Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1

Molecular Genetics and Genomics

Volumn 287, Issue 6, 2012, Pages 485-494

  Babrzadeh, Farbod ^a   Jalili, Roxana ^a   Wang, Chunlin ^a   Shokralla, Shadi ^a   Pierce, Sarah ^a   Robinson Mosher, Avi ^a   Nyren, Pål ^b   Shafer, Robert W ^a   Basso, Luiz C ^c   De Amorim, Henrique V ^d   De Oliveira, Antonio J ^d   Davis, Ronald W ^a   Ronaghi, Mostafa ^a   Gharizadeh, Baback ^a   Stambuk, Boris U ^e  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

^d FERMENTEC LTDA   (Brazil)

^e FEDERAL UNIVERSITY OF SANTA CATARINA   (Brazil)

Author keywords

Bioethanol; Genome; Industrial strains; Saccharomyces; Sugarcane

Indexed keywords

BIOETHANOL; BIOFUEL; UNCLASSIFIED DRUG; ALCOHOL;

ALLELE; ARTICLE; BIOFUEL PRODUCTION; DIPLOIDY; FERMENTATION; FUNGAL GENOME; FUNGAL STRAIN; GENE DELETION; GENE DUPLICATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC TRAIT; GENETIC VARIABILITY; HETEROZYGOSITY LOSS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SINGLE NUCLEOTIDE POLYMORPHISM; SUGARCANE; TELOMERE; TRANSPOSON; BIOTECHNOLOGY; CLASSIFICATION; DNA SEQUENCE; GENE DOSAGE; GENETICS; METABOLISM; SPECIES DIFFERENCE;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

BIOFUELS; BIOTECHNOLOGY; DIPLOIDY; ETHANOL; FERMENTATION; GENE DOSAGE; GENOME, FUNGAL; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 84864319268     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-012-0695-7     Document Type: Article

References (67)

1. Akache B, Turcotte B (2002) New regulators of drug sensitivity in the familyof yeast zinc cluster proteins. J Biol Chem 277:21254-21260
2. Akao T, Yashiro I, Hosoyama A, Kitagaki H, Horikawa H, Watanabe D, Akada R, Ando Y et al (2011) Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7. DNA Res 18:423-434
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
4. Alves-Jr SL, Herberts RA, Hollatz C, Trichez D, Miletti LC, de Araujo PS, Stambuk BU (2008) Molecular analysis of maltotriose active transport and fermentation by Saccharomyces cerevisiae reveals a determinant role for the AGT1 permease. Appl Environ Microbiol 74:1494-1501
5. Amorim-Neto HB, Yohannan BK, Bringhurst TA, Brosnan JM, Pearson SY, Walker JM, Walker GM (2009) Evaluation of a Brazilian fuel alcohol yeast strain for Scotch Whisky fermentations. J Inst Brew 115:198-207
6. Andrietta MGS, Andrietta SR, Steckelberg C, Stupiello ENA (2007) Bioethanol-Brazil, 30 years of Proálcool. Int SugarJ 109:195-200
7. Araya CL, Payen C, Dunham MJ, Fields S (2010) Whole-genome sequencing of a laboratory-evolved yeast strain. BMC Genomics 11:88
8. Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, Missawa SK, Galzerani F et al (2009) Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res 19:2258-2270
9. Basso LC, de Amorim HV, de Oliveira AJ, Lopes ML (2008) Yeast selection for fuel ethanol production in Brazil. FEMS Yeast Res 8:1155-1163
10. Basso TO, de Kok S, Dario M, do Espirito-Santo JC, Müller G, Schlölg PS, Silva CP et al (2011) Engineering topology and kinetics of sucrose metabolism in Saccharomyces cerevisiae for improved ethanol yield. Metab Eng 13:694-703
11. Benitez T, Gasent-Ramirez JM, Castrejon F, Codon AC (1996) Development of new strains for the food industry. Biotechnol Prog 12:149-163
12. Bobrowicz P, Wysocki R, Owsianik G, Goffeau A, Ulaszewski S (1997) Isolation of three contiguous genes, ACR1, ACR2 and ACR3, involved in resistance to arsenic compounds in the yeast Saccharomyces cerevisiae. Yeast 13:819-828
13. Borneman AR, Forgan AH, Pretorius IS, Chambers PJ (2008) Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res 8:1185-1195
14. Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, Pretorius IS, Egholm M, Chambers PJ (2011) Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet 7:e1001287
15. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296:752-755
16. Broach JR (1991) Ras-regulated signaling processes in Saccharomyces cerevisiae. Curr Opin Genet Dev 1:370-377
17. Codon AC, Benitez T, Korhola M (1998) Chromosomal polymorphism and adaptation to specific industrial environments of Saccharomyces strains. Appl Microbiol Biotechnol 49:154-163
18. Dowell RD, Ryan O, Jansen A, Cheung D, Agarwala S, Danford T, Bernstein DA, Rolfe PA et al (2010) Genotype to phenotype: a complex problem. Science 328:469
19. Dunn B, Richter C, Kvitek DJ, Pugh T, Sherlock G (2012) Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res. doi:10.1101/gr.130310.111
20. Duval EH, Alves-Jr SL, Dunn B, Sherlock G, Stambuk BU (2010) Microarray karyotyping of maltose-fermenting Saccharomyces yeasts with differing maltotriose utilization profiles reveals copy number variation in genes involved in maltose and maltotriose utilization. J Appl Microbiol 109:248-259
21. Esberg A, Muller LA, McCusker JH (2011) Genomic structure of and genome-wide recombination in the Saccharomyces cerevisiae S288C progenitor isolate EM93. PLoS ONE 6:e25211
22. Farrell AE, Plevin RJ, Turner BT, Jones AD, O'Hare M, Kammen DM (2006) Ethanol can contribute to energy and environmental goals. Science 311:506-508
23. Felsenstein J (1989) Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166
24. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M et al (1996) Life with 6000 genes. Science 274:546-563
25. Goldemberg J (2007) Ethanol for a sustainable energy future. Science 315:808-810
26. Goldemberg J, Guardabassi P (2010) The potential for first-generation ethanol production from sugarcane. Biofuels Bioprod Bioref 4:17-24
27. Hardison RC (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 16:369-372
28. Hardison RC (2003) Comparative genomics. PLoS Biol 1:e58
29. Huang X, Zhang J (1996) Methods for comparing a DNA sequence with a protein sequence. Comput Appl Biosci 12:497-506
30. Ide S, Watanabe K, Watanabe H, Shirahige K, Kobayashi T, Maki H (2007) Abnormality in initiation program of DNA replication is monitored by the highly repetitive rRNA gene array on chromosome XII in budding yeast. Mol Cell Biol 27:568-578
31. Ide S, Miyazaki T, Maki H, Kobayashi T (2010) Abundance of ribosomal RNA gene copies maintains genome integrity. Science 327:693-696
32. Isnard AD, Thomas D, Surdin-Kerjan Y (1996) The study of methionine uptake in Saccharomyces cerevisiae reveals a new family of amino acid permeases. J Mol Biol 262:473-484
33. Jacquot C, Julien R, Guilloton M (1997) The Saccharomyces cerevisiae MFS superfamily SGE1 gene confers resistance to cationic dyes. Yeast 13:891-902
34. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254
35. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12
36. Larroy C, Pares X, Biosca JA (2002) Characterization of a Saccharomyces cerevisiae NADP (H)-dependent alcohol dehydrogenase (ADHVII), a member of the cinnamyl alcohol dehydrogenase family. Eur J Biochem 269:5738-5745
37. Leal MRLV, Walter AD (2010) Sustainability of the production of ethanol from sugarcane: the Brazilian experience. Int Sugar J 112:390-396
38. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G et al (2007) The diploid genome sequence of an individual human. PLoS Biol 5:e254
39. Li Y, Carroll DS, Gardner SN, Walsh MC, Vitalis EA, Damon IK (2007) On the origin of smallpox: correlating variola phylogenics with historical smallpox records. Proc Natl Acad Sci USA 104:15787-15792
40. Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V et al (2009) Population genomics of domestic and wild yeasts. Nature 458:337-341
41. Litvin O, Causton HC, Chen BJ, Pe'er D (2009) Modularity and interactions in the genetics of gene expression. Proc Natl Acad Sci USA 106:6441-6446
42. Liu H, Styles CA, Fink GR (1996) Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. Genetics 144:967-978
43. Madsen KM, Udatha GD, Semba S, Otero JM, Koetter P, Nielsen J, Ebizuka Y, Kushiro T, Panagiotou G (2011) Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyperproducers. PLoS ONE 6:e14763
44. Magwene PM, Kayikçi Ö, Granek JA, Reininga JM, Scholl Z, Murray D (2011) Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 108:1987-1992
45. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380
46. Ness F, Aigle M (1995) RTM 1: a member of a new family of telomeric repeated genes in yeast. Genetics 140:945-956
47. Novo M, Bigey F, Beyne E, Galeote V, Gavory F, Mallet S, Cambon B, Legras JL, Wincker P, Casaregola S, Dequin S (2009) Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci USA 106:16333-16338
48. Ogihara F, Kitagaki H, Wang Q, Shimoi H (2008) Common industrial sake yeast strains have three copies of the AQY1-ARR3 region of chromosome XVI in their genomes. Yeast 25:419-432
49. Otero JM, Vongsangnak W, Asadollahi MA, Olivares-Hernandes R, Maury J, Farinelli L et al (2010) Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications. BMC Genomics 11:723
50. Park JI, Grant CM, Dawes IW (2005) The high-affinity cAMP phosphodiesterase of Saccharomyces cerevisiae is the major determinant of cAMP levels in stationary phase: involvement of different branches of the Ras-cyclic AMP pathway in stress responses. Biochem Biophys Res Commun 327:311-319
51. Pereira FB, Guimarães PM, Teixeira JA, Domingues L (2010) Selection of Saccharomyces cerevisiae strains for efficient very high gravity bio-ethanol fermentation processes. Biotechnol Lett 32:1655-1661
52. Riveros-Rosas H, Julián-Sánchez A, Villalobos-Molina R, Pardo JP, Piña E (2003) Diversity, taxonomy and evolution of mediumchain dehydrogenase/reductase superfamily. Eur J Biochem 270:3309-3334
53. Rose MD, Winston F, Hieter P (1990) Methods in yeast genetics. Cold Spring Harbor Laboratory Press, New York
54. Rouillon A, Surdin-Kerjan Y, Thomas D (1999) Transport of sulfonium compounds. Characterization of the s-adenosylmethionine and s-methylmethionine permeases from the yeast Saccharomyces cerevisiae. J Biol Chem 274:28096-28105
55. Sidow A (2002) Sequence first: ask questions later. Cell 111:13-16
56. Silva-Filho EA, dos Santos SKB, Resende AM, de Morais JO, De Morais MA Jr, Simoes DA (2005) Yeast population dynamics of industrial fuel-ethanol fermentation process assessed by PCR-fingerprinting. Antonie Van Leeuwenhoek 88:13-23
57. Smith EN, Kruglyak L (2008) Gene-environment interaction in yeast gene expression. PLoS Biol 6:e83
58. Stambuk BU, Dunn B, Alves-Jr SL, 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
59. Stanke M, Schoffmann O, Morgenstern B, Waack S (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7:62
60. Stephens C, Harrison SJ, Kazan K, Smith FW, Goulter KC, Maclean DJ, Manners JM (2005) Altered fungal sensitivity to a plant antimicrobial peptide through over-expression of yeast cDNAs. Curr Genet 47:194-201
61. Tanaka K, Nakafuku M, Tamanoi F, Kaziro Y, Matsumoto K, Toh-e A (1990) IRA2, a second gene of Saccharomyces cerevisiae that encodes a protein with a domain homologous to mammalian ras GTPase-activating protein. Mol Cell Biol 10:4303-4313
62. Thevelein JM, de Winde JH (1999) Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae. Mol Microbiol 33:904-918
63. Vinci CR, Clarke SG (2010) Homocysteine methyltransferases Mht1 and Sam4 prevent the accumulation of age-damaged (R, S) - AdoMet in the yeast Saccharomyces cerevisiae. J Biol Chem 285:20526-20531
64. Wang P, Kim Y, Pollack J, Narasimhan B, Tibshirani R (2005) A method for calling gains and losses in array CGH data. Biostatistics 6:45-58
65. Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17:1195-1201
66. Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, Cao Z, Gu Z, Bruno D, Miranda M, Nguyen M et al. (2007) Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci USA 104:12825-12830
67. Zaman S, Lippman SI, Schneper L, Slonim N, Broach JR (2009) Glucose regulates transcription in yeast through a network of signaling pathways. Mol Syst Biol 5:245