Fungal CSL transcription factors

. 2007 Jul 13 ; 8 () : 233. [epub] 20070713

Jazyk angličtina Země Velká Británie, Anglie Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid17629904

BACKGROUND: The CSL (CBF1/RBP-Jkappa/Suppressor of Hairless/LAG-1) transcription factor family members are well-known components of the transmembrane receptor Notch signaling pathway, which plays a critical role in metazoan development. They function as context-dependent activators or repressors of transcription of their responsive genes, the promoters of which harbor the GTG(G/A)GAA consensus elements. Recently, several studies described Notch-independent activities of the CSL proteins. RESULTS: We have identified putative CSL genes in several fungal species, showing that this family is not confined to metazoans. We have analyzed their sequence conservation and identified the presence of well-defined domains typical of genuine CSL proteins. Furthermore, we have shown that the candidate fungal protein sequences contain highly conserved regions known to be required for sequence-specific DNA binding in their metazoan counterparts. The phylogenetic analysis of the newly identified fungal CSL proteins revealed the existence of two distinct classes, both of which are present in all the species studied. CONCLUSION: Our findings support the evolutionary origin of the CSL transcription factor family in the last common ancestor of fungi and metazoans. We hypothesize that the ancestral CSL function involved DNA binding and Notch-independent regulation of transcription and that this function may still be shared, to a certain degree, by the present CSL family members from both fungi and metazoans.

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Pursglove SE, Mackay JP. CSL: a notch above the rest. Int J Biochem Cell Biol. 2005;37:2472–2477. doi: 10.1016/j.biocel.2005.06.013. PubMed DOI

Artavanis-Tsakonas S, Rand MD, Lake RJ. Notch signaling: cell fate control and signal integration in development. Science. 1999;284:770–776. doi: 10.1126/science.284.5415.770. PubMed DOI

Weinmaster G, Kintner C. Modulation of Notch signaling during somitogenesis. Annu Rev Cell Dev Biol. 2003;19:367–395. doi: 10.1146/annurev.cellbio.19.111301.115434. PubMed DOI

Weng AP, Aster JC. Multiple niches for Notch in cancer: context is everything. Curr Opin Genet Dev. 2004;14:48–54. doi: 10.1016/j.gde.2003.11.004. PubMed DOI

Hayward SD. Viral interactions with the Notch pathway. Semin Cancer Biol. 2004;14:387–396. doi: 10.1016/j.semcancer.2004.04.018. PubMed DOI

Oka C, Nakano T, Wakeham A, de la Pompa JL, Mori C, Sakai T, Okazaki S, Kawaichi M, Shiota K, Mak TW, Honjo T. Disruption of the mouse RBP-J kappa gene results in early embryonic death. Development. 1995;121:3291–3301. PubMed

Koelzer S, Klein T. A Notch-independent function of Suppressor of Hairless during the development of the bristle sensory organ precursor cell of Drosophila. Development. 2003;130:1973–1988. doi: 10.1242/dev.00426. PubMed DOI

Kaspar M, Klein T. Functional analysis of murine CBF1 during Drosophila development. Dev Dyn. 2006;235:918–927. doi: 10.1002/dvdy.20667. PubMed DOI

Bray S, Furriols M. Notch pathway: making sense of suppressor of hairless. Curr Biol. 2001;11:R217–R221. doi: 10.1016/S0960-9822(01)00109-9. PubMed DOI

Barolo S, Walker RG, Polyanovsky AD, Freschi G, Keil T, Posakony JW. A notch-independent activity of suppressor of hairless is required for normal mechanoreceptor physiology. Cell. 2000;103:957–969. doi: 10.1016/S0092-8674(00)00198-7. PubMed DOI

Beres TM, Masui T, Swift GH, Shi L, Henke RM, MacDonald RJ. PTF1 is an organ-specific and Notch-independent basic helix-loop-helix complex containing the mammalian Suppressor of Hairless (RBP-J) or its paralogue, RBP-L. Mol Cell Biol. 2006;26:117–130. doi: 10.1128/MCB.26.1.117-130.2006. PubMed DOI PMC

Minoguchi S, Taniguchi Y, Kato H, Okazaki T, Strobl LJ, Zimber-Strobl U, Bornkamm GW, Honjo T. RBP-L, a transcription factor related to RBP-Jkappa. Mol Cell Biol. 1997;17:2679–2687. PubMed PMC

Lai EC. Keeping a good pathway down: transcriptional repression of Notch pathway target genes by CSL proteins. EMBO Rep. 2002;3:840–845. doi: 10.1093/embo-reports/kvf170. PubMed DOI PMC

James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung GH, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schussler A, Longcore JE, O'Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature. 2006;443:818–822. doi: 10.1038/nature05110. PubMed DOI

Rep M, Duyvesteijn RG, Gale L, Usgaard T, Cornelissen BJ, Ma LJ, Ward TJ. The presence of GC-AG introns in Neurospora crassa and other euascomycetes determined from analyses of complete genomes: implications for automated gene prediction. Genomics. 2006;87:338–347. doi: 10.1016/j.ygeno.2005.11.014. PubMed DOI

Matsuyama A, Arai R, Yashiroda Y, Shirai A, Kamata A, Sekido S, Kobayashi Y, Hashimoto A, Hamamoto M, Hiraoka Y, Horinouchi S, Yoshida M. ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol. 2006;24:841–847. doi: 10.1038/nbt1222. PubMed DOI

Kovall RA, Hendrickson WA. Crystal structure of the nuclear effector of Notch signaling, CSL, bound to DNA. EMBO J. 2004;23:3441–3451. doi: 10.1038/sj.emboj.7600349. PubMed DOI PMC

Tang Z, Kadesch T. Identification of a novel activation domain in the Notch-responsive transcription factor CSL. Nucleic Acids Res. 2001;29:2284–2291. doi: 10.1093/nar/29.11.2284. PubMed DOI PMC

Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Pfam: clans, web tools and services. Nucleic Acids Res. 2006;34:D247–D251. doi: 10.1093/nar/gkj149. PubMed DOI PMC

Sakai T, Taniguchi Y, Tamura K, Minoguchi S, Fukuhara T, Strobl LJ, Zimber-Strobl U, Bornkamm GW, Honjo T. Functional replacement of the intracellular region of the Notch1 receptor by Epstein-Barr virus nuclear antigen 2. J Virol. 1998;72:6034–6039. PubMed PMC

Fuchs KP, Bommer G, Dumont E, Christoph B, Vidal M, Kremmer E, Kempkes B. Mutational analysis of the J recombination signal sequence binding protein (RBP-J)/Epstein-Barr virus nuclear antigen 2 (EBNA2) and RBP-J/Notch interaction. Eur J Biochem. 2001;268:4639–4646. doi: 10.1046/j.1432-1327.2001.02387.x. PubMed DOI

Hsieh JJ, Zhou S, Chen L, Young DB, Hayward SD. CIR, a corepressor linking the DNA binding factor CBF1 to the histone deacetylase complex. Proc Natl Acad Sci U S A. 1999;96:23–28. doi: 10.1073/pnas.96.1.23. PubMed DOI PMC

Kuramae EE, Robert V, Snel B, Weiss M, Boekhout T. Phylogenomics reveal a robust fungal tree of life. FEMS Yeast Res. 2006;6:1213–1220. doi: 10.1111/j.1567-1364.2006.00119.x. PubMed DOI

Furukawa T, Kawaichi M, Matsunami N, Ryo H, Nishida Y, Honjo T. The Drosophila RBP-J kappa gene encodes the binding protein for the immunoglobulin J kappa recombination signal sequence. J Biol Chem. 1991;266:23334–23340. PubMed

Hedges SB. The origin and evolution of model organisms. Nat Rev Genet. 2002;3:838–849. doi: 10.1038/nrg929. PubMed DOI

Ciccarelli FD, Doerks T, von MC, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science. 2006;311:1283–1287. doi: 10.1126/science.1123061. PubMed DOI

Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El AH, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares CP. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature. 2001;414:450–453. doi: 10.1038/35106579. PubMed DOI

Sluder AE, Maina CV. Nuclear receptors in nematodes: themes and variations. Trends Genet. 2001;17:206–213. doi: 10.1016/S0168-9525(01)02242-9. PubMed DOI

Rosel D, Puta F, Blahuskova A, Smykal P, Folk P. Molecular characterization of a calmodulin-like dictyostelium protein CalB. FEBS Lett. 2000;473:323–327. doi: 10.1016/S0014-5793(00)01551-9. PubMed DOI

Nakayashiki H, Kadotani N, Mayama S. Evolution and diversification of RNA silencing proteins in fungi. J Mol Evol. 2006;63:127–135. doi: 10.1007/s00239-005-0257-2. PubMed DOI

Schizosaccharomyces japonicus Sequencing Project. Broad Institute of MIT and Harvard

Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Dusterhoft A, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Benito J, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg SL, Cerutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P, Cerrutti L. The genome sequence of Schizosaccharomyces pombe. Nature. 2002;415:871–880. doi: 10.1038/nature724. PubMed DOI

Cryptococcus neoformans Sequencing Project. Broad Institute of MIT and Harvard

Kuramae EE, Robert V, Snel B, Boekhout T. Conflicting phylogenetic position of Schizosaccharomyces pombe. Genomics. 2006;88:387–393. doi: 10.1016/j.ygeno.2006.07.001. PubMed DOI

Coeytaux K, Poupon A. Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics. 2005;21:1891–1900. doi: 10.1093/bioinformatics/bti266. PubMed DOI

Gregan J, Rabitsch PK, Sakem B, Csutak O, Latypov V, Lehmann E, Kohli J, Nasmyth K. Novel genes required for meiotic chromosome segregation are identified by a high-throughput knockout screen in fission yeast. Curr Biol. 2005;15:1663–1669. doi: 10.1016/j.cub.2005.07.059. PubMed DOI

Decottignies A, Sanchez-Perez I, Nurse P. Schizosaccharomyces pombe essential genes: a pilot study. Genome Res. 2003;13:399–406. doi: 10.1101/gr.636103. PubMed DOI PMC

Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bahler J. Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell. 2003;14:214–229. doi: 10.1091/mbc.E02-08-0499. PubMed DOI PMC

Mata J, Lyne R, Burns G, Bahler J. The transcriptional program of meiosis and sporulation in fission yeast. Nat Genet. 2002;32:143–147. doi: 10.1038/ng951. PubMed DOI

NCBI Protein

UniProt Knowledgebase

Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268:78–94. doi: 10.1006/jmbi.1997.0951. PubMed DOI

Milanesi L, D'Angelo D, Rogozin IB. GeneBuilder: interactive in silico prediction of gene structure. Bioinformatics. 1999;15:612–621. doi: 10.1093/bioinformatics/15.7.612. PubMed DOI

Hua S, Sun Z. Support vector machine approach for protein subcellular localization prediction. Bioinformatics. 2001;17:721–728. doi: 10.1093/bioinformatics/17.8.721. PubMed DOI

Yu CS, Chen YC, Lu CH, Hwang JK. Prediction of protein subcellular localization. Proteins. 2006;64:643–651. doi: 10.1002/prot.21018. PubMed DOI

Nakai K, Horton P. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci. 1999;24:34–36. doi: 10.1016/S0968-0004(98)01336-X. PubMed DOI

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003;31:3497–3500. doi: 10.1093/nar/gkg500. PubMed DOI PMC

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876–4882. doi: 10.1093/nar/25.24.4876. PubMed DOI PMC

Kumar S, Tamura K, Nei M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 2004;5:150–163. doi: 10.1093/bib/5.2.150. PubMed DOI

Gouet P, Courcelle E, Stuart DI, Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics. 1999;15:305–308. doi: 10.1093/bioinformatics/15.4.305. PubMed DOI

Rhizopus oryzae Sequencing Project. Broad Institute of MIT and Harvard

Coprinus cinereus Sequencing Project. Broad Institute of MIT and Harvard

JGI Phanerochaete chrysosporium v2.0

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