004).
   PubMed Web of Science ®Google Scholar