Abstract
Furfural from lignocellulosic hydrolysates is the key inhibitor for bio-ethanol fermentation. In this study, we report a strategy of improving the furfural tolerance in Zymomonas mobilis on the transcriptional level by engineering its global transcription sigma factor (σ70, RpoD) protein. Three furfural tolerance RpoD mutants (ZM4-MF1, ZM4-MF2, and ZM4-MF3) were identified from error-prone PCR libraries. The best furfural-tolerance strain ZM4-MF2 reached to the maximal cell density (OD600) about 2.0 after approximately 30 h, while control strain ZM4-rpoD reached its highest cell density of about 1.3 under the same conditions. ZM4-MF2 also consumed glucose faster and yield higher ethanol; expression levels and key Entner-Doudoroff (ED) pathway enzymatic activities were also compared to control strain under furfural stress condition. Our results suggest that global transcription machinery engineering could potentially be used to improve stress tolerance and ethanol production in Z. mobilis.
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References
Agrawal M, Chen RR (2011) Discovery and characterization of a xylose reductase from Zymomonas mobilis ZM4. Biotechnol Lett 33(11):2127–2133
Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314(5805):1565–1568
Alper H, Stephanopoulos G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 9(3):258–267
Barakat A, Monlau F, Steyer J-P, Carrere H (2012) Effect of lignin-derived and furan compounds found in lignocellulosic hydrolysates on biomethane production. Bioresour Technol 104:90–99
Barciszewski J, Siboska GE, Pedersen BO, Clark BF, Rattan SI (1997) A mechanism for the in vivo formation of N6-furfuryladenine, kinetin, as a secondary oxidative damage product of DNA. FEBS Lett 414(2):457–460
Burgess RR, Anthony L (2001) How sigma docks to RNA polymerase and what sigma does. Curr Opin Microbiol 4(2):126–131
Chong HQ, Huang L, Yeow JW, Wang I, Zhang HF, Song H, Jiang RR (2013) Improving ethanol tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein(CRP). PLoS ONE 8(2):1–9
Conway T, Osman YA, Konnan JI, Hoffmann EM, Ingram LO (1987) Promoter and nucleotide sequences of the Zymomonas mobilis pyruvate decarboxylase. J Bacteriol 169(3):949–954
Dunlop MJ (2011) Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels 4(1):32–41
Gardella T, Moyle H, Susskind MM (1989) A mutant Escherichia coli σ70 subunit of RNA polymerase with altered promoter specificity. J Mol Biol 206(4):579–590
Geddes CC, Peterson JJ, Mullinnix MT, Svoronos SA, Shanmugam KT, Ingram LO (2010a) Optimizing cellulase usage for improved mixing and rheological properties of acid-pretreated sugarcane bagasse. Bioresour Technol 101(23):9128–9136
Geddes CC, Peterson JJ, Roslander C, Zacchi G, Mullinnix MT, Shanmugam KT, Ingram LO (2010b) Optimizing the saccharification of sugar cane bagasse using dilute phosphoric acid followed by fungal cellulases. Bioresour Technol 101(6):1851–1857
Geddes RD, Wang X, Yomano LP, Miller EN, Zheng H, Shanmugam KT, Ingram LO (2014) Polyamine transporters and polyamines increase furfural tolerance during xylose fermentation with ethanologenic Escherichia coli Strain LY180. Appl Environ Microbiol 80(19):5955–5964
Gorsich SW, Dien BS, Nichols NN, Slininger PJ, Liu ZL, Skory CD (2006) Tolerance to furfural-induced stress is associated with pentose phosphate pathway genes ZWF1, GND1, RPE1, and TKL1 in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 71(3):339–349
He MX, Wu B, Shui ZX, Hu QC, Wang WG, Tan FR, Tang XY, Zhu QL, Pan K, Li Q (2012a) Transcriptome profiling of Zymomonas mobilis under furfural stress. Appl Microbiol Biotechnol 95(1):189–199
He MX, Wu B, Qin H, Ruan ZY, Tan FR, Wang JL, Shui ZX, Dai LC, Zhu QL, Pan K (2014) Zymomonas mobilis: a novel platform for future biorefineries. Biotechnol Biofuels 7(1):101–115
He MX, Wu B, Shui ZX, Hu QC, Wang WG, Tan FR, Tang XY, Zhu QL, Pan K, Li Q, Su XH (2012b) Transcriptome profiling of Zymomonas mobilis under ethonal stress. Biotechnol Biofuels 5:75–84
Hong SH, Lee J, Wood TK (2010a) Engineering global regulator Hha of Escherichia coli to control biofilm dispersal. Microb Biotechnol 3(6):717–728
Hong SH, Wang X, Wood TK (2010b) Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H-NS of Escherichia coli. Microb Biotechnol 3(3):344–356
Hristozova T, Gotcheva V, Tzvetkova B, Paskaleva D, Angelov A (2008) Effect of furfural on nitrogen assimilating enzymes of the lactose utilizing yeasts Candida blankii 35 and Candida pseudotropicalis 11. Enzym Microb Technol 43(3):284–288
Joachimsthal E, Rogers P (2000) Characterization of a high-productivity recombinant strain of Zymomonas mobilis for ethanol production from glucose/xylose mixtures. In: Finkelstein M, Davison B (eds) Twenty-first symposium on biotechnology for fuels and chemicals. Applied Biochemistry and Biotechnology. Humana Press, pp 343–356
Katahira S, Mizuike A, Fukuda H, Kondo A (2006) Ethanol fermentation from lignocellulosic hydrolysate by a recombinant xylose- and cellooligosaccharide-assimilating yeast strain. Appl Microbiol Biotechnol 72(6):1136–1143
Khan QA, Shamsi FA, Hadi S (1995) Mutagenicity of furfural in plasmid DNA. Cancer Lett 89(1):95–99
Klein-Marcuschamer D, Stephanopoulos G (2008) Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Proc Natl Acad Sci U S A 105(7):2319–2324
Lee JY, Sung BH, Yu BJ, Lee JH, Lee SH, Kim MS, Koob MD, Kim SC (2008) Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli. Nucleic Acids Res 36(16):102–111
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25(4):402–408
Luo LH, Seo PS, Seo JW, Heo SY, Kim DH, Kim CH (2009) Improved ethanol tolerance in Escherichia coli by changing the cellular fatty acids composition through genetic manipulation. Biotechnol Lett 31(12):1867–1871
Kovach ME, Elzer PH, Steven Hill D, Robertson GT, Farris MA, II Martin Roop R, Peterson KM (1995) Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175–176
Mackenzie KF, Eddy CK, Ingram LO (1989) Modulation of alcohol dehydrogenase isoenzyme levels in Zymomonas mobilis by iron and zinc. J Bacteriol 171(2):1063–1068
Miller EN, Jarboe LR, Turner PC, Pharkya P, Yomano LP, York SW, Nunn D, Shanmugam K, Ingram LO (2009) Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol 75(19):6132–6141
NCBI conserved domain (2015) Search for conserved domains within a protein or coding nucleotide sequence.
Neale AD, Scopes RK, Kelly JM, Wettenhall REH (1986) The two alcohol dehydrogenases of Zymomonas mobilis purification by differential dye ligand chromatography, molecular characterisation and physiological roles. Eur J Biochem 154:119–124
Nichols NN, Hector RE, Saha BC, Frazer SE, Kennedy GJ (2014) Biological abatement of inhibitors in rice hull hydrolyzate and fermentation to ethanol using conventional and engineered microbes. Biomass Bioenergy 67:79–88
Owens JT, Miyake R, Murakami K, Chmura AJ, Fujita N, Ishihama A, Meares CF (1998) Mapping the σ70 subunit contact sites on Escherichia coli RNA polymerase with a σ70-conjugated chemical protease. Proc Natl Acad Sci U S A 95(11):6021–6026
Parawira W, Tekere M (2011) Biotechnological strategies to overcome inhibitors in lignocellulose hydrolysates for ethanol production: review. Crit Rev Biotechnol 31(1):20–31
Park KS, Lee DK, Lee H, Lee Y, Jang YS, Kim YH, Yang HY, Lee SI, Seol W, Kim JS (2003) Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors. Nat Biotechnol 21(10):1208–1214
Rogers PL, Jeon YJ, Lee KJ, Lawford HG (2007) Zymomonas mobilis for fuel ethanol and higher value products. Adv Biochem Eng Biotechnol 108:263–288
Sharma UK, Ravishankar S, Shandil RK, Praveen P, Balganesh T (1999) Study of the interaction between bacteriophage T4 asiA and Escherichia coli ς70, using the yeast two-hybrid system: neutralization of asiA toxicity to E. coli cells by coexpression of a truncated ς70 fragment. J Bacteriol 181(18):5855–5859
Shi DJ, Wang CL, Wang KM (2009) Genome shuffling to improve thermotolerance, ethanol tolerance and ethanol productivity of Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 36(1):139–147
Sridhar M, Kiran Sree N, Venkateswar Rao L (2002) Effect of UV radiation on thermotolerance, ethanol tolerance and osmotolerance of Saccharomyces cerevisiae VS1 and VS3 strains. Bioresour Technol 83(3):199–202
Tao F, Miao JY, Shi GY, Zhang KC (2005) Ethanol fermentation by an acid-tolerant Zymomonas mobilis under non-sterilized condition. Process Biochem 40(1):183–187
Tokiwa Y, Calabia BP (2008) Biological production of functional chemicals from renewable resources. Can J Chem 86(6):548–555
Uppugundla N, da Costa Sousa L, Chundawat SPS, Yu X, Simmons B, Singh S, Gao X, Kumar R, Wyman CE, Dale BE, Balan V (2014) A comparative study of ethanol production using dilute acid, ionic liquid and AFEX™ pretreated corn stover. Biotechnol Biofuels 7:72–86
Wang X, Yomano LP, Lee JY, York SW, Zheng H, Mullinnix MT, Shanmugam K, Ingram LO (2013) Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals. Proc Natl Acad Sci U S A 110(10):4021–4026
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 (2013) Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. PLoS ONE 8(7):68886–68899
Zhang Y, Ma R, Zhao Z, Zhou Z, Lu W, Zhang W, Chen M (2010) irrE, an exogenous gene from Deinococcus radiodurans, improves the growth of and ethanol production by a Zymomonas mobilis strain under ethanol and acid stresses. J Microbiol Biotechnol 20(7):1156–1162
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This work was supported by Applied Basic Research Programs of Sichuan province (NO. 2014JY0065) and partially supported by Youth Science and Technology Foundation of Sichuan Province in China (Grant NO: 2015JQ0047). Open Funds of Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin (Tarim University, BRZD1403). Open Funds of State Key Laboratory of Microbial Technology (Shandong University, M2013-07), Open Funds of Key Laboratory of Microbial Resources Collection and Preservation (Ministry of Agriculture, MOA, 2013),
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Tan, FR., Dai, LC., Wu, B. et al. Improving furfural tolerance of Zymomonas mobilis by rewiring a sigma factor RpoD protein. Appl Microbiol Biotechnol 99, 5363–5371 (2015). https://doi.org/10.1007/s00253-015-6577-2
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DOI: https://doi.org/10.1007/s00253-015-6577-2