Research Progress for Genetic Modification of Butanol-producing Clostridia

doi:10.13560/j.cnki.biotech.bull.1985.2017.01.011

Abstract

Abstract: Butanol-producing Clostridia as butanol fermentation strains have been studied frequently in recent years. As a new renewable energy sources,butanol has obviously more advantages than ethanol. Therefore,it is of great significance to study gene modification of butanol-producing Clostridia. In this review,from three aspects of key genes,glycolytic pathway,and butanol tolerance,we introduced the latest research progress on gene modification of butanol-producing Clostridia. Meanwhile,we discussed the issues in the current research,and put forward suggestions on how to improve the butanol yield,aiming at providing some new ideas for the researchers.

Key words: butanol-producing Clostridia, ABE fermentation, EMP, gene overexpress, gene inactivation, butanol tolerance

ZHANG Chao, WANG Yi-qiang, WANG Qi-ye, HUANG Rui-chun, MI Xiao-qin. Research Progress for Genetic Modification of Butanol-producing Clostridia[J]. Biotechnology Bulletin, 2017, 33(1): 106-113.

References

[1] Moon HG, Jang Y, Cho C, et al. One hundred years of clostridial butanol fermentation[J]. Fems Microbiology Letters, 2016, 363：3-18.
[2] Berezina OV, Zakharova NV, Yarotsky CV, et al. Microbial producers of butanol[J]. Applied Biochemistry And Microbiology, 2012, 48（7）：625-638.
[3] Cho C, Jang YS, Moon HG, et al. Metabolic engineering of clostridia for the production of chemicals[J]. Biofuels, Bioproducts and Biorefining, 2015, 9：211-225.
[4] Ding J, Xu G, Han R, et al. Biobutanol production from corn stover hydrolysate pretreated with recycled ionic liquid by Clostridium saccharobutylicum DSM 13864[J]. Bioresource Technology, 2016, 199：228-234.
[5] Jin C, Yao M, Liu H, et al. Progress in the production and application of n-butanol as a biofuel[J]. Renewable and Sustainable Energy Reviews, 2011, 15（8）：4080-4106.
[6] Uyttebroek M, Van Hecke W, Vanbroekhoven K. Sustainability metrics of 1-butanol[J]. Catalysis Today, 2015, 239：7-10.
[7] Wang QY, Zhang C, Yao R, et al. Butanol Fermentation by Clostridium saccharobutylicum based on poplar wood[J]. Biores-ources, 2015, 10（3）：5395-5406.
[8] 钟洁, 王义强, 华涟滩, 等. 基于杨木纤维发酵产丁醇工艺条件的研究[J]. 中南林业科技大学学报, 2015（7）：125-130.
[9] 彭牡丹, 王义强, 王启业, 等. 糖丁酸梭状芽孢杆菌BAA-117利用不同碳源发酵产燃料丁醇的研究[J]. 可再生能源, 2014（11）：1703-1709.
[10] Li H, Zhang Q, Yu X, et al. Enhancement of butanol production in Clostridium acetobutylicum SE25 through accelerating phase shift by different phases pH regulation from cassava flour[J]. Bioresource Technology, 2016, 201：148-155.
[11] Zheng J, Tashiro Y, Wang Q, et al. Recent advances to improve fermentative butanol production：Genetic engineering and fermentation technology[J]. Journal of Bioscience and Bioengineering, 2015, 119（1）：1-9.
[12] 毛绍名, 章怀云. 丙酮丁醇梭菌高耐丁醇突变株的选育及其生理特性的研究[J]. 中南林业科技大学学报, 2012（8）：103-107.
[13] 王义强, 王启业, 华连滩, 等. 高产丁醇菌株诱变选育及发酵研究[J]. 中南林业科技大学学报, 2015（10）：120-126.
[14] Xu M, Zhao J, Yu L, et al. Engineering Clostridium acetobutylicum with a histidine kinase knockout for enhanced n-butanol tolerance and production[J]. Applied Microbiology and Biotechnol, 2015, 99（2）：1011-1022.
[15] Ehsaan M, Kuit W, Zhang Y, et al. Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824[J]. Biotechnology for Biofuels, 2016, 9（1）：4-24.
[16] 顾阳, 杨晟, 姜卫红. 产溶剂梭菌分子遗传操作技术研究进展[J]. 生物工程学报, 2013（8）：1133-1145.
[17] Lutke-Eversloh T, Bahl H. Metabolic engineering of Clostridium acetobutylicum：recent advances to improve butanol production[J]. Current Opinion in Biotechnology, 2011, 22（5）：634-647.
[18] Grimmler C, Janssen H, Krauβe D, et al. Genome-wide gene expression analysis of the switch between acidogenesis and solventogenesis in continuous cultures ofClostridium acetobutylicum[J]. Journal of Molecular Microbiology and Biotechnology, 2011, 20（1）：1-15.
[19] Lee JW, Na D, Park JM, et al. Systems metabolic engineering of microorganisms for natural and non-natural chemicals[J]. Nature Chemical Biology, 2012, 8（6）：536-546.
[20] Ventura JS, Hu H, Jahng D. Enhanced butanol production in Clostridium acetobutylicum ATCC 824 by double overexpression of 6-phosphofructokinase and pyruvate kinase genes[J]. Applied Microbiology and Biotechnology, 2013, 97（16）：7505-7516.
[21] Jiang Y, Xu C, Dong F, et al. Disruption of the acetoacetate decarboxylase gene in solvent-producing Clostridium acetobutylicum increases the butanol ratio[J]. Metabolic Engineering, 2009, 11（4-5）：284-291.
[22] Tummala SB, Welker NE, Papoutsakis ET. Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum[J]. Journal of Bacteriology, 2003, 185（6）：1923-1934.
[23] Hönicke D, Lütke-Eversloh T, Liu Z, et al. Chemostat cultivation and transcriptional analyses of Clostridium acetobutylicum mutants with defects in the acid and acetone biosynthetic pathways[J]. Applied Microbiology and Biotechnology, 2014, 98（23）：9777-9794.
[24] Cooksley CM, Zhang Y, Wang H, et al. Targeted mutagenesis of the Clostridium acetobutylicum acetone-butanol-ethanol fermentation pathway[J]. Metabolic Engineering, 2012, 14（6）：630-641.
[25] Kuit W, Minton NP, López-Contreras AM, et al. Disruption of the acetate kinase（ack）gene of Clostridium acetobutylicum results in delayed acetate production[J]. Applied Microbiology and Biotechnology, 2012, 94（3）：729-741.
[26] Jang YS, Lee JY, Lee J, et al. Enhanced butanol production obtained by reinforcing the direct butanol-forming route in Clostridium acetobutylicum[J]. Mcrobiology, 2012, 3（5）：e312-e314.
[27] Lehmann D, Hönicke D, Ehrenreich A, et al. Modifying the product pattern of Clostridium acetobutylicum[J]. Applied Microbiology and Biotechnology, 2012, 94（3）：743-754.
[28] Wang Y, Li X, Milne CB, et al. Development of a gene knockout system using mobile group II introns（targetron）and genetic disruption of acid production pathways in Clostridium beijerinckii[J]. Applied and Environmental Microbiology, 2013, 79（19）：5853-5863.
[29] Shao L, Hu S, Yang Y, et al. Targeted gene disruption by use of a group II intron（targetron）vector in Clostridium acetobutylicum[J]. Cell Res, 2007, 17（11）：963-965.
[30] Harris LM, Desai RP, Welker NE, et al. Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant：need for new phenomenological models for solventogenesis and butanol inhibition?[J]. Biotechnology and Bioengineering, 2000, 67（1）：1-11.
[31] Harris LM, Blank L, Desai RP, et al. Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivatedsolR gene[J]. Journal of Industrial Microbiology and Biotechnology, 2001, 27（5）：322-328.
[32] Lehmann D, Radomski N, Lütke-Eversloh T. New insights into the butyric acid metabolism of Clostridium acetobutylicum[J]. Applied Microbiology and Biotechnology, 2012, 96（5）：1325-1339.
[33] Liu J, Guo T, Wang D, et al. Enhanced butanol production by increasing NADH and ATP levels in Clostridium beijerinckii NCIMB 8052 by insertional inactivation ofCbei_4110[J]. Applied Microbiology and Biotechnology, 2016, 100（11）：4985-4996.
[34] Tomas CA, Beamish J, Papoutsakis ET. Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum[J]. Journal of Bacteriology, 2004, 186（7）：2006-2018.
[35] Mann MS, Dragovic Z, Schirrmacher G, et al. Over-expression of stress protein-encoding genes helps Clostridium acetobutylicum to rapidly adapt to butanol stress[J]. Biotechnology Letters, 2012, 34（9）：1643-1649.
[36] Jia K, Zhang Y, Li Y. Identification and characterization of two functionally unknown genes involved in butanol tolerance of Clostridium acetobutylicum[J]. PLoS One, 2012, 7（6）：e38815.
[37] Nair RV, Green EM, Watson DE, et al. Regulation of the sol locus genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 by a putative transcriptional repressor[J]. Journal of Bacteriology, 1999, 181（1）：319-330.
[38] Harris LM, Welker NE, Papoutsakis ET. Northern, morphological, and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824[J]. Journal of Bacteriology, 2002, 184（13）：3586-3597.
[39] Scotcher MC, Bennett GN. SpoIIE regulates sporulation but does not directly affect solventogenesis in Clostridium acetobutylicum ATCC 824[J]. Journal of Bacteriology, 2005, 187（6）：1930-1936.
[40] Dong H, Zhang Y, Dai Z, et al. Engineering Clostridium Strain to Accept Unmethylated DNA[J]. PLoS One, 2010, 5：e90382.
[41] Truffaut N, Hubert J, Reysset G. Construction of shuttle vectors useful for transforming Clostridium acetobutylicum[J]. Fems Microbiol Letters, 1989, 49（1）：15-20.
[42] Mermelstein LD, Papoutsakis ET. In vivo methylation in Escherichia coli by the Bacillus subtilis phage phi 3T I methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824[J]. Applied and Environmental Microbiology, 1993, 59（4）：1077-1081.
[43] Croux C, Nguyen N, Lee J, et al. Construction of a restriction-less, marker-less mutant useful for functional genomic and metabolic engineering of the biofuel producer Clostridium acetobutylicum[J]. Biotechnology for Biofuels, 2016, 9（1）：23.
[44] Green EM, Bennett GN. Genetic manipulation of acid and solvent formation in clostridium acetobutylicum ATCC 824[J]. Biotechnology and Bioengineering, 1998, 58（2-3）：215-221.
[45] Desai RP, Papoutsakis ET. Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum[J]. Applied and Environmental Microbiology, 1999, 65（3）：936-945.
[46] Tummala SB, Junne SG, Papoutsakis ET. Antisense RNA downregulation of coenzyme A transferase combined with alcohol-aldehyde dehydrogenase overexpression leads to predominantly alcohologenic Clostridium acetobutylicum fermentations[J]. Journal of Bacteriology, 2003, 185（12）：3644-3653.
[47] Al-Hinai MA, Fast AG, Papoutsakis ET. Novel system for efficient isolation of Clostridium double-crossover allelic exchange mutants enabling markerless chromosomal gene deletions and DNA integration[J]. Applied And Environmental Microbiology, 2012, 78（22）：8112-8121.
[48] Soucaille P, Figge R, Croux C. Process for chromosomal integration and DNA sequence replacement in Clostridia[Z]. Google Patents, 2014.
[49] Shao L, Hu S, Yang Y, et al. Targeted gene disruption by use of a group II intron（targetron）vector in Clostridium acetobutylicum[J]. Cell Research, 2007, 17（11）：963-965.
[50] Heap JT, Pennington OJ, Cartman ST, et al. The ClosTron：a universal gene knock-out system for the genus Clostridium[J]. Journal of Microbiological Methods, 2007, 70（3）：452-464.
[51] Liao C, Seo S, Lu T. System-level modeling of acetone-butanol-ethanol fermentation[J]. Fems Microbiology Letters, 2016, 363（9）：w74.
[52] Wang Y, Li X, Blaschek HP. Effects of supplementary butyrate on butanol production and the metabolic switch in Clostridium beijerinckii NCIMB 8052：genome-wide transcriptional analysis with RNA-Seq[J]. Biotechnology for Biofuels, 2013, 6（1）：138.
[53] Mao S, Luo Y, Zhang T, et al. Proteome reference map and comparative proteomic analysis between a wild type Clostridium acetobutylicum DSM 1731 and its mutant with enhanced butanol tolerance and butanol yield[J]. Journal of Proteome Research, 2010, 9（6）：3046-3061.
[54] Liao C, Seo S, Celik V, et al. Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum[J]. Proceedings of the National Academy of Sciences, 2015, 112（27）：8505-8510.
[55] Ng CY, Takahashi K, Liu Z. Isolation, characterization, and optimization of an aerobic butanol-producing bacterium from Singapore[J]. Biotechnology And Applied Biochemistry, 2016, 63（1）：86-91.