Two-component signal transduction in Agaricus bisporus: A comparative genomic analysis with other basidiomycetes through the web-based tool BASID2CS

Fungal Genetics and Biology

Volumn 55, Issue , 2013, Pages 77-84

  Lavín, José L ^a   García Yoldi, Alberto ^a   Ramírez, Lucía ^a   Pisabarro, Antonio G ^a   Oguiza, José A ^a  

^a PUBLIC UNIVERSITY OF NAVARRE   (Spain)

Author keywords

Agaricus bisporus; Basidiomycetes; Comparative genomics; Histidine kinase; Response regulator; Signal transduction

Indexed keywords

FUNGAL PROTEIN; HISTIDINE CONTAINING PHOSPHOTRANSFER PROTEIN; PROTEIN HISTIDINE KINASE; PROTEIN RIM15; PROTEIN SKN7; PROTEIN SSK1; TCO1 NIK1 FUSION PROTEIN; TRANSCRIPTOME; UNCLASSIFIED DRUG;

AGARICUS BISPORUS; AMINO TERMINAL SEQUENCE; ARTICLE; BIOINFORMATICS; CARBOXY TERMINAL SEQUENCE; COMPUTER PROGRAM; CRYPTOCOCCUS NEOFORMANS; FUNGAL EXAMINATION; GENE; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; GENOME ANALYSIS; HPT GENE; NONHUMAN; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN EXPRESSION; RIM15 GENE; SIGNAL TRANSDUCTION; SPECIES COMPARISON; SSK1 GENE; TCO1 NIK1 GENE; TRANSCRIPTOMICS; TWO COMPONENT SIGNAL SYSTEM;

AGARICUS; BASIDIOMYCOTA; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; GENOMICS; INTERNET; SIGNAL TRANSDUCTION; SOIL MICROBIOLOGY;

AGARICUS; AGARICUS BISPORUS; BASIDIOMYCOTA; EUKARYOTA; FUNGI;

EID: 84879018601     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2012.09.012     Document Type: Article

References (52)

1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
2. Appleby J.L., Parkinson J.S., Bourret R.B. Signal transduction via the multistep phosphorelay: not necessarily a road less traveled. Cell 1996, 86:845-848.
3. Bahn Y.S., Kojima K., Cox G.M., Heitman J. A unique fungal two-component system regulates stress responses, drug sensitivity, sexual development, and virulence of Cryptococcus neoformans. Mol. Biol. Cell 2006, 17:3122-3135.
4. Bahn Y.S. Master and commander in fungal pathogens: the two-component system and the HOG signaling pathway. Eukaryot. Cell 2008, 7:2017-2036.
5. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., Studholme D.J., Yeats C., Eddy S.R. The Pfam protein families database. Nucleic Acids Res. 2004, 32:D138-D141.
6. Cashin P., Goldsack L., Hall D., O'Toole R. Contrasting signal transduction mechanisms in bacterial and eukaryotic gene transcription. FEMS Microbiol. Lett. 2006, 261:155-164.
7. Catlett N.L., Yoder O.C., Turgeon B.G. Whole-genome analysis of two-component signal transduction genes in fungal pathogens. Eukaryot. Cell 2003, 2:1151-1161.
8. Chauhan N., Calderone R. Two-component signal transduction proteins as potential drug targets in medically important fungi. Infect. Immun. 2008, 76:4795-4803.
9. Chun C.D., Liu O.W., Madhani H.D. A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans. PLoS Pathogens 2007, 3:e22.
10. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
11. Fassler J.S., West A.H. Fungal Skn7 stress responses and their relationship to virulence. Eukaryot. Cell 2011, 10:156-167.
12. Finn R.D., Clements J., Eddy S.R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011, 39:W29-W37.
13. Galperin M.Y. Diversity of structure and function of response regulator output domains. Curr. Opin. Microbiol. 2010, 13:150-159.
14. Grebe T.W., Stock J.B. The histidine protein kinase superfamily. Adv. Microb. Physiol. 1999, 41:139-227.
15. Grigoriev I.V., Nordberg H., Shabalov I., Aerts A., Cantor M., Goodstein D., Kuo A., Minovitsky S., Nikitin R., Ohm R.A., Otillar R., Poliakov A., Ratnere I., Riley R., Smirnova T., Rokhsar D., Dubchak I. The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 2012, 40:D26-D32.
16. Hagiwara D., Asano Y., Marui J., Furukawa K., Kanamaru K., Kato M., Abe K., Kobayashi T., Yamashino T., Mizuno T. The SskA and SrrA response regulators are implicated in oxidative stress responses of hyphae and asexual spores in the phosphorelay signaling network of Aspergillus nidulans. Biosci. Biotechnol. Biochem. 2007, 71:1003-1014.
17. Hibbett D.S., Binder M., Bischoff J.F., Blackwell M., Cannon P.F., Eriksson O.E., Huhndorf S., James T., Kirk P.M., Lücking R., Thorsten Lumbsch H., Lutzoni F., Matheny P.B., McLaughlin D.J., Powell M.J., Redhead S., Schoch C.L., Spatafora J.W., Stalpers J.A., Vilgalys R., Aime M.C., Aptroot A., Bauer R., Begerow D., Benny G.L., Castlebury L.A., Crous P.W., Dai Y.C., Gams W., Geiser D.M., Griffith G.W., Gueidan C., Hawksworth D.L., Hestmark G., Hosaka K., Humber R.A., Hyde K.D., Ironside J.E., Kõljalg U., Kurtzman C.P., Larsson K.H., Lichtwardt R., Longcore J., Miadlikowska J., Miller A., Moncalvo J.M., Mozley-Standridge S., Oberwinkler F., Parmasto E., Reeb V., Rogers J.D., Roux C., Ryvarden L., Sampaio J.P., Schüssler A., Sugiyama J., Thorn R.G., Tibell L., Untereiner W.A., Walker C., Wang Z., Weir A., Weiss M., White M.M., Winka K., Yao Y.J., Zhang N. A higher-level phylogenetic classification of the fungi. Mycol. Res. 2007, 111:509-547.
18. Hohmann S., Krantz M., Nordlander B. Yeast osmoregulation. Methods Enzymol. 2007, 428:29-45.
19. James T.Y., Kauff F., Schoch C.L., Matheny P.B., Hofstetter V., Cox C.J., Celio G., Gueidan C., Fraker E., Miadlikowska J., Lumbsch H.T., Rauhut A., Reeb V., Arnold A.E., Amtoft A., Stajich J.E., Hosaka K., Sung G.H., Johnson D., O'Rourke B., Crockett M., Binder M., Curtis J.M., Slot J.C., Wang Z., Wilson A.W., Schussler A., Longcore J.E., O'Donnell K., Mozley-Standridge S., Porter D., Letcher P.M., Powell M.J., Taylor J.W., White M.M., Griffith G.W., Davies D.R., Humber R.A., Morton J.B., Sugiyama J., Rossman A.Y., Rogers J.D., Pfister D.H., Hewitt D., Hansen K., Hambleton S., Shoemaker R.A., Kohlmeyer J., Volkmann-Kohlmeyer B., Spotts R.A., Serdani M., Crous P.W., Hughes K.W., Matsuura K., Langer E., Langer G., Untereiner W.A., Lucking R., Budel B., Geiser D.M., Aptroot A., Diederich P., Schmitt I., Schultz M., Yahr R., Hibbett D.S., Lutzoni F., McLaughlin D.J., Spatafora J.W., Vilgalys R. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 2006, 443:818-822.
20. Kirk P.M., Cannon P.F., David J.C., Stalpers J. Ainsworth and Bisby's Dictionary of the Fungi 2001, CAB International, Wallingford, UK. nineth ed.
21. Klein B.S., Tebbets B. Dimorphism and virulence in fungi. Curr. Opin. Microbiol. 2007, 10:314-319.
22. Kobayashi T., Abe K., Asai K., Gomi K., Juvvadi P.R., Kato M., Kitamoto K., Takeuchi M., Machida M. Genomics of Aspergillus oryzae. Biosci. Biotechnol. Biochem. 2007, 71:646-670.
23. Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 2001, 305:567-580.
24. Kruppa M., Calderone R. Two-component signal transduction in human fungal pathogens. FEMS Yeast Res. 2006, 6:149-159.
25. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
26. Laub M.T., Goulian M. Specificity in two-component signal transduction pathways. Annu. Rev. Genet. 2007, 41:121-145.
27. Lavín J.L., Ramírez L., Ussery D.W., Pisabarro A.G., Oguiza J.A. Genomic analysis of two-component signal transduction proteins in basidiomycetes. J. Mol. Microbiol. Biotechnol. 2010, 18:63-73.
28. Lee J.W., Ko Y.J., Kim S.Y., Bahn Y.S. Multiple roles of Ypd1 phosphotransfer protein in viability, stress response, and virulence factor regulation in Cryptococcus neoformans. Eukaryot. Cell 2011, 10:998-1002.
29. Li D., Agrellos O.A., Calderone R. Histidine kinases keep fungi safe and vigorous. Curr. Opin. Microbiol. 2010, 13:424-430.
30. Loomis W.F., Shaulsky G., Wang N. Histidine kinases in signal transduction pathways of eukaryotes. J. Cell Sci. 1997, 110:1141-1145.
31. Loomis W.F., Kuspa A., Shaulsky G. Two-component signal transduction systems in eukaryotic microorganisms. Curr. Opin. Microbiol. 1998, 1:643-648.
32. Marchler-Bauer A., Anderson J.B., DeWeese-Scott C., Fedorova N.D., Geer L.Y., He S., Hurwitz D.I., Jackson J.D., Jacobs A.R., Lanczycki C.J., Liebert C.A., Liu C., Madej T., Marchler G.H., Mazumder R., Nikolskaya A.N., Panchenko A.R., Rao B.S., Shoemaker B.A., Simonyan V., Song J.S., Thiessen P.A., Vasudevan S., Wang Y., Yamashita R.A., Yin J.J., Bryant S.H. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res. 2003, 31:383-387.
33. Martinez D., Challacombe J., Morgenstern I., Hibbett D., Schmoll M., Kubicek C.P., Ferreira P., Ruiz-Duenas F.J., Martinez A.T., Kersten P., Hammel K.E., Vanden Wymelenberg A., Gaskell J., Lindquist E., Sabat G., Bondurant S.S., Larrondo L.F., Canessa P., Vicuna R., Yadav J., Doddapaneni H., Subramanian V., Pisabarro A.G., Lavín J.L., Oguiza J.A., Master E., Henrissat B., Coutinho P.M., Harris P., Magnuson J.K., Baker S.E., Bruno K., Kenealy W., Hoegger P.J., Kües U., Ramaiya P., Lucas S., Salamov A., Shapiro H., Tu H., Chee C.L., Misra M., Xie G., Teter S., Yaver D., James T., Mokrejs M., Pospisek M., Grigoriev I.V., Brettin T., Rokhsar D., Berka R., Cullen D. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc. Natl. Acad. Sci. USA 2009, 106:1954-1959.
34. Morin E., Kohler A., Baker A.R., Foulogne-Oriol M., Lombard V., Nagy L.G., Ohm R.A., Patyshakuliyeva A., Brun A., Aerts A.L., Bailey A.M., Billette C., Coutinho P.M., Deakin G., Doddapaneni H., Floudas D., Grimwood J., Hildén K., Kües U., LaButti K.M., Lapidus A., Lindquist E.A., Lucas S.M., Murat C., Riley R.W., Salamov A.A., Schmutz J., Subramanian V., Wösten H.A.B., Xu J., Eastwood D.C., Foster G.D., Sonnenberg A.S.M., Cullen D., de Vries R.P., Lundell T., Hibbett D.S., Henrissat B., Burton K.S., Kerrigan R.W., Challen M.P., Grigoriev I.V., Martin F. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc. Natl. Acad. Sci. USA 2012, 109:17501-17506.
35. Motoyama T., Ochiai N., Morita M., Iida Y., Usami R., Kudo T. Involvement of putative response regulator genes of the rice blast fungus Magnaporthe oryzae in osmotic stress response, fungicide action, and pathogenicity. Curr. Genet. 2008, 54:185-195.
36. Ohm R.A., de Jong J.F., Lugones L.G., Aerts A., Kothe E., Stajich J.E., de Vries R.P., Record E., Levasseur A., Baker S.E., Bartholomew K.A., Coutinho P.M., Erdmann S., Fowler T.J., Gathman A.C., Lombard V., Henrissat B., Knabe N., Kües U., Lilly W.W., Lindquist E., Lucas S., Magnuson J.K., Piumi F., Raudaskoski M., Salamov A., Schmutz J., Schwarze F.W., vanKuyk P.A., Horton J.S., Grigoriev I.V., Wösten H.A. Genome sequence of the model mushroom Schizophyllum commune. Nat. Biotechnol. 2010, 28:957-963.
37. Padamsee M., Kumar T.K., Riley R., Binder M., Boyd A., Calvo A.M., Furukawa K., Hesse C., Hohmann S., James T.Y., LaButti K., Lapidus A., Lindquist E., Lucas S., Miller K., Shantappa S., Grigoriev I.V., Hibbett D.S., McLaughlin D.J., Spatafora J.W., Aime M.C. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet. Biol. 2012, 49:217-226.
38. 0. Mol. Cell. 2003, 12:1607-1613.
39. Perraud A.L., Weiss V., Gross R. Signalling pathways in two-component phosphorelay systems. Trends Microbiol. 1999, 7:115-120.
40. Purschwitz J., Müller S., Kastner C., Fischer R. Seeing the rainbow: light sensing in fungi. Curr. Opin. Microbiol. 2006, 9:566-571.
41. Ronning C.M., Fedorova N.D., Bowyer P., Coulson R., Goldman G., Kim H.S., Turner G., Wortman J.R., Yu J., Anderson M.J., Denning D.W., Nierman W.C. Genomics of Aspergillus fumigatus. Rev. Iberoam. Micol. 2005, 22:223-228.
42. Sánchez C. Cultivation of Pleurotus ostreatus and other edible mushrooms. Appl. Microbiol. Biotechnol. 2010, 85:1321-1337.
43. Santos J.L., Shiozaki K. Fungal histidine kinases. Sci. STKE 2001, 4:RE1.
44. Schmoll M. The information highways of a biotechnological workhorse - signal transduction in Hypocrea jecorina. BMC Genomics 2008, 9:430.
45. Stock A.M., Robinson V.L., Goudreau P.N. Two-component signal transduction. Annu. Rev. Biochem. 2000, 69:183-215.
46. Szeto C.Y., Wong Q.W., Leung G.S., Kwan H.S. Isolation and transcript analysis of two-component histidine kinase gene Le.nik1 in Shiitake mushroom, Lentinula edodes. Mycol. Res. 2008, 112:108-116.
47. Thomason P., Kay R. Eukaryotic signal transduction via histidine-aspartate phosphorelay. J. Cell Sci. 2000, 113:3141-3150.
48. van der Heijden R.T., Snel B., van Noort V., Huynen M.A. Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics 2007, 8:83.
49. Vidan S., Mitchell A.P. Stimulation of yeast meiotic gene expression by the glucose-repressible protein kinase Rim15p. Mol. Cell. Biol. 1997, 17:2688-2697.
50. West A.H., Stock A.M. Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem. Sci. 2001, 26:369-376.
51. Wolanin P.M., Thomason P.A., Stock J.B. Histidine protein kinases: key signal transducers outside the animal kingdom. Genome Biol. 2002, 3. REVIEWS3013.
52. Wormley F.L., Heinrich G., Miller J.L., Perfect J.R., Cox G.M. Identification and characterization of an SKN7 homologue in Cryptococcus neoformans. Infect. Immun. 2005, 73:5022-5030.