The yin and yang of yeast: biodiversity research and systems biology as complementary forces driving innovation in biotechnology

Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314:1565–1568 Avery SV (2006) Microbial cell individuality and the underlying sources of heterogeneity. Nat Rev Microbiol 4:577–587 Barnett JA (2000) A history of research on yeasts 2: Louis Pasteur and his contemporaries, 1850–1880. Yeast 16:755–771 Barnett JA (2003) Beginnings of microbiology and biochemistry: the contribution of yeast research. Microbiology 149:557–567 Barnett JA, Lichtenthaler FW (2001) A history of research on yeasts 3: Emil Fischer, Eduard Buchner and their contemporaries, 1880–1900. Yeast 18:363–388 Beggs JD (1978) Transformation of yeast by a replicating hybrid plasmid. Nature 275:104–109 Borneman AR, Forgan AH, Pretorius IS, Chambers PJ (2008) Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res 8:1185–1195 Boundy-Mills K (2010) Yeast culture collections of the world: more than a source of cultures SIM News (in press) Bouton JH (2007) Molecular breeding of switchgrass for use as a biofuel crop. Curr Opin Genet Dev 17:553–558 Bro C, Regenberg B, Förster J, Nielsen J (2006) In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng 8:102–111 Bryan JT (2007) Developing an HPV vaccine to prevent cervical cancer and genital warts. Vaccine 25:3001–3006 Cereghino JL, Cregg JM (2000) Heterologous protein expression in the methylotrophic yeast Pichia pastoris. FEMS Microbiol Rev 24:45–66 De Pourcq K, De Schutter K, Callewaert N (2010) Engineering of glycosylation in yeast and other fungi: current state and perspectives. Appl Microbiol Biotechnol 87:1617–1631 Dimitrov LN, Brem RB, Kruglyak L, Gottschling DE (2009) Polymorphisms in multiple genes contribute to the spontaneous mitochondrial genome instability of Saccharomyces cerevisiae S288C strains. Genetics 183:365–383 Doniger SW, Kim HS, Swain D, Corcuera D, Williams M, Yang SP, Fay JC (2008) A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet 4:e1000183 Dowell RD, Ryan O, Jansen A, Cheung D, Agarwala S, Danford T, Bernstein DA, Rolfe PA, Heisler LE, Chin B, Nislow C, Giaever G, Phillips PC, Fink GR, Gifford DK, Boone C (2010) Genotype to phenotype: a complex problem. Science 328:469 Dujon B (2006) Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet 22:375–387 Dunn B, Sherlock G (2008) Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus. Genome Res 18:1610–1623 EFSA (2009) EFSA delivers its first series of opinions on ‘general function’ health claims http://www.efsa.europa.eu/EFSA/efsa_locale-1178620753812_1211902914361.htm Engel SR, Balakrishnan R, Binkley G et al. (2010) Saccharomyces genome database provides mutant phenotype data. Nucleic Acids Res 38:D433–D436 Foligné B, Dewulf J, Vandekerckove P, Pignède G, Pot B (2010) Probiotic yeasts: anti-inflammatory potential of various non-pathogenic strains in experimental colitis in mice. World J Gastroenterol 16:2134–2145 Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274:563–567 Guadalupe Medina V, Almering MJ, van Maris AJ, Pronk JT (2010) Elimination of glycerol production in anaerobic cultures of a Saccharomyces cerevisiae strain engineered to use acetic acid as an electron acceptor. Appl Environ Microbiol 76:190–195 Herrgård MJ, Swainston N, Dobson P et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26:1155–1160 Hinnen A, Hicks JB, Fink GR (1978) Transformation of yeast. Proc Natl Acad Sci USA 75:1929–1933 Hofmann KJ, Neeper MP, Markus HZ et al (1996) Sequence conservation within the major capsid protein of human papillomavirus (HPV) type 18 and formation of HPV-18 virus-like particles in Saccharomyces cerevisiae. J Gen Virol 77:465–468 Ide S, Miyazaki T, Maki H, Kobayashi T (2010) Abundance of ribosomal RNA gene copies maintains genome integrity. Science 327:693–696 Kim HS, Fay JC (2009) A combined-cross analysis reveals genes with drug-specific and background-dependent effects on drug sensitivity in Saccharomyces cerevisiae. Genetics 183:1141–1151 King RD, Rowland J, Oliver SG, Young M, Aubrey W, Byrne E, Liakata M, Markham M, Pir P, Soldatova LN, Sparkes A, Whelan KE, Clare A (2009) The automation of science. Science 324:85–89 Kobayashi T, Heck DJ, Nomura M, Horiuchi T (1998) Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev 12:3821–3830 Kumar SV, Wigge PA (2010) H2A.Z-containing nucleosomes mediate the thermosensory response in arabidopsis. Cell 140:136–147 Kurtzman CP (2003) Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. FEMS Yeast Res 4:233–245 Kurtzman CP, Fell JW (1998) The Yeasts—a taxonomic study, 4th edn. Elsevier, Amsterdam, p 3 Li P, Anumanthan A, Gao XG, Ilangovan K, Suzara VV, Duezguenes N, Renugopalakrishnan V (2007) Expression of recombinant proteins in Pichia pastoris. Appl Biochem Biotechnol 142:105–124 Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O’Kelly MJT, van Oudenaarden A, Barton DB, Bailes E, Jones M, Durbin R, Louis EJ (2009) Population genomics of domestic and wild yeasts. Nature 458:337–341 Mattanovich D, Graf A, Stadlmann J, Dragosits M, Redl A, Maurer M, Kleinheinz M, Sauer M, Altmann F, Gasser B (2009) Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris. Microb Cell Fact 8:29 McAleer WJ, Buynak EB, Maigetter RZ, Wampler DE, Miller WJ, Hilleman MR (1984) Human hepatitis B vaccine from recombinant yeast. Nature 307:178–180 Mewes HW, Albermann K, Bähr M, Frishman D, Gleissner D, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, Pfeiffer F, Zollner A (1997) Overview of the yeast genome. Nature 387(Suppl):7–65 Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KF, Münsterkötter M, Ruepp A, Spannagl M, Stümpflen V, Rattei T (2008) MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res 36:D196–D201 Neeper MP, Hofmann KJ, Jansen KU (1996) Expression of the major capsid protein of human papillomavirus type 11 in Saccharomyces cerevisae. Gene 180:1–6 Omara W, Rash BM, Hayes A, Wickham MSJ, Oliver SG, Stateva LI (2010) Conditional cell wall mutants of Saccharomyces cerevisiae as delivery vehicles for therapeutic agents in vivo in the GI tract. J Biotechnol 147:136–143 Pscheidt B, Glieder A (2008) Yeast cell factories for fine chemical and API production. Microb Cell Fact 7:25 Qin J, Li R, Raes J, Arumugam M et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65 Ro DK, Paradise EM, Ouellet M et al. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440:940–943 Romanos MA, Hughes FJ, Comerford SA, Scorer CA (1995) Production of a phosphorylated GST:HPV-6 E7 fusion protein using a yeast expression vector and glutathione S-transferase fusions. Gene 152:137–138 Saloheimo A, Rauta J, Stasyk OV, Sibirny AA, Penttilä M, Ruohonen L (2007) Xylose transport studies with xylose-utilizing Saccharomyces cerevisiae strains expressing heterologous and homologous permeases. Appl Microbiol Biotechnol 74:1041–1052 Salusjärvi L, Kankainen M, Soliymani R, Pitkänen J-P, Penttilä M, Ruohonen L (2008) Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae. Microb Cell Fact 7:18 (16 pages) Scanlan PD, Marchesi JR (2008) Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J 2:1183–1193 Scannell DR, Frank AC, Conant GC, Byrne KP, Woolfit M, Wolfe KH (2007) Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc Natl Acad Sci USA 104:8397–8402 Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458:342–345 Scherens B, Goffeau A (2004) The uses of genome-wide yeast mutant collections. Genome Biol 5:229 Scorzetti G, Fell JW, Fonseca A, Statzell-Tallman A (2002) Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Res 2:495–517 Sohn SB, Graf AB, Kim TY, Gasser B, Maurer M, Ferrer P, Mattanovich D, Lee SY (2010) Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production. Biotechnol J 5:705–715 Stambuk BU, Dunn B, Alves SL Jr, Duval EH, Sherlock G (2009) Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis. Genome Res 19:2271–2278 Suh SO, McHugh JV, Pollock DD, Blackwell M (2005) The beetle gut: a hyperdiverse source of novel yeasts. Mycol Res 109:261–265 Suh SO, Blackwell M, Kurtzman CP, Lachance MA (2006) Phylogenetics of Saccharomycetales, the ascomycete yeasts. Mycologia 98:1006–1017 Szczebara FM, Chandelier C, Villeret C et al. (2003) Total biosynthesis of hydrocortisone from a simple carbon source in yeast. Nature Biotechnol 21:143–149 Uruburu F (2003) History and services of culture collections. Int Microbiol 6:101–103 Verho R, Londesborough J, Penttilä M, Richard P (2003) Engineering redox cofactor regeneration for improved pentose fermentation in Saccharomyces cerevisiae. Appl Environ Microbiol 69:5892–5897 Wei W, McCusker JH, Hyman RW et al. (2007) Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci USA 104:12825–12830 Wolf K (1996) Non-conventional yeasts in biotechnology: a handbook. Springer, Berlin Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708–713 Zanello G, Meurens F, Berri M, Salmon H (2009) Saccharomyces boulardii effects on gastrointestinal diseases. Curr Issues Mol Biol 11:47–58 Zhang X, Zhang H, Li X, Su Z, Wang J, Zhang C (2009) Isolation and characterization of Sporobolomyces sp. LF1 capable of degrading chlorimuron-ethyl. J Environ Sci China 21:1253–1260