Phylogenetic diversity of stress signalling pathways in fungi

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Nikolaou, Elissavet ^a   Agrafioti, Ino ^b   Stumpf, Michael ^b   Quinn, Janet ^c   Stansfield, Ian ^a   Brown, Alistair Jp ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CONGO RED; HYDROGEN PEROXIDE; MENADIONE; SODIUM CHLORIDE; SORBITOL; BENZENESULFONIC ACID DERIVATIVE; C.I. FLUORESCENT BRIGHTENING AGENT 28; FUNGAL DNA; FUNGAL PROTEIN;

ARTICLE; ASCOMYCETES; BASIDIOMYCETES; CANDIDA ALBICANS; CELL STRESS; CELL WALL; COMPARATIVE STUDY; CONSERVATION BIOLOGY; CONTROLLED STUDY; ENVIRONMENT; ENVIRONMENTAL STRESS; FUNGUS; GENETIC VARIABILITY; HOST; MAMMAL; MICROSPORIDA; MOLECULAR EVOLUTION; NONHUMAN; OSMOTIC STRESS; OXIDATIVE STRESS; PHYLOGENY; PLANT; SACCHAROMYCES CEREVISIAE; SENSOR; SPECIES; DRUG EFFECT; FUNGAL GENOME; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; OSMOTIC PRESSURE; SIGNAL TRANSDUCTION;

ASCOMYCOTA; BASIDIOMYCOTA; CANDIDA ALBICANS; FUNGI; MAMMALIA; MICROSPORIDIA; SACCHAROMYCES CEREVISIAE;

BENZENESULFONATES; CANDIDA ALBICANS; CELL WALL; CONGO RED; DNA, FUNGAL; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; HYDROGEN PEROXIDE; OSMOTIC PRESSURE; OXIDATIVE STRESS; PHYLOGENY; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SODIUM CHLORIDE; SORBITOL; VITAMIN K 3;

EID: 64249092397     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-44     Document Type: Article

References (155)

1. Novel insights into the osmotic stress response of yeast. WH Mager M Siderius, FEMS Yeast Res 2002 2 251 257 12702273
2. Saccharomyces cerevisiae has distinct adaptive responses to both hydrogen peroxide and menadione. DJ Jamieson, J Bacteriol 1992 174 20 6678 6681 1400218
3. Adaptive response of the yeast Saccharomyces cerevisiae to reactive oxygen species: defenses, damage and death. P Moradas-Ferreira V Costa, Redox Rep 2000 5 5 277 285 11145102
4. Osmotic stress signalling and osmoadaptation in yeasts. S Hohmann, Microbiol Mol Biol Rev 2002 66 2 300 372 12040128
5. Multiple pathways differentially regulate global oxidative stress responses in fission yeast. D Chen CRM Wilkinson S Watt CJ Penkett WM Toone N Jones J Bahler, Mol Biol Cell 2008 19 1 308 317 18003976
6. Cloning and sequencing of a Candida albicans catalase gene and effects of disruption of this gene. DR Wysong L Christin AM Sugar PW Robbins RD Diamond, Infect Immun 1998 66 5 1953 1961 9573075
7. The bZip transcription factor Cap1p is involved in multidrug resistance and oxidative stress response in Candida albicans. AM Alarco M Raymond, J Bacteriol 1999 181 3 700 708 9922230
8. Copper- and zinc-containing superoxide dismutase (Cu/ZnSOD) is required for the protection of Candida albicans against oxidative stresses and the expression of its full virulence. CS Hwang GE Rhie JH Oh WK Huh HS Yim SO Kang, Microbiology 2002 148 Pt 11 3705 3713 12427960
9. The HOG1 mitogen-activated protein kinase is essential in the oxidative stress response and chlamydospore formation in Candida albicans. R Alonso-Monge F Navarro-Garcia E Roman AI Negredo B Eisman C Nombela J Pla, Eukaryotic Cell 2003 2 2 351 361 12684384
10. Superoxide dismutases in Candida albicans: Transcriptional regulation and functional characterization of the hyphal-induced SOD5 gene. M Martchenko AM Alarco D Harcus M Whiteway, Mol Biol Cell 2004 15 2 456 467 14617819
11. Granulocytes govern the transcriptional response, morphology and proliferation of Candida albicans in human blood. C Fradin P De Groot D MacCallum M Schaller F Klis FC Odds B Hube, Mol Microbiol 2005 56 2 397 415 15813733
12. MAP kinase pathways in the yeast Saccharomyces cerevisiae. MC Gustin J Albertyn M Alexander K Davenport, Microbiol Mol Biol Rev 1998 62 4 1264 1300 9841672
13. Yeast HOG1 MAP kinase cascade is regulated by a multistep phosphorelay mechanism in the SLN1-YPD1-SSK1 "two-component" osmosensor. F Posas SM Wurgler-Murphy T Maeda EA Witten TC Thai H Saito, Cell 1996 86 6 865 75 8808622
14. A two-component system that regulates an osmosensing MAP kinase cascade in yeast. T Maeda SM Wurgler-Murphy H Saito, Nature 1994 369 242 245 8183345
15. Control of MAP kinase signalling specificity or how not to go HOG wild. GF Sprague, Genes Dev 1998 12 18 2817 20 9744858
16. Osmotic activation of the HOG MAPK pathway via Ste11p MAPKKK: scaffold role of Pbs2p MAPKK. F Posas H Saito, Science 1997 276 5319 1702 5 9180081
17. Yeast osmosensor Sln1 and plant cytokinin receptor Cre1 respond to changes in turgor pressure. V Reiser DC Raitt H Saito, J Cell Biol 2003 161 6 1035 40 12821642
18. Comparative genomics of the HOG-signalling system in fungi. M Krantz E Becit S Hohmann, Curr Genet 2006 49 3 137 151 16468042
19. Regulation of the transcriptional response to oxidative stress in fungi: Similarities and differences. SW Moye-Rowley, Eukaryot Cell 2003 2 3 381 389 12796283
20. Yeast signalling pathways in the oxidative stress response. A Ikner K Shiozaki, Mutat Res 2005 569 1-2 13 27 15603750
21. Yeast YAP1 encodes a novel form of the jun family of transcriptional activator proteins. WS Moye-Rowley KD Harshman CS Parker, Genes Dev 1989 3 283 292 2542125
22. AP-1 transcription factors in yeast. WM Toone N Jones, Curr Opin Genet Dev 1999 9 1 55 61 10072349
23. Mutated yeast heat shock transcription factor exhibits elevated basal transcriptional activation and confers metal resistance. AK Sewell F Yokoya W Yu T Miyagawa T Murayama DR Winge, J Biol Chem 1995 270 42 25079 25086 7559639
24. Oxidative stress induces heat shock factor phosphorylation and HSF-dependent activation of yeast metallothionein gene transcription. XD Liu DJ Thiele, Genes Dev 1996 10 5 592 603 8598289
25. Cell wall integrity signalling in Saccharomyces cerevisiae. D Levin, Microbiol Mol Biol Rev 2005 69 2 262 291 15944456
26. Characterization of the Wsc1 protein, a putative receptor in the stress response of Saccharomyces cerevisiae. AL Lodder TK Lee R Ballester, Genetics 1999 152 4 1487 1499 10430578
27. Mid2 is a putative sensor for cell integrity signalling in Saccharomyces cerevisiae. M Rajavel B Philip BM Buehrer B Errede DE Levin, Mol Cell Biol 1999 19 6 3969 3976 10330137
28. Growth site localization of Rho1 small GTP-binding protein and its involvement in bud formation in Saccharomyces cerevisiae. W Yamochi K Tanaka H Nonaka A Maeda T Musha Y Takai, J Cell Biol 1994 125 1077 1093 8195291
29. Rom1p and Rom2p are GDP/GTP exchange proteins (GEPs) for the Rho1p small GTP binding protein in Saccharomyces cerevisiae. K Ozaki K Tanaka H Imamura T Hihara T Kameyama H Nonaka H Hirano Y Matsuura Y Takai, EMBO J 1996 15 9 2196 2207 8641285
30. Cell polarity and morphogenesis in budding yeast. K Madden M Snyder, Annu Rev Microbiol 1998 52 687 744 9891811
31. Isolation and characterization of the gene encoding phosphoenolpyruvate carboxykinase from Saccharomyces cerevisiae. MD Valdés-Hevia R de la Guerra C Gancedo, FEBS Lett 1989 258 2 313 316 2689220
32. Mkk1 and Mkk2, which encode Saccharomyces cerevisiae mitogen-activated protein kinase-kinase homologs, function in the pathway mediated by protein kinase C. K Irie M Takase KS Lee DE Levin H Araki K Matsumoto Y Oshima, Mol Cell Biol 1993 13 5 3076 3083 8386320
33. A yeast mitogen-activated protein kinase homolog (Mpk1p) mediates signalling by protein kinase C. KS Lee K Irie Y Watanabe H Araki E Nishida K Matsumoto DE Levin, Mol Cell Biol 1993 13 5 3067 75 8386319
34. A role for the Pkc1p/Mpk1p kinase cascade in the morphogenesis checkpoint. JC Harrison ES Bardes Y Ohya DJ Lew, Nat Cell Biol 2001 3 4 417 20 11283616
35. Distinct regulatory proteins control the graded transcriptional response to increasing H 2 O 2 levels in fission yeast Schizosaccharomyces pombe. J Quinn VJ Findlay K Dawson JB Millar N Jones BA Morgan WM Toone, Mol Biol Cell 2002 13 3 805 816 11907263
36. Msn2/4-like transcription factors play no obvious roles in the stress responses of the fungal pathogen, Candida albicans. S Nicholls M Straffon B Enjalbert A Nantel S Macaskill M Whiteway AJP Brown, Eukaryot Cell 2004 3 1111 1123 15470239
37. Role of the Hog1 stress-activated protein kinase in the global transcriptional response to stress in the fungal pathogen Candida albicans. B Enjalbert DA Smith MJ Cornell I Alam S Nicholls AJP Brown J Quinn, Mol Biol Cell 2006 17 2 1018 1032 16339080
38. A single MAPKKK regulates the Hog1 MAPK pathway in the pathogenic fungus Candida albicans. J Cheetham DA Smith A da Silva Dantas KS Doris MJ Patterson CR Bruce J Quinn, Mol Biol Cell 2007 18 11 4603 4614 17804815
39. Comparative genomics of the environmental stress response in ascomycete fungi. AP Gasch, Yeast 24 11 961 976 17605132
40. DL Hawksworth PM Kirk BC Sutton DN Pegler, Ainsworth and Bisby's Dictionary of the Fungi United Kingdom: CAB International 1995
41. CJ Alexopoulos CW Mims M Blackwell, Introductory Mycology New York: John Wiley and Sons 1996
42. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. M Pellegrini EM Marcotte MJ Thompson D Eisenberg TO Yeates, Proc Natl Acad Sci U S A 1999 96 8 4285 4288 10200254
43. Detecting protein function and protein-protein interactions from genome sequences. EM Marcotte M Pellegrini HL Ng DW Rice TO Yeates D Eisenberg, Science 1999 285 5428 751 753 10427000
44. Gene homology resources on the World Wide Web. A Turchin IS Kohane, Physiol Genomics 2002 11 3 165 177 12464690
45. Do essential genes evolve slowly? LD Hurst NG Smith, Curr Biol 1999 9 14 747 750 10421576
46. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. IK Jordan IB Rogozin YI Wolf EV Koonin, Genome Res 2002 12 6 962 968 12045149
47. A simple dependence between protein evolution rate and the number of protein-protein interactions. HB Fraser DP Wall AE Hirsh, BMC Evol Biol 2003 3 11 12769820
48. The impact of comparative genomics on our understanding of evolution. EV Koonin L Aravind A Kondrashov, Cell 2000 101 6 573 576 10892642
49. A comparative genomics approach to the evolution of eukaryotes and their mitochondria. BF Lang E Seif MW Gray CJ O'Kelly G Burger, J Eukaryot Microbiol 1999 46 4 320 326 10461380
50. Comparative genomics of the eukaryotes. GM Rubin MD Yandell JR Wortman GL Gabor Miklos CR Nelson IK Hariharan ME Fortini PW Li R Apweiler W Fleischmann JM Cherry S Henikoff MP Skupski S Misra M Ashburner E Birney MS Boguski T Brody P Brokstein SE Celniker SA Chervitz D Coates A Cravchik A Gabrielian RF Galle WM Gelbart RA George LS Goldstein F Gong P Guan NL Harris BA Hay RA Hoskins J Li Z Li RO Hynes SJ Jones PM Kuehl B Lemaitre JT Littleton DK Morrison C Mungall PH O'Farrell OK Pickeral C Shue LB Vosshall J Zhang Q Zhao XH Zheng S Lewis, Science 2000 287 5461 2204 2215 10731134
51. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. D Fitzpatrick M Logue J Stajich G Butler, BMC Evol Biol 2006 6 99 17121679
52. Initial molecular characterisation of a novel Rho-type GTPase RhoH in the filamentous ascomycete Ashbya gossypii. A Walther J Wendland, Curr Genet 2005 48 4 247 255 16160833
53. Deletion of the regulatory subunit of protein kinase A in Aspergillus fumigatus alters morphology, sensitivity to oxidative damage and virulence. W Zhao JC Panepinto JR Fortwendel L Fox BG Oliver DS Askew JC Rhodes, Infect Immun 2006 74 8 4865 4874 16861675
54. Comparison of transcriptional responses to osmotic stresses induced by NaCl and sorbitol additions in Saccharomyces cerevisiae using DNA microarray. T Hirasawa K Ashitani K Yoshikawa K Nagahisa C Furusawa Y Katakura H Shimizu S Shioya, J Biosci Bioeng 2006 102 6 568 71 17270724
55. High resistance to oxidative stress in the fungal pathogen Candida glabrata is mediated by a single catalase, Cta1p, and is controlled by the transcription factors Yap1p, Skn7p, Msn2p, and Msn4p. M Cuellar-Cruz M Briones-Martin-del-Campo I Canas-Villamar J Montalvo-Arredondo L Riego-Ruiz I Castano A De las Penas, Eukaryot Cell 2008 7 5 814 25 18375620
56. Genomic expression programs in the response of yeast cells to environmental changes. AP Gasch PT Spellman CM Kao O Carmel-Harel MB Eisen G Storz D Botstein PO Brown, Mol Biol Cell 2000 11 12 4241 4257 11102521
57. Characterization and gene cloning of 1,3-beta-D-glucan synthase from Saccharomyces cerevisiae. SB Inoue N Takewaki T Takasuka T Mio M Adachi Y Fujii C Miyamoto M Arisawa Y Furuichi T Watanabe, Eur J Biochem 1995 231 3 845 54 7649185
58. Dynamics of cell wall structure in Saccharomyces cerevisiae. FM Klis P Mol K Hellingwerf B Stanley, FEMS Microbiol Rev 2002 26 3 239 256 12165426
59. Salt tolerance in plants and microorganisms: toxicity targets and defense responses. R Serrano, Int Rev Cytol 1996 165 1 52 8900956
60. Studies on marine occurring yeasts: Growth related to pH, NaCl concentration and temperature. B Norkrans, Arch Microbiol 1966 54 4 374 392
61. Osmophilic yeasts. H Onishi, Adv Food Res 1963 12 53 94 14280864
62. On the mechanism of salt tolerance. Production of glycerol and heat during growth of Debaryomyces hansenii. L Gustafsson B Norkans, Arch Microbiol 1976 110 2-3 177 183 1015945
63. The accumulation of polyols by the yeast Debaryomyces hansenii in response to water stress. MF Nobre MS da Costa, Canadian J Microbiol 1985 31 11 1061 1064
64. Regulation of the potassium to sodium ratio and of the osmotic potential in relation to salt tolerance in yeasts. B Norkrans A Kylin, J Bacteriol 1969 100 2 836 845 5354950
65. Effects of four oxidants, menadione, 1-chloro-2, 4-dinitrobenzene, hydrogen peroxide and cumene hydroperoxide, on fission yeast Schizosaccharomyces pombe. N Mutoh M Kawabata S Kitajima, J Biochem 2005 138 6 797 804 16428309
66. Oxidative stress responses of the yeast Saccharomyces cerevisiae. DJ Jamieson, Yeast 1998 14 16 1511 1527 9885153
67. Hydrogen peroxide sensing and signalling. E Veal A Day B Morgan, Mol Cell 2007 26 1 1 14 17434122
68. Oxidative stress and living cells. G Gille K Sigler, Folia Microbiol (Praha) 1995 40 2 131 152 8851559
69. Calcofluor white alters the assembly of chitin fibrils in Saccharomyces cerevisiae and Candida albicans cells. MV Elorza H Rico R Sentandreu, J Gen Microbiol 1983 129 Pt 5 1577 82 6352860
70. Calcofluor white inhibits Neurospora chitin synthetase activity [bleaching agent for fabrics]. CP Selitrennikoff, Plant Physiol Bioch 1984 8 3 269 272
71. Effect of Calcofluor white and Congo red on fungal cell wall morphogenesis: in vivo activation of chitin polymerization. C Roncero A Duran, J Bacteriol 1985 163 3 1180 1185 3897187
72. Isolation and characterization of Saccharomyces cerevisiae mutants resistant to Calcofluor white. C Roncero MH Valdivieso JC Ribas A Duran, J Bacteriol 1988 170 4 1950 1954 3280554
73. The dependence of the conformation of a (1 3) - D-glucan on chain-length in alkaline solution. K Ogawa J Tsurugi T Watanabe, Carbohydr Res 1973 29 397 403
74. Circular dichroism of the complex of a (1-3)-bD-glucan with Congo Red. K Ogawa M Hatano, Carbohydr Res 1978 67 527 535
75. The influence of Congo red on the cell wall and (1 3) - d-glucan microfibril biogenesis in Saccharomyces cerevisiae. M Kopecka M Gabriel, Arch Microbiol 1992 158 2 115 126 1417414
76. A novel endoplasmic reticulum membrane protein Rcr1 regulates chitin deposition in the cell wall of Saccharomyces cerevisiae. K Imai Y Noda H Adachi K Yoda, J Biol Chem 2005 280 9 8275 8284 15590673
77. A new approach for isolating cell wall mutants in Saccharomyces cerevisiae by screening for hypersensitivity to calcofluor white. AFJ Ram A Wolters RT Hoopen FM Klis, Yeast 1994 10 8 1019 1030 7992502
78. Identification of two cell cycle regulated genes affecting the 1, 3-glucan content of cell walls in Saccharomyces cerevisiae. AFJ Ram SSC Brekelmans LJWM Oehlen FM Klis, FEBS Lett 1995 358 2 165 170 7828729
79. The structure of a P-(1-*3)-D-glucan from yeast cell walls. DJ Manners AJ Masson JC Patterson, Biochem J 1973 135 19 30 4359920
80. Cell walls. GH Fleet, The Yeasts New York: Academic Press, Rose AH, Harrison JS, 1991 199 277
81. Isolation of chitin synthetase from Saccharomyces cerevisiae. Purification of an enzyme by entrapment in the reaction product. MS Kang N Elango E Mattia J Au-Young PW Robbins E Cabib, J Biol Chem 1984 259 23 14966 14972 6238967
82. Characterization of Aspergillus nidulans mutants deficient in cell wall chitin or glucan. PT Borgia CL Dodge, J Bacteriol 1992 174 2 377 83 1729232
83. The wall structure of Schizosaccharomyces pombe. DA Bush M Horisberger I Horman P Wursch, J Gen Microbiol 1974 81 199 206 4822119
84. Localization of -galactomannan and of wheat germ agglutinin receptors in Schizosaccharomyces pombe. M Horisberger M Vonlanthen J Rosset, Arch Microbiol 1978 119 2 107 111 727851
85. The S. cerevisiae structural gene for chitin synthase is not required for chitin synthesis in vivo. CE Bulawa M Slater E Cabib J Au-Young A Sburlati WLJr Adair PW Robbins, Cell 1986 46 2 213 25 2941152
86. The occurrence of glucosaminoglycan in the wall of Schizosaccharomyces pombe. JH Sietsma JG Wessels, J Gen Microbiol 1990 136 2261 5 2079623
87. Cell Wall Chemistry, Morphogenesis, and Taxonomy of Fungi. S Bartnicki-Garcia, Ann Rev Microbiol 1968 22 87 108
88. J Ruiz-Herrera, Fungal cell wall: Structure, synthesis and assembly USA: CRC Press 1992
89. Cell wall perturbation in yeast results in dual phosphorylation of the Slt2/Mpk1 MAP kinase and in an Slt2-mediated increase in FKS2-lacZ expression, glucanase resistance and thermotolerance. H De Nobel C Ruiz H Martin W Morris S Brul M Molina FM Klis, Microbiology 2000 146 2121 2132 10974100
90. The chsD and chsE genes of Aspergillus nidulans and their roles in chitin synthesis. CA Specht Y Liu PW Robbins CE Bulawa N Iartchouk KR Winter PJ Riggle JC Rhodes CL Dodge DW Culp PT Borgia, Fungal Genet Biol 1996 20 153 167 8810520
91. Interactions of fungi with phagocytes. MK Mansour SM Levitz, Curr Opin Microbiol 2002 5 4 359 365 12160853
92. Role of antioxidant enzymatic defences against oxidative stress (H 2 O 2 ) and the acquisition of oxidative tolerance in Candida albicans. P Gonzalez-Parraga JA Hernandez JC Arguelles, Yeast 2003 20 14 1161 1169 14587100
93. Cells have distinct mechanisms to maintain protection against different reactive oxygen species: Oxidative-stress-response genes. GW Thorpe CS Fong N AliC VJ Higgins IW Dawes, PNAS 2004 101 17 6564 6569 15087496
94. Phagocytosis by neutrophils induces an amino acid deprivation response in Saccharomyces cerevisiae and Candida albicans. I Rubin-Bejerano I Fraser P Grisafi GR Fink, Proc Natl Acad Sci USA 2003 100 19 11007 11012 12958213
95. Transcriptional response of Candida albicans upon internalization by macrophages. MC Lorenz JA Bender GR Fink, Eukaryot Cell 2004 3 5 1076 1087 15470236
96. Niche-specific activation of the oxidative stress responses by the pathogenic fungus Candida albicans. B Enjalbert DM MacCallum FC Odds AJP Brown, Infect Immun 2007 75 5 2143 2151 17339352
97. Stress Responses in Candida albicans. J Quinn AJP Brown, Candida: comparative and functional genomics UK: Caister Academic Press, d'Enfert C, Hube B, 2007 217 261
98. Analysis of the adaptive oxidative stress response of Candida albicans. DJ Jamieson DW Stephen EC Terriere, FEMS Microbiol Lett 1996 138 1 83 88 8674975
99. Saccharomyces cerevisiae expresses three phospholipid hydroperoxide glutathione peroxidases. AM Avery SV Avery, J Biol Chem 2001 276 36 33730 33735 11445588
100. Candida albicans response regulator gene SSK1 regulates a subset of genes whose functions are associated with cell wall biosynthesis and adaptation to oxidative stress. N Chauhan D Inglis E Roman J Pla D Li JA Calera R Calderone, Eukaryot Cell 2003 2 5 1018 1024 14555484
101. "Sleeping beauty": Quiescence in Saccharomyces cerevisiae. JV Gray GA Petsko GC Johnston D Ringe RA Singer M Werner-Washburne, Microbiol Mol Biol Rev 2004 68 2 187 206 15187181
102. A yeast by any other name: Candida glabrata and its interaction with the host. R Kaur R Domergue ML Zupancic BP Cormack, Curr Opin Microbiol 2005 8 4 378 384 15996895
103. Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae. JM Thevelein JH de Winde, Mol Microbiol 1999 33 5 904 918 10476026
104. A conserved stress-activated protein kinase regulates a core stress response in the human pathogen Candida albicans. DA Smith S Nicholls BA Morgan AJP Brown J Quinn, Mol Biol Cell 2004 15 9 4179 4190 15229284
105. Molecular evidence for an ancient duplication of the entire yeast genome. KH Wolfe DC Shields, Nature 1997 387 6634 708 713 9192896
106. A genomic perspective on protein families. RL Tatusov EV Koonin DJ Lipman, Science 1997 278 5338 631 637 9381173
107. The COG database: a tool for genome-scale analysis of protein functions and evolution. RL Tatusov MY Galperin DA Natale EV Koonin, Nucleic Acids Res 2000 28 1 33 36 10592175
108. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. M Remm CEV Storm ELL Sonnhammer, J Mol Biol 2001 314 5 1041 1052 11743721
109. Inparanoid: a comprehensive database of eukaryotic orthologs. KP O'Brien M Remm ELL Sonnhammer, Nucleic Acids Res 2005 33 Database D476 D480 15608241
110. Database resources of the National Center for Biotechnology Information. DL Wheeler T Barrett DA Benson SH Bryant K Canese DM Church M DiCuccio R Edgar S Federhen W Helmberg DL Kenton O Khovayko DJ Lipman TL Madden DR Maglott J Ostell JU Pontius KD Pruitt GD Schuler LM Schriml E Sequeira ST Sherry K Sirotkin G Starchenko TO Suzek R Tatusov TA Tatusova L Wagner E Yaschenko, Nucleic Acids Res 2005 33 Database D39 D45 15608222
111. F Sherman GR Fink JB Hicks, Methods in yeast genetics New York: Cold Spring Harbor Laboratory Press 1987
112. Getting started with yeast. F Sherman, Methods Enzymol 1991 194 3 21 2005794
113. The fungi of stigmatomycosis. SF Ashby W Nowell, Annual Botany 1926 40 69 84
114. AgTHR4, a new selection marker for the transformation of the filamentous fungus Ashbya gossypii, maps in a four-gene cluster that is conserved between A. gossypii and Saccharomyces cerevisiae. R Altmann-Johl P Philippsen, Mol Gen Genet 1996 250 1 69 80 8569689
115. The zrfA and zrfB genes of Aspergillus fumigatus encode the zinc transporter proteins of a zinc uptake system induced in an acid, inc-depleted environment. R Vicentefranqueira MA Moreno F Leal JA Calera, Eukaryot Cell 2005 4 5 837 848 15879518
116. Meiotic and mitotic recombination in Aspergillus, and its chromosomal aberrations. E Kafer, Adv Genet 1977 19 33 131 327767
117. Functional characterization of Aspergillus nidulans homologues of Saccharomyces cerevisiae Spa2 and Bud6. A Virag SD Harris, Eukaryot Cell 2006 5 6 881 895 16757736
118. Untersuchungen über die morphologische und biologische Differenzierung in der Fusarium -Sektion Liseola. HI Nirenberg, Mitt Biol Bundesanst 1976 169 1 117
119. Arabidopsis is susceptible to the cereal ear blight fungal pathogens Fusarium graminearum and Fusarium culmorum. M Urban S Daniels E Mott K Hammond-Kosack, Plant 2002 32 6 961 973
120. Identification and Characterization of MPG1, a gene involved in pathogenicity from the rice blast fungus Magnaporthe grisea. NJ Talbot DJ Ebbole JE Hamer, Plant Cell 1993 5 11 1575 1590 8312740
121. Vogel, A convenient medium for Neurospora (medium N). HJ Vogel, Microb Genet Bull 1956 13 42 43
122. Lipofectin increases transformation of Neurospora crassa. C Selitrennikoff MS Sachs, Fungal Genet Newsl 1991 38 90 91
123. Isolation of Ashbya gossypii mutant for an improved riboflavin production targeting for biorefinery technology. EY Park JH Zhang S Tajima L Dwiarti, J Appl Microbiol 2007 103 2 468 476 17650208
124. Genetic, biochemical and molecular techniques. RH Davis, Neurospora: contributions of a model organism USA: Oxford University Press, Davis RH, 2000 293
125. Aspergillus nidulans is frequently resistant to amphotericin B. DP Kontoyiannis RE Lewis GS May N Osherov MG Rinaldi, Mycoses 2002 45 9-10 406 407 12421291
126. How to convert wild-type spreading growth to colonial. DD Perkins, 2006 http://www.fgsc.net/Neurospora/NeurosporaProtocolGuide.htm
127. Isolation and sequence of the gene actin in Saccharomyces cerevisiae. R Ng J Abelson, Proc Natl Acad Sci USA 1980 77 7 3912 3916 7001447
128. Isolation and characterization of the yeast 3-phosphoglycerokinase gene (PGK) by an immunological screening technique. RA Hitzeman L Clarke J Carbon, J Biol Chem 1980 255 24 12073 12080 6254992
129. Identification of the two genes coding for the translation elongation factor EF-1a of S. cerevisiae. F Schirmaier P Philippsen, EMBO 1984 3 3311 3315
130. Cell cycle control in Saccharomyces cerevisiae. DJ Lew T Weinert JR Pringle, The molecular and cellular biology of the yeast Saccharomyces: Cell cycle and cell biology New York: Cold Spring Harbor Laboratory Press, Pringle JR, Broach JR, Jones EW, 1997 607 695
131. DNA sequence and characterization of the S. cerevisiae gene encoding adenylate cyclase. T Kataoka D Broek M Wigler, Cell 1985 43 2Pt1 493 505 2934138
132. Isolation of the gene encoding adenylate cyclase in Saccharomyces cerevisiae. GF Casperson N Walker HR Bourne, Proc Natl Acad Sci USA 1985 82 15 5060 3 2991907
133. Positive regulation in the general amino acid control of Saccharomyces cerevisiae. AG Hinnebusch GR Fink, Proc Natl Acad Sci USA 1983 80 5374 5378 6351059
134. Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. LL Lutfiyya VR Iyer J DeRisi J DeVit P O'Brown M Johnston, Genetics 1998 150 1377 1391 9832517
135. FAP1, a homologue of human transcription factor NF-X1, competes with rapamycin for binding to FKBP12 in yeast. J Kunz A Loeschmann M Deuter-Reinhard MN Hall, Mol Microbiol 2000 37 6 1480 93 10998178
136. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 9254694
137. MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. S Kumar K Tamura M Nei, Brief Bioinform 2004 5 2 150 163 15260895
138. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 22 4673 4680 7984417
139. The neighbor-joining method: a new method for constructing phylogenetic trees. N Saitou M Nei, Mol Biol Evol 1987 4 406 425 3447015
140. TREEVIEW: An application to display phylogenetic trees on personal computers. RDM Page, Comput Appl Biosci 1996 12 4 357 358 8902363
141. Protein dispensability and rate of evolution. AE Hirsh HB Fraser, Nature 2001 411 6841 1046 1049 11429604
142. Detecting putative orthologues. DP Wall HB Fraser AE Hirsh, Bioinformatics 2003 19 1710 1711 15593400
143. Functional genomic analysis of the rates of protein evolution. DP Wall AE Hirsh HB Fraser J Kumm G Giaever MB Eisen MW Feldman, PNAS 2005 102 15 5483 5488 15800036
144. Assessment of phylogenomic and orthology approaches for phylogenetic inference. BE Dutilh V van Noort RTJM van der Heijden T Boekhout B Snel MA Huynen, Bioinformatics 2007 23 7 815 824 17237036
145. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. FS Dietrich S Voegeli S Brachat A Lerch K Gates S Steiner C Mohr R Pöhlmann P Luedi S Choi RA Wing A Flavier TD Gaffney P Philippsen, Science 2004 304 5668 304 307 15001715
146. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. WC Nierman A Pain MJ Anderson JR Wortman HS Kim J Arroyo M Berriman K Abe DB Archer C Bermejo J Bennett P Bowyer D Chen M Collins R Coulsen R Davies PS Dyer M Farman N Fedorova N Fedorova TV Feldblyum R Fischer N Fosker A Fraser JL García MJ García A Goble GH Goldman K Gomi S Griffith-Jones R Gwilliam B Haas H Haas D Harris H Horiuchi J Huang S Humphray J Jiménez N Keller H Khouri K Kitamoto T Kobayashi S Konzack R Kulkarni T Kumagai A Lafon JP Latgé W Li A Lord C Lu WH Majoros GS May BL Miller Y Mohamoud M Molina M Monod I Mouyna S Mulligan L Murphy S O'Neil I Paulsen MA Pẽalva M Pertea C Price BL Pritchard MA Quail E Rabbinowitsch N Rawlins MA Rajandream U Reichard H Renauld GD Robson S Rodriguez de Crdoba JM Rodríguez-Pẽa CM Ronning S Rutter SL Salzberg M Sanchez JC Sánchez-Ferrero D Saunders K Seeger R Squares S Squares M Takeuchi F Tekaia G Turner CR Vazquez de Aldana J Weidman O White J Woodward JH Yu C Fraser JE Galagan K Asai M Machida N Hall B Barrell DW Denning, Nature 2005 438 1151 1156 16372009
147. Sequencing of Aspergillus nidulans and comparative analysis with the A. fumigatus and A. oryzae. JE Galagan SE Calvo C Cuomo LJ Ma JR Wortman S Batzoglou SI Lee M Batürkmen CC Spevak J Clutterbuck V Kapitonov J Jurka C Scazzocchio M Farman J Butler S Purcell S Harris GH Braus O Draht S Busch C D'Enfert C Bouchier GH Goldman D Bell-Pedersen S Griffiths-Jones JH Doonan J Yu K Vienken A Pain M Freitag EU Selker DB Archer MA Pẽalva BR Oakley M Momany T Tanaka T Kumagai K Asai M Machida WC Nierman DW Denning M Caddick M Hynes M Paoletti R Fischer B Miller P Dyer MS Sachs SA Osmani BW Birren, Nature 2005 438 7071 1105 1115 16372000
148. The diploid genome sequence of Candida albicans. T Jones NA Federspiel H Chibana J Dungan S Kalman BB Magee G Newport YR Thorstenson N Agabian PT Magee RW Davis S Scherer, Proc Natl Acad Sci USA 2004 101 19 7329 7334 15123810
149. Genome evolution in yeasts. B Dujon D Sherman G Fischer P Durrens S Casaregola I Lafontaine J de Montigny C Marck C Neuveglise E Talla N Goffard L Frangeul M Aigle V Anthouard A Babour V Barbe S Barnay S Blanchin JM Beckerich B Beyne C Bleykasten A Boisrame J Boyer L Cattolico F Confanioleri A de Daruvar L Despons E Fabre C Fairhead H Ferry-Dumazet A Groppi F Hantraye C Hennequin N Jauniaux P Joyet R Kachouri A Kerrest R Koszul M Lemaire I Lesur L Ma H Muller JM Nicaud M Nikolski S Oztas O Ozier-Kalogeropoulos S Pellenz S Potier GF Richard ML Straub A Suleau D Swennen F Tekaia M We'solowski-Louvel E Westhofl B Wirth M Zeniou-Meyer I Zivanovic M Bolotin-Fukuhara A Thierry C Bouchier B Caudron C Scarpelli C Gaillardin J Weissenbach P Wincker JL Souciet, Nature 2004 430 35 44 15229592
150. The Genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. BJ Loftus E Fung P Roncaglia D Rowley P Amedeo D Bruno J Vamathevan M Miranda IJ Anderson JA Fraser JE Allen IE Bosdet MR Brent R Chiu TL Doering MJ Donlin CA D'Souza DS Fox V Grinberg J Fu M Fukushima BJ Haas JC Huang G Janbon SJM Jones HL Koo MI Krzywinski JK Kwon-Chung KB Lengeler R Maiti MA Marra RE Marra CE MathewsoN TG Mitchell M Pertea FR Riggs SL Salzberg JE Schein A Shvartsbeyn H Shin M Shumway CA Specht BB Suh A Tenney TR Utterback BL Wickes JR Wortman NH Wye JW Kronstad JK Lodge J Heitman RW Davis CM Fraser RW Hyman, Science 2005 307 5713 1321 1324 15653466
151. Genome sequence and gene compaction of the eukaryotic parasite Encephalitozoon cuniculi. MD Katinka S Duprat E Cornillot G Mété nier F Thomarat G Prensier V Barbe E Peyretaillade P Brottier P Wincker F Delbac H El Alaoui P Peyret W Saurin M Gouy J Weissenbach CP Vivarès, Nature 2001 414 6862 450 453 11719806
152. The genome sequence of the rice blast fungus Magnaporthe grisea. RA Dean NJ Talbot DJ Ebbole ML Farman TK Mitchell MJ Orbach M Thon R Kulkarni JR Xu H Pan ND Read YH Lee I Carbone D Brown YY Oh N Donofrio JS Jeong DM Soanes S Djonovic E Kolomiets C Rehmeyer W Li M Harding S Kim MH Lebrun H Bohnert S Coughlan J Butler S Calvo LJ Ma R Nicol S Purcell C Nusbaum JE Galagan BW Birren, Nature 2005 434 7036 980 986 15846337
153. The genome sequence of the filamentous fungus Neurospora crassa. JE Galagan SE Calvo KA Borkovich EU Selker ND Read D Jaffe W FitzHugh L Ma S Smirnov S Purcell B Rehman T Elkins R Engels S Wang CB Nielsen J Butler M Endrizzi D Qui P Ianakiev D Bell-Pedersen MA Nelson M Werner-Washburne CP
154. Life with 6000 genes. A Goffeau BG Barrell H Bussey RW Davis B Dujon H Feldmann F Galibert JD Hoheisel C Jacq M Johnston EJ Louis HW Mewes Y Murakami P Philippsen H Tettelin SG Oliver, Science 1996 274 5287 546 567 8849441
155. The genome sequence of Schizosaccharomyces pombe. V Wood R Gwilliam MA Rajandream M Lyne R Lyne A Stewart J Sgouros N Peat J Hayles S Baker D Basham S Bowman K Brooks D Brown S Brown T Chillingworth C Churcher M Collins R Connor A Cronin P Davis T Feltwell A Fraser S Gentles A Goble N Hamlin D Harris J Hidalgo G Hodgson S Holroyd T Hornsby S Howarth EJ Huckle S Hunt K Jagels K James L Jones M Jones S Leather S McDonald J McLean P Mooney S Moule K Mungall L Murphy D Niblett C Odell K Oliver S O'Neil D Pearson MA Quail E Rabbinowitsch K Rutherford S Rutter D Saunders K Seeger S Sharp J Skelton M Simmonds R Squares S Squares K Stevens K Taylor RG Taylor A Tivey S Walsh T Warren S Whitehead J Woodward G Volckaert R Aert J Robben B Grymonprez I Weltjens E Vanstreels M Rieger M Schaefre S Mueller-Auer S Gabel M Fuchs C Fritzc E Holzer D Moestl H Hilbert K Borzym I Langer A Beck H Lehrach R Reinhardt TM Pohl P Eger W Zimmermann H Wedler R Wambutt B Purnelle A Goffeau E Cadieu S Dreano S Gloux V Lelaure S Mottier F Galibert SJ Aves Z Xiang C Hunt K Moore SM Hurst M Lucas M Rochet C Gaillardin VA Tallada A Garzon G Thode RR Daga L Cruzado J Jimenez M Sanchez F del Rey J Benito A Domnguez JL Revuelta S Moreno J Armstrong SL Forsburg L Cerrutti T Lowe WR McCombie I Paulsen J Potashkin GV Shpakovski D Ussery BG Barrell P Nurse, Nature 2002 415 6874 871 880 11859360