Improving Saccharomyces cerevisiae ethanol production and tolerance via RNA polymerase II subunit Rpb7

Biotechnology for Biofuels

Volumn 10, Issue 1, 2017, Pages

  Qiu, Zilong ^a   Jiang, Rongrong ^a  

^a Nanyang Technological University   (Singapore)

Author keywords

Ethanol productivity; Ethanol titers; Ethanol tolerance; Global transcription machinery engineering (gTME); Oxidative tolerance; RNA polymerase II; Subunit Rpb7; Transcriptional engineering; VHG fermentation

Indexed keywords

FERMENTATION; GENE EXPRESSION; GENES; MACHINERY; NUCLEIC ACIDS; POLYMERASE CHAIN REACTION; POLYMERS; PRODUCTIVITY; RNA; TRANSCRIPTION; YEAST;

ETHANOL PRODUCTIVITY; ETHANOL TOLERANCE; MACHINERY ENGINEERINGS; RNA POLYMERASE II; SUBUNIT RPB7; TRANSCRIPTIONAL ENGINEERINGS;

ETHANOL;

BIOFUEL; CELLULAR AUTOMATON; ETHANOL; FERMENTATION; OXIDATIVE STRESS; PHENOTYPE; POLYMERASE CHAIN REACTION; RNA;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 85020862104     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/s13068-017-0806-0     Document Type: Article

References (55)

1. Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G. Engineering yeast transcription machinery for improved ethanol tolerance and production. Science. 2006;314:1565-8.
2. Alper H, Stephanopoulos G. Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng. 2007;9:258-67.
3. Ansanay-Galeote V, Blondin B, Dequin S, Sablayrolles JM. Stress effect of ethanol on fermentation kinetics by stationary-phase cells of Saccharomyces cerevisiae. Biotechnol Lett. 2001;23:677-81.
4. Armache KJ, Kettenberger H, Cramer P. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci USA. 2003;100:6964-8.
5. Bai FW, Anderson WA, Moo-Young M. Ethanol fermentation technologies from sugar and starch feedstocks. Biotechnol Adv. 2008;26:89-105.
6. Bai FW, Chen LJ, Zhang Z, Anderson WA, Moo-Young M. Continuous ethanol production and evaluation of yeast cell lysis and viability loss under very high gravity medium conditions. J Biotechnol. 2004;110:287-93.
7. Benatuil L, Perez JM, Belk J, Hsieh CM. An improved yeast transformation method for the generation of very large human antibody libraries. Protein Eng Des Sel. 2010;23:155-9.
8. Cao TS, Chi Z, Liu GL, Chi ZM. Expression of TPS1 gene from Saccharomycopsis fibuligera A11 in Saccharomyces sp. W0 enhances trehalose accumulation, ethanol tolerance, and ethanol production. Mol Biotechnol. 2014;56:72-8.
9. Chen T, Wang J, Yang R, Li J, Lin M, Lin Z. Laboratory-evolved mutants of an exogenous global regulator, IrrE from Deinococcus radiodurans, enhance stress tolerances of Escherichia coli. PLoS ONE. 2011;6:16228.
10. Choder M. Rpb4 and Rpb7: subunits of RNA polymerase II and beyond. Trends Biochem Sci. 2004;29:674-81.
11. Chong H, Geng H, Zhang H, Song H, Huang L, Jiang R. Enhancing E. coli isobutanol tolerance through engineering its global transcription factor cAMP receptor protein (CRP). Biotechnol Bioeng. 2014;111:700-8.
12. Chong H, Huang L, Yeow J, Wang I, Zhang H, Song H, Jiang R. Improving ethanol tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PLoS ONE. 2013;8:e57628.
13. Costa V, Amorim MA, Reis E, Quintanilha A, Moradas-Ferreira P. Mitochondria1 superoxide disrnutase is essential for ethanol tolerance of Saccharomyces cerevisiae in the post-diauxic phase. Microbiology. 1997;143:1649-56.
14. Cramer P. Architecture of RNA polymerase II and implications for the transcription mechanism. Science. 2000;288:640-9.
15. Cramer P. RNA polymerase II structure: from core to functional complexes. Curr Opin Genet Dev. 2004;14:218-26.
16. Demasi AP, Pereira GA, Netto LE. Yeast oxidative stress response. Influences of cytosolic thioredoxin peroxidase I and of the mitochondrial functional state. FEBS J. 2006;273:805-16.
17. Du X, Takagi H. N-Acetyltransferase Mpr1 confers ethanol tolerance on Saccharomyces cerevisiae by reducing reactive oxygen species. Appl Microbiol Biotechnol. 2007;75:1343-51.
18. Gibson BR, Lawrence SJ, Leclaire JP, Powell CD, Smart KA. Yeast responses to stresses associated with industrial brewery handling. FEMS Microbiol Rev. 2007;31:535-69.
19. Harel-Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M. RNA polymerase II subunits link transcription and mRNA decay to translation. Cell. 2010;143:552-63.
20. Henderson CM, Lozada-Contreras M, Jiranek V, Longo ML, Block DE. Ethanol production and maximum cell growth are highly correlated with membrane lipid composition during fermentation as determined by lipidomic analysis of 22 Saccharomyces cerevisiae strains. Appl Environ Microbiol. 2013;79:91-104.
21. Hong SH, Hegde M, Kim J, Wang X, Jayaraman A, Wood TK. Synthetic quorum-sensing circuit to control consortial biofilm formation and dispersal in a microfluidic device. Nat Commun. 2012;3:613.
22. Hong SH, Wang X, Wood TK. Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H-NS of Escherichia coli. Microb Biotechnol. 2010;3:344-56.
23. Izawa S, Inoue Y, Kimura A. Importance of catalase in the adaptive response to hydrogen peroxide. Biochem J. 1996;15:61-7.
24. Jasiak AJ, Hartmann H, Karakasili E, Kalocsay M, Flatley A, Kremmer E, Strasser K, Martin DE, Soding J, Cramer P. Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. J Biol Chem. 2008;283:26423-7.
25. Jung YJ, Park HD. Antisense-mediated inhibition of acid trehalase (ATH1) gene expression promotes ethanol fermentation and tolerance in Saccharomyces cerevisiae. Biotechnol Lett. 2005;27:1855-9.
26. Kim HS, Kim NR, Choi W. Total fatty acid content of the plasma membrane of Saccharomyces cerevisiae is more responsible for ethanol tolerance than the degree of unsaturation. Biotechnol Lett. 2011;33:509-15.
27. Klein-Marcuschamer D, Santos CN, Yu H, Stephanopoulos G. Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes. Appl Environ Microbiol. 2009;75:2705-11.
28. Koleske AJ, Young RA. An RNA polymerase II holoenzyme responsive to activators. Nature. 1994;368:466-9.
29. Lam FH, Ghaderi A, Fink GR, Stephanopoulos G. Biofuels. Engineering alcohol tolerance in yeast. Science. 2014;346:71-5.
30. Lin Z, Zhang Y, Wang J. Engineering of transcriptional regulators enhances microbial stress tolerance. Biotechnol Adv. 2013;31:986-91.
31. Liu H, Liu K, Yan M, Xu L, Ouyang P. gTME for improved adaptation of Saccharomyces cerevisiae to corn cob acid hydrolysate. Appl Biochem Biotechnol. 2011;164:1150-9.
32. Lotan R, Goler-Baron V, Duek L, Haimovich G, Choder M. The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol. 2007;178:1133-43.
33. Meka H, Werner F, Cordell SC, Onesti S, Brick P. Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II. Nucleic Acids Res. 2005;33:6435-44.
34. Moon MH, Ryu J, Choeng YH, Hong SK, Kang HA, Chang YK. Enhancement of stress tolerance and ethanol production in Saccharomyces cerevisiae by heterologous expression of a trehalose biosynthetic gene from Streptomyces albus. Biotechnol Bioprocess Eng. 2012;17:986-96.
35. Nijkamp JF, vanden Broek M, Datema E, de Kok S, Bosman L, Luttik MA, Daran-Lapujade P, Vongsangnak W, Nielsen J, Heijne WH, Klaassen P, Paddon CJ, Platt D, Kotter P, van Ham RC, Reinders MJ, Pronk JT, de Ridder D, Daran JM. 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. 2012;11:36.
36. Özcan S, Johnston M. Function and regulation of yeast hexose transporters. Microbiol Mol Biol Rev. 1999;63:554-69.
37. Pais TM, Foulquie-Moreno MR, Hubmann G, Duitama J, Swinnen S, Goovaerts A, Yang Y, Dumortier F, Thevelein JM. Comparative polygenic analysis of maximal ethanol accumulation capacity and tolerance to high ethanol levels of cell proliferation in yeast. PLoS Genet. 2013;9:e1003548.
38. Park KS, Lee DK, Lee H, Lee Y, Jang YS, Kim YH, Yang HY, Lee SI, Seol W, Kim JS. Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors. Nat Biotechnol. 2003;21:1208-14.
39. Pronk JT, Steensmays HY, Dijken JPV. Pyruvate metabolism in Saccharomyces cerevisiae. Yeast. 1996;12:1607-33.
40. Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation by RNA polymerase II. Nat Rev Mol Cell Biol. 2015;16:129-43.
41. Sampath V, Sadhale P. Rpb4 and Rpb7: a sub-complex integral to multi-subunit RNA polymerases performs a multitude of functions. IUBMB Life. 2005;57:93-102.
42. Sheffer A, Varon M, Choder M. Rpb7 can interact with RNA polymerase II and support transcription during some stresses independently of Rpb4. Mol Biol Cell. 1999;19:2672-80.
43. Shpakovski GV, Gadal O, Labarre-Mariotte S, Lebedenko EN, Miklos I, Sakurai H, Proshkin SA, Mullem VV, Ishihama A, Thuriaux P. Functional conservation of RNA polymerase II in fission and budding yeasts. J Mol Biol. 2000;295:1119-27.
44. Spencer J, Phister TG, Smart KA, Greetham D. Tolerance of pentose utilising yeast to hydrogen peroxide-induced oxidative stress. BMC Res Notes. 2014;17:151.
45. Tan FR, Dai LC, Wu B, Qin H, Shui ZX, Wang JL, Zhu QL, Hu QC, Ruan ZY, He MX. Improving furfural tolerance of Zymomonas mobilis by rewiring a sigma factor RpoD protein. Appl Microbiol Biotechnol. 2015;99:5363-71.
46. Thammasittirong SNR, Thirasaktana T, Thammasittirong A, Srisodsuk M. Improvement of ethanol production by ethanol-tolerant Saccharomyces cerevisiae UVNR56.SpringerPlus. 2013;2:583.
47. Thatipamala R, Rohani S, Hill GA. Effects of high product and substrate inhibitions on the kinetics and biomass and product yields during ethanol batch fermentation. Biotechnol Bioeng. 1992;40:289-97
48. Vanegas JM, Contreras MF, Faller R, Longo ML. Role of unsaturated lipid and ergosterol in ethanol tolerance of model yeast biomembranes. Biophys J. 2012;102:507-16.
49. Vemuri GN, Eiteman MA, McEwen JE, Olsson L, Nielsen J. Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 2007;104:2402-7.
50. Watson TG. Effects of sodium chloride on steady-state growth and metabolism of Saccharomyces cerevisiae. J Gen Microbiol. 1970;64:91-9.
51. Wong CM, Zhou Y, Ng RW, Kung Hf HF, Jin DY. Cooperation of yeast peroxiredoxins Tsa1p and Tsa2p in the cellular defense against oxidative and nitrosative stress. J Biol Chem. 2002;277:5385-94.
52. Woychik NA, Hampsey M. The RNA polymerase II machinery structure illuminates function. Cell. 2002;108:453-63.
53. Zhang H, Chong H, Ching CB, Jiang R. Random mutagenesis of global transcription factor cAMP receptor protein for improved osmotolerance. Biotechnol Bioeng. 2012;109:1165-72.
54. Zhao H, Li J, Han B, Li X, Chen J. Improvement of oxidative stress tolerance in Saccharomyces cerevisiae through global transcription machinery engineering. J Ind Microbiol Biotechnol. 2014;41:869-78.
55. Zhao XQ, Bai FW. Mechanisms of yeast stress tolerance and its manipulation for efficient fuel ethanol production. J Biotechnol. 2009;144:23-30.