Deconstructing the genetic basis of spent sulphite liquor tolerance using deep sequencing of genome-shuffled yeast
详细信息    查看全文
  • 作者：Dominic Pinel (1) (3)
    David Colatriano (1)
    Heng Jiang (1) (4)
    Hung Lee (2)
    Vincent JJ Martin (1)

    1. Department of Biology     ; Centre for Structural and Functional Genomics ; Concordia University ; 7141 Sherbrooke Street West ; Montr茅al ; Qu茅bec ; H4B 1R6 ; Canada
    3. Current address     ; Energy Biosciences Institute ; University of California ; Berkeley ; Berkeley ; CA ; 94704 ; USA
    4. Current address     ; Crabtree Nutrition Laboratories ; McGill University Health Center ; Montreal ; Quebec ; H3A 1A1 ; Canada
    2. School of Environmental Sciences     ; University of Guelph ; Guelph ; Ontario ; N1G 2 W1 ; Canada
  • 关键词：Evolutionary engineering ; Genome shuffling ; Reverse engineering ; Complex trait ; Tolerance ; Yeast
  • 刊名：Biotechnology for Biofuels
  • 出版年：2015
  • 出版时间：December 2015
  • 年：2015
  • 卷：8
  • 期：1
  • 全文大小：1,317 KB
  • 参考文献：1. Oud, B, Maris, AJ, Daran, JM, Pronk, JT (2012) Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast. FEMS Yeast Res 12: pp. 183-96 CrossRef
    2. Smith, DR, Quinlan, AR, Peckham, HE, Makowsky, K, Tao, W, Woolf, B (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 18: pp. 1638-42 CrossRef
    3. Crom, S, Schackwitz, W, Pennacchio, L, Magnuson, JK, Culley, DE, Collett, JR (2009) Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106: pp. 16151-6 CrossRef
    4. Sarin, S, Bertrand, V, Bigelow, H, Boyanov, A, Doitsidou, M, Poole, RJ (2010) Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis elegans strains by whole-genome sequencing. Genetics 185: pp. 417-30 CrossRef
    5. Harper, MA, Chen, Z, Toy, T, Machado, IM, Nelson, SF, Liao, JC (2011) Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants. PLoS One 6: pp. e16517 CrossRef
    6. Parts, L, Cubillos, FA, Warringer, J, Jain, K, Salinas, F, Bumpstead, SJ (2011) Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res 21: pp. 1131-8 CrossRef
    7. Zhang, YX, Perry, K, Vinci, VA, Powell, K, Stemmer, WPC, Cardayre, SB (2002) Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415: pp. 644-6 CrossRef
    8. Pinel, D, D鈥橝oust, F, Cardayre, SB, Bajwa, PK, Lee, H, Martin, VJJ (2011) Saccharomyces cerevisiae genome shuffling through recursive population mating leads to improved tolerance to spent sulfite liquor. Appl Environ Microbiol 77: pp. 4736-43 CrossRef
    9. Patnaik, R, Louie, S, Gavrilovic, V, Perry, K, Stemmer, WPC, Ryan, CM (2002) Genome shuffling of Lactobacillus for improved acid tolerance. Nat Biotechnol 20: pp. 707-12 CrossRef
    10. Dai, MH, Copley, SD (2004) Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Appl Environ Microbiol 70: pp. 2391-7 CrossRef
    11. Biot-Pelletier, D, Martin, VJJ (2014) Evolutionary engineering by genome shuffling. Appl Microbiol Biotechnol 98: pp. 3877-87 CrossRef
    12. Almeida, JRM, Modig, T, Petersson, A, Hahn-H盲gerdal, B, Lid茅n, G, Gorwa-Grauslund, MF (2007) Increased tolerance and conversion of inhibitors in lignocellulosic hydrolysates by Saccharomyces cerevisiae. J Chem Technol Biotechnol 82: pp. 340-9 CrossRef
    13. Liu, ZL (2011) Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates. Appl Microbiol Biotechnol 90: pp. 809-25 CrossRef
    14. Liu, ZL, Blaschek, HP Lignocellulosic biomass conversion to ethanol by Saccharomyces. In: Vertes, A, Qureshi, N, Yukawa, H, Blaschek, H eds. (2010) Biomass to biofuels: strategies for global industries. John Wiley & Sons, Ltd, West Sussex, U. K, pp. 17-36
    15. Palmqvist, E, Hahn-H盲gerdal, B (2000) Fermentation of lignocellulosic hydrolysates. I: Inhibition and detoxification. Biores Technol 74: pp. 17-24 CrossRef
    16. Richardson, TL, Harner, NK, Bajwa, PK, Trevors, JT, Lee, H (2011) Approaches to deal with toxic inhibitors during fermentation of lignocellulosic substrates. Acs Sym Ser 1067: pp. 171-202 CrossRef
    17. Pinel, D, Gawand, P, Mahadevan, R, Martin, VJJ (2011) 鈥極mics鈥?technologies and systems biology for engineering Saccharomyces cerevisiae strains for lignocellulosic bioethanol production. Biofuels 2: pp. 659-75 CrossRef
    18. Gorsich, SW, Slininger, PJ, Liu, ZL (2005) Physiological responses to furfural and HMF and the link to other stress pathways. J Biotechnol 118: pp. S91-1
    19. Petersson, A, Almeida, JRM, Modig, T, Karhumaa, K, Hahn-H盲gerdal, B, Gorwa-Grauslund, MF (2006) A 5-hydroxymethyl furfural reducing enzyme encoded by the Saccharomyces cerevisiae ADH6 gene conveys HMF tolerance. Yeast 23: pp. 455-64 CrossRef
    20. Keating, JD, Panganiban, C, Mansfield, SD (2006) Tolerance and adaptation of ethanologenic yeasts to lignocellulosic inhibitory compounds. Biotechnol Bioeng 93: pp. 1196-206 CrossRef
    21. Pinel, D, Martin, VJJ Meiotic recombination-based genome shuffling of Saccharomyces cerevisiae and Schefferomyces stiptis for increased inhibitor tolerance to lignocellulosic substrate toxicity. In: Patnaik, R eds. (2012) Engineering complex phenotypes in industrial strains. John Wiley & Sons, Inc, Hoboken, New Jersey, pp. 233-50 CrossRef
    22. Helle, SS, Murray, A, Lam, J, Cameron, DR, Duff, SJ (2004) Xylose fermentation by genetically modified Saccharomyces cerevisiae 259ST in spent sulfite liquor. Bioresour Technol 92: pp. 163-71 CrossRef
    23. Olsson, L, HahnHagerdal, B (1996) Fermentation of lignocellulosic hydrolysates for ethanol production. Enzyme Microb Tech 18: pp. 312-31 CrossRef
    24. Paraj贸, JC, Dom铆ngues, H, Dom铆nguez, JM (1998) Biotechnological production of xylitol. Part 3: operation in culture media made from lignocellulose hydrolysates. Bioresour Technol 66: pp. 25-40 CrossRef
    25. Helle S, Duff S. Supplementing spent sulfite liquor with a lignocellulosic hydrolysate to increase pentose/hexose co-fermentation efficiency and ethanol yield. Final report-Natural Resources Canada-Tembec Industries; 2004. http://www.lifesciencesbc.ca/files/dufffinal_report.pdf.
    26. Yassour, M, Kaplan, T, Fraser, HB, Levin, JZ, Pfiffner, J, Adiconis, X (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A 106: pp. 3264-9 CrossRef
    27. Nagalakshmi, U, Wang, Z, Waern, K, Shou, C, Raha, D, Gerstein, M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: pp. 1344-9 CrossRef
    28. Kumar, P, Henikoff, S, Ng, PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: pp. 1073-81 CrossRef
    29. Ng, PC, Henikoff, S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31: pp. 3812-4 CrossRef
    30. Sim, NL, Kumar, P, Hu, J, Henikoff, S, Schneider, G, Ng, PC (2012) SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res 40: pp. W452-7 CrossRef
    31. Ozkaynak, E, Finley, D, Solomon, MJ, Varshavsky, A (1987) The yeast ubiquitin genes: a family of natural gene fusions. EMBO J 6: pp. 1429-39
    32. Modig, T, Lid茅n, G, Taherzadeh, MJ (2002) Inhibition effects of furfural on alcohol dehydrogenase, aldehyde dehydrogenase and pyruvate dehydrogenase. Biochem J 363: pp. 769-76 CrossRef
    33. Goldberg, AL (2003) Protein degradation and protection against misfolded or damaged proteins. Nature 426: pp. 895-9 CrossRef
    34. Hochstrasser, M (1996) Ubiquitin-dependent protein degradation. Annu Rev Genet 30: pp. 405-39 CrossRef
    35. Kimura, Y, Tanaka, K (2010) Regulatory mechanisms involved in the control of ubiquitin homeostasis. J Biochem 147: pp. 793-8 CrossRef
    36. Hershko, A, Ciechanover, A (1998) The ubiquitin system. Annu Rev Biochem 67: pp. 425-79 CrossRef
    37. Mukhopadhyay, D, Riezman, H (2007) Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science 315: pp. 201-5 CrossRef
    38. Finley, D, Ozkaynak, E, Varshavsky, A (1987) The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses. Cell 48: pp. 1035-46 CrossRef
    39. Hanna, J, Meides, A, Zhang, DP, Finley, D (2007) A ubiquitin stress response induces altered proteasome composition. Cell 129: pp. 747-59 CrossRef
    40. Leggett, DS, Hanna, J, Borodovsky, A, Crosas, B, Schmidt, M, Baker, RT (2002) Multiple associated proteins regulate proteasome structure and function. Mol Cell 10: pp. 495-507 CrossRef
    41. Hanna, J, Leggett, DS, Finley, D (2003) Ubiquitin depletion as a key mediator of toxicity by translational inhibitors. Mol Cell Biol 23: pp. 9251-61 CrossRef
    42. Chernova, TA, Allen, KD, Wesoloski, LM, Shanks, JR, Chernoff, YO, Wilkinson, KD (2003) Pleiotropic effects of Ubp6 loss on drug sensitivities and yeast prion are due to depletion of the free ubiquitin pool. J Biol Chem 278: pp. 52102-15 CrossRef
    43. Hern谩ndez-L贸pez, MJ, Garcia-Marqu茅s, S, Randez-Gil, F, Prieto, JA (2011) Multicopy suppression screening of Saccharomyces cerevisiae identifies the ubiquitination machinery as a main target for improving growth at low temperatures. Appl Environ Microbiol 77: pp. 7517-25 CrossRef
    44. Kolling, R, Hollenberg, CP (1994) The ABC-transporter Ste6 accumulates in the plasma membrane in a ubiquitinated form in endocytosis mutants. EMBO J 13: pp. 3261-71
    45. Hein, C, Springael, JY, Volland, C, Haguenauer-Tsapis, R, Andre, B (1995) NPl1, an essential yeast gene involved in induced degradation of Gap1 and Fur4 permeases, encodes the Rsp5 ubiquitin-protein ligase. Mol Microbiol 18: pp. 77-87 CrossRef
    46. Hicke, L, Riezman, H (1996) Ubiquitination of a yeast plasma membrane receptor signals its ligand-stimulated endocytosis. Cell 84: pp. 277-87 CrossRef
    47. Lin, CH, MacGurn, JA, Chu, T, Stefan, CJ, Emr, SD (2008) Arrestin-related ubiquitin-ligase adaptors regulate endocytosis and protein turnover at the cell surface. Cell 135: pp. 714-25 CrossRef
    48. Goh, WS, Orlov, Y, Li, J, Clarke, ND (2010) Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol 6: pp. e1000649 CrossRef
    49. Harbison, CT, Gordon, DB, Lee, TI, Rinaldi, NJ, Macisaac, KD, Danford, TW (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: pp. 99-104 CrossRef
    50. Lee, TI, Rinaldi, NJ, Robert, F, Odom, DT, Bar-Joseph, Z, Gerber, GK (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: pp. 799-804 CrossRef
    51. Workman, CT, Mak, HC, McCuine, S, Tagne, JB, Agarwal, M, Ozier, O (2006) A systems approach to mapping DNA damage response pathways. Science 312: pp. 1054-9 CrossRef
    52. Zhu, C, Byers, KJ, McCord, RP, Shi, Z, Berger, MF, Newburger, DE (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19: pp. 556-66 CrossRef
    53. Vyas, VK, Berkey, CD, Miyao, T, Carlson, M (2005) Repressors Nrg1 and Nrg2 regulate a set of stress-responsive genes in Saccharomyces cerevisiae. Eukaryot Cell 4: pp. 1882-91 CrossRef
    54. Kuchin, S, Vyas, VK, Carlson, M (2002) Snf1 protein kinase and the repressors Nrg1 and Nrg2 regulate FLO11, haploid invasive growth, and diploid pseudohyphal differentiation. Mol Cell Biol 22: pp. 3994-4000 CrossRef
    55. Mayordomo, I, Estruch, F, Sanz, P (2002) Convergence of the target of rapamycin and the Snf1 protein kinase pathways in the regulation of the subcellular localization of Msn2, a transcriptional activator of STRE (Stress Response Element)-regulated genes. J Biol Chem 277: pp. 35650-6 CrossRef
    56. Mira, NP, Becker, JD, S谩-Correia, I (2010) Genomic expression program involving the Haa1p-regulon in Saccharomyces cerevisiae response to acetic acid. OMICS 14: pp. 587-601 CrossRef
    57. Fernandes, AR, Mira, NP, Vargas, RC, Canelhas, I, S谩-Correia, I (2005) Saccharomyces cerevisiae adaptation to weak acids involves the transcription factor Haa1p and Haa1p-regulated genes. Biochem Biophys Res Commun 337: pp. 95-103 CrossRef
    58. Magasanik, B (2003) Ammonia assimilation by Saccharomyces cerevisiae. Eukaryot Cell 2: pp. 827-9 CrossRef
    59. Ding, MZ, Wang, X, Liu, W, Cheng, JS, Yang, Y, Yuan, YJ (2012) Proteomic research reveals the stress response and detoxification of yeast to combined inhibitors. PLoS One 7: pp. e43474 CrossRef
    60. Mira, NP, Palma, M, Guerreiro, JF, S谩-Correia, I (2010) Genome-wide identification of Saccharomyces cerevisiae genes required for tolerance to acetic acid. Microb Cell Fact 9: pp. 79 CrossRef
    61. Hess, DC, Lu, W, Rabinowitz, JD, Botstein, D (2006) Ammonium toxicity and potassium limitation in yeast. PLoS Biol 4: pp. e351 CrossRef
    62. Bayer, TS, Hoff, KG, Beisel, CL, Lee, JJ, Smolke, CD (2009) Synthetic control of a fitness tradeoff in yeast nitrogen metabolism. J Biol Eng 3: pp. 1 CrossRef
    63. Wegele, H, M眉ller, L, Buchner, J (2004) Hsp70 and Hsp90鈥揳 relay team for protein folding. Rev Physiol Biochem Pharmacol 151: pp. 1-44 CrossRef
    64. Verghese, J, Abrams, J, Wang, Y, Morano, KA (2012) Biology of the heat shock response and protein chaperones: budding yeast (Saccharomyces cerevisiae) as a model system. Microbiol Mol Biol Rev 76: pp. 115-58 CrossRef
    65. Jones, GW, Masison, DC (2003) Saccharomyces cerevisiae Hsp70 mutations affect [PSI+] prion propagation and cell growth differently and implicate Hsp40 and tetratricopeptide repeat cochaperones in impairment of [PSI+]. Genetics 163: pp. 495-506
    66. Loovers, HM, Guinan, E, Jones, GW (2007) Importance of the Hsp70 ATPase domain in yeast prion propagation. Genetics 175: pp. 621-30 CrossRef
    67. Duncan, K, Edwards, RM, Coggins, JR (1987) The pentafunctional arom enzyme of Saccharomyces cerevisiae is a mosaic of monofunctional domains. Biochem J 246: pp. 375-86
    68. Bauer, BE, Rossington, D, Mollapour, M, Mamnun, Y, Kuchler, K, Piper, PW (2003) Weak organic acid stress inhibits aromatic amino acid uptake by yeast, causing a strong influence of amino acid auxotrophies on the phenotypes of membrane transporter mutants. Eur J Biochem 270: pp. 3189-95 CrossRef
    69. Yoshikawa, K, Tanaka, T, Furusawa, C, Nagahisa, K, Hirasawa, T, Shimizu, H (2009) Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae. Fems Yeast Research 9: pp. 32-44 CrossRef
    70. Stambuk, BU, Panek, AD, Crowe, JH, Crowe, LM, Araujo, PS (1998) Expression of high-affinity trehalose-H+ symport in Saccharomyces cerevisiae. Biochim Biophys Acta 1379: pp. 118-28 CrossRef
    71. Jules, M, Guillou, V, Francois, J, Parrou, JL (2004) Two distinct pathways for trehalose assimilation in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol 70: pp. 2771-8 CrossRef
    72. Babrzadeh, F, Jalili, R, Wang, C, Shokralla, S, Pierce, S, Robinson-Mosher, A (2012) Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1. Mol Genet Genomics 287: pp. 485-94 CrossRef
    73. Carreto, L, Eiriz, MF, Gomes, AC, Pereira, PM, Schuller, D, Santos, MA (2008) Comparative genomics of wild type yeast strains unveils important genome diversity. BMC Genomics 9: pp. 524 CrossRef
    74. Dunn, B, Levine, RP, Sherlock, G (2005) Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures. BMC Genomics 6: pp. 53 CrossRef
    75. Ask, M, Mapelli, V, Hock, H, Olsson, L, Bettiga, M (2013) Engineering glutathione biosynthesis of Saccharomyces cerevisiae increases robustness to inhibitors in pretreated lignocellulosic materials. Microb Cell Fact 12: pp. 87 CrossRef
    76. Stephen, DW, Jamieson, DJ (1997) Amino acid-dependent regulation of the Saccharomyces cerevisiae GSH1 gene by hydrogen peroxide. Mol Microbiol 23: pp. 203-10 CrossRef
    77. Nijkamp, JF, Broek, M, Datema, E, Kok, S, Bosman, L, Luttik, MA (2012) De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact 11: pp. 36 CrossRef
    78. Langmead, B, Trapnell, C, Pop, M, Salzberg, SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: pp. R25 CrossRef
    79. Li, H, Ruan, J, Durbin, R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: pp. 1851-8 CrossRef
    80. Nakamura, K, Oshima, T, Morimoto, T, Ikeda, S, Yoshikawa, H, Shiwa, Y (2011) Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 39: pp. e90 CrossRef
    81. Oyola, SO, Otto, TD, Gu, Y, Maslen, G, Manske, M, Campino, S (2012) Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 13: pp. 1 CrossRef
    82. Xie, C, Tammi, MT (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. Bmc Bioinformatics 10: pp. 80 CrossRef
    83. Artimo, P, Jonnalagedda, M, Arnold, K, Baratin, D, Csardi, G, Castro, E (2012) ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res 40: pp. W597-603 CrossRef
    84. Baggerly, KA, Deng, L, Morris, JS, Aldaz, CM (2003) Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics 19: pp. 1477-83 formatics/btg173" target="_blank" title="It opens in new window">CrossRef
    85. Huang, W, Sherman, BT, Lempicki, RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: pp. 44-57 CrossRef
    86. Merico, D, Isserlin, R, Bader, GD (2011) Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. Methods Mol Biol 781: pp. 257-77 CrossRef
    87. Merico, D, Isserlin, R, Stueker, O, Emili, A, Bader, GD (2010) Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 5: pp. e13984 CrossRef
    88. Cherry, JM, Hong, EL, Amundsen, C, Balakrishnan, R, Binkley, G, Chan, ET (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 40: pp. D700-5 CrossRef
    89. Abdulrehman, D, Monteiro, PT, Teixeira, MC, Mira, NP, Lourenco, AB, Santos, SC (2011) YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res 39: pp. D136-40 CrossRef
    90. Monteiro, PT, Mendes, ND, Teixeira, MC, d鈥橭rey, S, Tenreiro, S, Mira, NP (2008) YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res 36: pp. D132-6 CrossRef
    91. Teixeira, MC, Monteiro, P, Jain, P, Tenreiro, S, Fernandes, AR, Mira, NP (2006) The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res 34: pp. D446-51 CrossRef
    92. Russell, DW, Jensen, R, Zoller, MJ, Burke, J, Errede, B, Smith, M (1986) Structure of the Saccharomyces cerevisiae HO gene and analysis of its upstream regulatory region. Mol Cell Biol 6: pp. 4281-94
  • 刊物类别：Chemistry and Materials Science
  • 刊物主题：Biotechnology
    Plant Breeding/Biotechnology
    Renewable and Green Energy
    Environmental Engineering/Biotechnology
  • 出版者：BioMed Central
  • ISSN：1754-6834
文摘
Background Identifying the genetic basis of complex microbial phenotypes is currently a major barrier to our understanding of multigenic traits and our ability to rationally design biocatalysts with highly specific attributes for the biotechnology industry. Here, we demonstrate that strain evolution by meiotic recombination-based genome shuffling coupled with deep sequencing can be used to deconstruct complex phenotypes and explore the nature of multigenic traits, while providing concrete targets for strain development. Results We determined genomic variations found within Saccharomyces cerevisiae previously evolved in our laboratory by genome shuffling for tolerance to spent sulphite liquor. The representation of these variations was backtracked through parental mutant pools and cross-referenced with RNA-seq gene expression analysis to elucidate the importance of single mutations and key biological processes that play a role in our trait of interest. Our findings pinpoint novel genes and biological determinants of lignocellulosic hydrolysate inhibitor tolerance in yeast. These include the following: protein homeostasis constituents, including Ubp7p and Art5p, related to ubiquitin-mediated proteolysis; stress response transcriptional repressor, Nrg1p; and NADPH-dependent glutamate dehydrogenase, Gdh1p. Reverse engineering a prominent mutation in ubiquitin-specific protease gene UBP7 in a laboratory S. cerevisiae strain effectively increased spent sulphite liquor tolerance. Conclusions This study advances understanding of yeast tolerance mechanisms to inhibitory substrates and biocatalyst design for a biomass-to-biofuel/biochemical industry, while providing insights into the process of mutation accumulation that occurs during genome shuffling.

© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号

地址：北京市海淀区学院路29号 邮编：100083

电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700