Disruption of PHO13 improves ethanol production via the xylose isomerase pathway

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• 作者：Takahiro Bamba ; Tomohisa Hasunuma ; Akihiko Kondo
• 关键词：Bioethanol ; PHO13 ; Saccharomyces cerevisiae ; Xylose fermentation ; Xylose isomerase
• 刊名：AMB Express
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：6
• 期：1
• 全文大小：1,145 KB
• 参考文献：Akada R, Kitagawa T, Kaneko S, Toyonaga D, Ito S, Kakihara Y, Hoshida H, Morimura S, Kondo A, Kida K. PCR-mediated seamless gene deletion and marker recycling in Saccharomyces cerevisiae. Yeast. 2006;23:399–405.PubMed CrossRef
  Blank LM, Lehmbeck F, Sauer U. Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res. 2005;5:545–58.PubMed CrossRef
  Chen DC, Yang BC, Kuo TT. One-step transformation of yeast in stationary phase. Curr Genet. 1992;21:83–4.PubMed CrossRef
  Chu BCH, Lee H. Genetic improvement of Saccharomyces cerevisiae for xylose fermentation. Biotechnol Adv. 2007;25:425–41.PubMed CrossRef
  De Preter K, Speleman F, Combaret V, Lunec J, Laureys G, Eussen BHJ, Francotte N, Board J, Pearson ADJ, De Paepe A, Van Roy N, Vandesompele J. Quantification of MYCN, DDX1, and NAG gene copy number in neuroblastoma using a real-time quantitative PCR assay. Mod Pathol. 2002;15:159–66.PubMed CrossRef
  Fiaux J, Cakar ZP, Sonderegger M, Wüthrich K, Szyperski T, Sauer U. Metabolic-flux profiling of the yeasts Saccharomyces cerevisiae and Pichia stipitis. Eukaryot Cell. 2003;2:170–80.PubMed PubMedCentral CrossRef
  Fujitomi K, Sanda T, Hasunuma T, Kondo A. Deletion of the PHO13 gene in Saccharomyces cerevisiae improves ethanol production from lignocellulosic hydrolysate in the presence of acetic and formic acids, and furfural. Bioresour Technol. 2012;111:161–6.PubMed CrossRef
  Grotkjær T, Christakopoulos P, Nielsen J, Olsson L. Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Metab Eng. 2005;7:437–44.PubMed CrossRef
  Hasunuma T, Sanda T, Yamada R, Yoshimura K, Ishii J, Kondo A. Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae. Microb Cell Fact. 2011;10:2.PubMed PubMedCentral CrossRef
  Hector RE, Bowman MJ, Skory CD, Cotta MA. The Saccharomyces cerevisiae YMR315 W gene encodes an NADP(H)-specific oxidoreductase regulated by the transcription factor Stb5p in response to NADPH limitation. N Biotechnol. 2009;26:171–80.PubMed CrossRef
  Ishii J, Izawa K, Matsumura S, Wakamura K, Tanino T, Tanaka T, Ogino C, Fukuda H, Kondo A. A simple and immediate method for simultaneously evaluating expression level and plasmid maintenance in yeast. J Biochem. 2009;145:701–8.PubMed CrossRef
  Jin Y, Ni H, Laplaza JM, Jeffries TW. Optimal growth and ethanol production from xylose by recombinant Saccharomyces cerevisiae require moderate d-xylulokinase activity. Appl Environ Microbiol. 2003;69:495–503.PubMed PubMedCentral CrossRef
  Jin Y, Alper H, Yang YT, Stephanopoulos G. Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach. Appl Environ Microbiol. 2005;71:8249–56.PubMed PubMedCentral CrossRef
  Johansson B, Christensson C, Hobley T, Hahn-Hägerdal B. Xylulokinase overexpression in two strains of Saccharomyces cerevisiae also expressing xylose reductase and xylitol dehydrogenase and its effect on fermentation of xylose and lignocellulosic hydrolysate. Appl Environ Microbiol. 2001;67:4249–55.PubMed PubMedCentral CrossRef
  Johansson B, Hahn-Hägerdal B. The non-oxidative pentose phosphate pathway controls the fermentation rate of xylulose but not of xylose in Saccharomyces cerevisiae TMB3001. FEMS Yeast Res. 2002;2:277–82.PubMed
  Karhumaa K, Hahn-Hägerdal B, Gorwa-Grauslund M-F. Investigation of limiting metabolic steps in the utilization of xylose by recombinant Saccharomyces cerevisiae using metabolic engineering. Yeast. 2005;22:359–68.PubMed CrossRef
  Karhumaa K, Garcia Sanchez R, Hahn-Hägerdal B, Gorwa-Grauslund M-F. Comparison of the xylose reductase-xylitol dehydrogenase and the xylose isomerase pathways for xylose fermentation by recombinant Saccharomyces cerevisiae. Microb Cell Fact. 2007;6:5.PubMed PubMedCentral CrossRef
  Kato H, Izumi Y, Hasunuma T, Matsuda F, Kondo A. Widely targeted metabolic profiling analysis of yeast central metabolites. J Biosci Bioeng. 2012;113:665–73.PubMed CrossRef
  Kim SR, Skerker JM, Kang W, Lesmana A, Wei N, Arkin AP, Jin Y-S. Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae. PLoS One. 2013;8:e57048.PubMed PubMedCentral CrossRef
  Kim SR, Xu H, Lesmana A, Kuzmanovic U, Au M, Florencia C, Oh EJ, Zhang G, Kim KH, Jin Y-S. Deletion of PHO13, encoding haloacid dehalogenase type IIA phosphatase, results in upregulation of the pentose phosphate pathway in Saccharomyces cerevisiae. Appl Environ Microbiol. 2015;81:1601–9.PubMed PubMedCentral CrossRef
  Kötter P, Ciriacy M. Xylose fermentation by Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 1993;38:776–83.CrossRef
  Kuyper M, Hartog MMP, Toirkens MJ, Almering MJH, Winkler AA, Van Dijken JP, Pronk JT. Metabolic engineering of a xylose-isomerase-expressing Saccharomyces cerevisiae strain for rapid anaerobic xylose fermentation. FEMS Yeast Res. 2005a;5:399–409.PubMed CrossRef
  Kuyper M, Toirkens MJ, Diderich JA, Winkler AA, Van Dijken JP, Pronk JT. Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting Saccharomyces cerevisiae strain. FEMS Yeast Res. 2005b;5:925–34.PubMed CrossRef
  Larochelle M, Drouin S, Robert F, Turcotte B. Oxidative stress-activated zinc cluster protein Stb5 has dual activator/repressor functions required for pentose phosphate pathway regulation and NADPH production. Mol Cell Biol. 2006;26:6690–701.PubMed PubMedCentral CrossRef
  Lee S-M, Jellison T, Alper HS. Systematic and evolutionary engineering of a xylose isomerase-based pathway in Saccharomyces cerevisiae for efficient conversion yields. Biotechnol Biofuels. 2014;7:122.PubMed PubMedCentral
  Li YC, Gou ZX, Liu ZS, Tang YQ, Akamatsu T, Kida K. Synergistic effects of TAL1 over-expression and PHO13 deletion on the weak acid inhibition of xylose fermentation by industrial Saccharomyces cerevisiae strain. Biotechnol Lett. 2014;36:2011–21.
  Lu C, Jeffries T. Shuffling of promoters for multiple genes to optimize xylose fermentation in an engineered Saccharomyces cerevisiae strain. Appl Environ Microbiol. 2007;73:6072–7.PubMed PubMedCentral CrossRef
  Madhavan A, Tamalampudi S, Ushida K, Kanai D, Katahira S, Srivastava A, Fukuda H, Bisaria VS, Kondo A. Xylose isomerase from polycentric fungus Orpinomyces: gene sequencing, cloning, and expression in Saccharomyces cerevisiae for bioconversion of xylose to ethanol. Appl Microbiol Biotechnol. 2009a;82:1067–78.PubMed CrossRef
  Madhavan A, Tamalampudi S, Srivastava A, Fukuda H, Bisaria VS, Kondo A. Alcoholic fermentation of xylose and mixed sugars using recombinant Saccharomyces cerevisiae engineered for xylose utilization. Appl Microbiol Biotechnol. 2009b;82:1037–47.PubMed CrossRef
  Matsushika A, Inoue H, Kodaki T, Sawayama S. Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives. Appl Microbiol Biotechnol. 2009;84:37–53.PubMed CrossRef
  Mosier N, Wyman C, Dale B, Elander R, Lee YY, Holtzapple M, Ladisch M. Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresour Technol. 2005;96:673–86.PubMed CrossRef
  Ni H, Laplaza JM, Jeffries TW. Transposon mutagenesis to improve the growth of recombinant Saccharomyces cerevisiae on d -xylose. Appl Environ Microbiol. 2007;73:2061–6.PubMed PubMedCentral CrossRef
  Shen Y, Chen X, Peng B, Chen L, Hou J, Bao X. An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile. Appl Microbiol Biotechnol. 2012;96:1079–91.PubMed CrossRef
  Van Maris AJA, Winkler AA, Kuyper M, De Laat WTAM, Van Dijken JP, Pronk JT. Development of efficient xylose fermentation in Saccharomyces cerevisiae: xylose isomerase as a key component. Adv Biochem Eng Biotechnol. 2007;108:179–204.PubMed
  Van Vleet JH, Jeffries TW, Olsson L. Deleting the para-nitrophenyl phosphatase (pNPPase), PHO13, in recombinant Saccharomyces cerevisiae improves growth and ethanol production on d -xylose. Metab Eng. 2008;10:360–9.PubMed CrossRef
  Van Vleet JH, Jeffries TW. Yeast metabolic engineering for hemicellulosic ethanol production. Curr Opin Biotechnol. 2009;20:300–6.PubMed CrossRef
  Wasylenko TM, Stephanopoulos G. Metabolomic and 13C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase. Biotechnol Bioeng. 2015;112:470–83.PubMed CrossRef
  Yamada R, Tanaka T, Ogino C, Fukuda H, Kondo A. Novel strategy for yeast construction using δ-integration and cell fusion to efficiently produce ethanol from raw starch. Appl Microbiol Biotechnol. 2010;85:1491–8.PubMed CrossRef
  Zhou H, Cheng J-S, Wang BL, Fink GR, Stephanopoulos G. Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metab Eng. 2012;14:611–22.PubMed CrossRef
  
• 作者单位：Takahiro Bamba (1)
  Tomohisa Hasunuma (2)
  Akihiko Kondo (1) (3)
  
  1. Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
  2. Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
  3. Biomass Engineering Program, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Biotechnology
  Microbiology
  Microbial Genetics and Genomics
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：2191-0855

文摘

Xylose is the second most abundant sugar in lignocellulosic materials and can be converted to ethanol by recombinant Saccharomyces cerevisiae yeast strains expressing heterologous genes involved in xylose assimilation pathways. Recent research demonstrated that disruption of the alkaline phosphatase gene, PHO13, enhances ethanol production from xylose by a strain expressing the xylose reductase (XR) and xylitol dehydrogenase (XDH) genes; however, the yield of ethanol is poor. In this study, PHO13 was disrupted in a recombinant strain harboring multiple copies of the xylose isomerase (XI) gene derived from Orpinomyces sp., coupled with overexpression of the endogenous xylulokinase (XK) gene and disruption of GRE3, which encodes aldose reductase. The resulting YΔGP/XK/XI strain consumed 2.08 g/L/h of xylose and produced 0.88 g/L/h of volumetric ethanol, for an 86.8 % theoretical ethanol yield, and only YΔGP/XK/XI demonstrated increase in cell concentration. Transcriptome analysis indicated that expression of genes involved in the pentose phosphate pathway (GND1, SOL3, TAL1, RKI1, and TKL1) and TCA cycle and respiratory chain (NDE1, ACO1, ACO2, SDH2, IDH1, IDH2, ATP7, ATP19, SDH4, SDH3, CMC2, and ATP15) was upregulated in the YΔGP/XK/XI strain. And the expression levels of 125 cell cycle genes were changed by deletion of PHO13. Keywords Bioethanol PHO13 Saccharomyces cerevisiae Xylose fermentation Xylose isomerase