Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment

Biotechnology for Biofuels

Volumn 8, Issue 1, 2015, Pages

  Yi, Xia ^a   Gu, Hanqi ^a   Gao, Qiuqiang ^a   Liu, Z Lewis ^b   Bao, Jie ^a  

^a EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

Author keywords

DNA microarray; Lignocellulose pretreatment; Phenolic aldehyde inhibitors; Recombinants; Stress tolerance; Zymomonas mobilis ZM4

Indexed keywords

CELLULOSE; DETOXIFICATION; ETHANOL; FURFURAL; GENE EXPRESSION; GENES; LIGNIN; PRODUCTIVITY; TOXICITY;

DNA MICRO-ARRAY; PRE-TREATMENT; RECOMBINANTS; STRESS TOLERANCE; ZYMOMONAS MOBILIS;

ALDEHYDES;

ALDEHYDE; BIOFUEL; CATALYST; CELLULOSE; HYDROXYL RADICAL; INHIBITOR; LIGNIN; MICROBIAL ACTIVITY; PHENOLIC COMPOUND; TOLERANCE;

BACTERIA (MICROORGANISMS); ZYMOMONAS MOBILIS;

EID: 84959557202     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/s13068-015-0333-9     Document Type: Article

References (32)

1. Klinke HB, Thomsen AB, Ahring BK. Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Appl Microbiol Biotechnol. 2004;66:10-26.
2. Palmqvist E, Hahn-Hagerdal B. Fermentation of lignocellulosic hydrolysates. II: Inhibitors and mechanisms of inhibition. Bioresour Technol. 2000;74:25-33.
3. Larsson S, Quintana-Sainz A, Reimann A, Nilvebrant NO, Jonsson LJ. Influence of lignocellulose-derived aromatic compounds on oxygen-limited growth and ethanolic fermentation by Saccharomyces cerevisiae. Appl Biochem Biotechnol. 2000;84-86:617-32.
4. Jing X, Zhang X, Bao J. Inhibition performance of lignocellulose degradation products on industrial cellulase enzymes during cellulose hydrolysis. Appl Biochem Biotechnol. 2009;159:696-707.
5. Rogers PL, Jeon YJ, Lee KJ, Lawford HG. Zymomonas mobilis for fuel ethanol and higher value products. Adv Biochem Eng Biotechnol. 2007;108:263-88.
6. Zhang M, Eddy C, Deanda K, Finkelstein M, Picataggio S. Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science. 1995;267:240-3.
7. Gu HQ, Zhang J, Bao J. High tolerance and physiological mechanism of Zymomonas mobilis to phenolic inhibitors in ethanol fermentation of corncob residue. Biotechnol Bioeng. 2015;112:1770-82.
8. Ranatunga TD, Jervis J, Helm RF, McMillan JD, Hatzis C. Identification of inhibitory components toxic toward Zymomonas mobilis CP4 (pZB5) xylose fermentation. Appl Biochem Biotechnol. 1997;67:185-98.
9. He MX, Wu B, Shui ZX, Hu QC, Wang WG, Tan FR, Tang XY, Zhu QL, Pan K, Li Q, Su XH. Transcriptome profiling of Zymomonas mobilis under ethanol stress. Biotechnol Biofuels. 2012;5:75-84.
10. Yang S, Pan C, Tschaplinski TJ, Hurst GB, Engle NL, Zhou W, Dam P, Xu Y, Rodriguez M Jr, Dice L, Johnson CM, Davison BH, Brown SD. Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. PLoS One. 2013;7:e68886-900.
11. He MX, Wu B, Shui ZX, Hu QC, Wang WG, Tan FR, Tang XY, Zhu QL, Pan K, Li Q, Su XH. Transcriptome profiling of Zymomonas mobilis under furfural stress. Appl Microbiol Biotechnol. 2012;95:189-99.
12. Franden MA, Pilath HM, Mohagheghi A, Pienkos PT, Zhang M. Inhibition of growth of Zymomonas mobilis by model compounds found in lignocellulosic hydrolysates. Biotechnol Biofuels. 2013;6:99-113.
13. Palmqvist E, Almeida JS, Hahn-Hagerdal B. Influence of furfural on anaerobic glycolytic kinetics of Saccharomyces cerevisiae in batch culture. Biotechnol Bioeng. 1999;62:447-54.
14. Nikaido H. Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev. 2003;67:593-656.
15. Dong HW, Bao J, Ryu DD, Zhong JJ. Design and construction of improved new vectors for Zymomonas mobilis recombinants. Biotechnol Bioeng. 2011;108:1616-27.
16. Müller A, Hauer B, Rosche B. Asymmetric alkene reduction by yeast old yellow enzymes and by a novel Zymomonas mobilis reductase. Biotechnol Bioeng. 2007;98:22-9.
17. Liu Z. Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates. Appl Microbiol Biotechnol. 2011;90:809-25.
18. Liu Z. Genomics of yeast tolerance and in situ detoxification. In: Liu ZL, editor. Microbial stress tolerance for biofuels, vol. 22., Microbiology monographsBerlin: Springer; 2011. p. 1-28.
19. Liu Z, Menggen M, Song MJ. Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways. Mol Genet Genom. 2009;282:233-44.
20. Moon J, Liu ZL. Engineered NADH-dependent GRE2 from Saccharomyces cerevisiae by directed enzyme evolution enhances HMF reduction using additional cofactor NADPH. Enzym Microb Technol. 2012;50:115-20.
21. Moon J, Liu ZL. Direct enzyme assay evidence confirms aldehyde reductase function of Ydr541cp and Ygl039wp from Saccharomyces cerevisiae. Yeast. 2015;32:399-407.
22. Ma M, Liu Z. Mechanisms of ethanol tolerance in Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 2010;87:829-45.
23. Segura A, Molina L, Fillet S, Krell T, Bernal P, Munõz-Rojas J, Ramos JL. Solvent tolerance in Gram-negative bacteria. Curr Opin Biotechnol. 2012;23:415-21.
24. Liu ZL. Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysate. Appl Microbiol Biotechnol. 2011;90:809-25.
25. Zhang Y, Liu ZL, Song M. ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion. Nucl Acids Res. 2015;43:4393-407. doi: 10.1093/nar/gkv358.
26. Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, de Longueville F, Fuscoe JC, Tong W, Shi L, Wolfinger RD. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol. 2006;24:1140-50.
27. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998;95:14863-8.
28. Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57:289-300.
29. Van de Guchte M, van der Vossen JM, Kok J, Venema G. Construction of a lactococcal expression vector: Expression of hen egg white lysozyme in Lactococcus lactis subsp. lactis. Appl Environ Microbiol. 1989;55:224-8.
30. Abd E-Mawla AM, Beerhues L. Benzoic acid biosynthesis in cell cultures of Hypericum androsaemum. Planta. 2002;214:727-33.
31. Klinke HB, Ahring BK, Schmidt AS, Thomsen AB. Characterization of degradation products from alkaline wet oxidation of wheat straw. Bioresour Technol. 2002;82:15-26.
32. Varga E, Klinke HB, Réczey K, Thomsen AB. High solid simultaneous saccharification and fermentation of wet oxidized corn stover to ethanol. Biotechnol Bioeng. 2004;88:567-74.