微生物遗传多样性的挖掘和代谢工程应用
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摘要
随着近年来系统生物学研究的深入,微生物的基因组、转录组、蛋白组及代谢组等不同层次的组学信息不断增加。我国具有丰富的微生物多样性,但目前对多样性的研究大多集中在物种多样性及生态多样性方面,对微生物菌株水平遗传多样性的研究还刚刚起步。以酿酒酵母和链霉菌为例,结合本课题组的成果,总结了近年来利用其基因组序列及转录组蛋白质等功能基因组信息,开发利用其遗传多样性的研究进展。在工业酿酒酵母中发现了多个独特的功能基因,包括絮凝基因及与环境胁迫耐性相关的调节蛋白基因,还发现了独特的启动子序列。此外,在海洋放线菌基因组中也发现了独特的调节基因。对微生物遗传多样性的挖掘利用,不仅有助于深入理解微生物不同菌株中独特的调节方式,也为微生物的代谢工程改造提供了大量新的可利用的遗传组件。
With the in-depth studies of systems bology,multi-omics( genomics,transcriptomics,proteomics andmetabolomics) data is increasingly emerging. It has been well studied and accepted that there is a vast diversity of microorganisms in China,however,so far most studies focus on the species diversity and its ecological implication,there is still few studies focusing on the genetic diversity of microorganisms. In this review,brewing yeast strains of Saccharomyces cerevisiae and streptomycetes were used as examples,and research progress in the exploration of the genetic diversity of genes responsible for yeast flocculation and stress tolerance,as well as special promoter sequence in industrial yeast strains was summarized. In addition,the effect of regulatory protein identified from marine actinobacteria on heterologous antibiotic production was also presented. Exploration and utilization of the genetic diversity of microorganisms provides basis for not only the understanding of specific regulatory mode in different strains of microorganisms,but also the metabolic engineering of microorganisms using diverse genetic elements.
With the in-depth studies of systems bology,multi-omics( genomics,transcriptomics,proteomics andmetabolomics) data is increasingly emerging. It has been well studied and accepted that there is a vast diversity of microorganisms in China,however,so far most studies focus on the species diversity and its ecological implication,there is still few studies focusing on the genetic diversity of microorganisms. In this review,brewing yeast strains of Saccharomyces cerevisiae and streptomycetes were used as examples,and research progress in the exploration of the genetic diversity of genes responsible for yeast flocculation and stress tolerance,as well as special promoter sequence in industrial yeast strains was summarized. In addition,the effect of regulatory protein identified from marine actinobacteria on heterologous antibiotic production was also presented. Exploration and utilization of the genetic diversity of microorganisms provides basis for not only the understanding of specific regulatory mode in different strains of microorganisms,but also the metabolic engineering of microorganisms using diverse genetic elements.
引文
[1]左颀,张明明,程诚,等.不同宿主木糖重组酿酒酵母的混合糖代谢比较[J].微生物学通报,2014,7:1270-1277.
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[12]彭炳银,陈晓,沈煜,等.不同启动子控制下木酮糖激酶的差异表达及其对酿酒酵母木糖代谢的影响[J].微生物学报,2011,51(7):914-922.
[13]刘秀颖,何秀萍,卢莹,等.基于基因组DNA诱变的遗传重组改造乙醇工业酵母的耐热性及发酵性能[J].生物工程学报,2011,21(7):1049-1056.
[14]张晓阳,杜风光,池小琴,等.代谢工程与全基因组重组构建酿酒酵母抗逆高产乙醇菌[J].中国生物工程杂志,2011,31(7):91-97.
[15]赵心清,姜如娇,李宁,等.利用SPT3的定向进化提高工业酿酒酵母乙醇耐受性[J].生物工程学报,2010,26:159-164.
[16]李倩,赵心清,Kim J.,等.三种选育高乙醇耐受性工业酿酒酵母方法的比较[J].生物工程学报,2013,29:1672-1675.
[17]赵心清,白凤武,李寅.系统生物学和合成生物学研究在生物燃料生产菌株改造中的应用[J].生物工程学报,2010,26:880-887.
[18]Ma C,Wei XW,Sun CH,et al.Improvement of acetic acid tolerance of Saccharomyces cerevisiae using a zinc-finger-based artificial transcription factor and identification of novel genes involved in acetic acid tolerance[J].Appl Microbiol Biotechnol,2015.In press.
[19]魏小文,马翠,熊亮,等.过表达液泡蛋白酶B基因提高酿酒酵母高温乙醇发酵效率[J].微生物学通报,2015,出版中.
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[21]Hirsch HH,Schiffer HH,Wolf DH.Biogenesis of the yeast vacuole(lysosome)Proteinase yscB contributes molecularly and kinetically to vacuolar hydrolase-precursor maturation[J].European J Biochem,1992,207(3):867-876.
[22]Chiang HL,Schekman R,Hamamoto S.Selective uptake of cytosolic,peroxisomal,and plasma membrane proteins into the yeast lysosome for degradation[J].J Biol Chem,1996,271(17):9934-9941.
[23]Van Den Hazel HB,Kielland-Brandt MC,Winther JR.Review:biosynthesis and function of yeast vacuolar proteases[J].Yeast,1996,12(1):1-16.
[24]Wan C,Zhang MM,Fang Q,et al.Impact of zinc sulfate addition on dynamic metabolic profiling of Saccharomyces cerevisiae subjected to long term acetic acid stress treatment and identification of key metabolites involved in antioxidant effect of zinc[J].Metallomics,2015,7:322-332.
[25]陈亮宇,王玉梅,赵心清.基因组挖掘技术在海洋放线菌天然产物研究开发中的应用及展望[J].微生物学通报,2013,40:1896-1908.
[26]Zhao XQ,Li WJ,Jiao WC,et al.Streptomyces xinghaiensis sp.nov.,a new marine actinomycete derived from a marine sediment sample[J].Int J Syst Evol Microbiol,2009,59:2870-2874.
[27]Chen C,Feng WW,Qin S,et al.Streptomyces xiaopingdaonensis sp.nov.,a novel marine actinomycete isolated from the sediment of Xiaopingdao in Dalian,China[J].Antonie van Leeuwenhoek,2015,107(2):511-518.
[28]Zhao XQ,Yang TH.Draft genome sequence of the marine derived actinomycete Streptomyces xinghaiensis NRRL B24674T[J].J Bacteriol,2011,193:5543.
[29]Zhao XQ,Geng X,Chen C,et al.Draft genome sequence of the marine actinomycete Streptomyces sulphureus L180,isolated from marine sediment[J].J Bacteriol,2012,194:4482.
[30]Chen C,Zhao XQ,Jin YY,et al.Effect of overexpression of endogenous and exogenous Streptomyces antibiotic regulatory proteins on tacrolimus(FK506)production in Streptomyces sp.KCCM 11116P[J].RSC Adv,2015,5:15756-15762.
[2]RomaníA,Pereira F,Johansson B,et al.Metabolic engineering of Saccharomyces cerevisiae ethanol strains PE-2 and CAT-1for efficient lignocellulosic fermentation[J].Bioresour Technol,2015,179:150-158.
[3]Sato TK,Liu T,Parreiras LS,et al.Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass[J].Appl Environ Microbiol,2014,80(2):540-554.
[4]Wang QM,Liu WQ,Liti G,et al.Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity[J].Mol Ecol,2012,21:5404-5417.
[5]苟梓希,李云成,谢采芸,等.工业酿酒酵母菌株KF-7对发酵抑制物的耐受性评价[J].应用与环境生物学报,2015,21(1):1-12.
[6]Zhao XQ,Bai FW.Mechanism of yeast ethanol tolerance and its manipulation for efficient fuel ethanol production[J].J Biotechnol,2009,27:849-856.
[7]Zhao XQ,Bai FW.Yeast flocculation:new story in fuel ethanol production[J].Biotechnol Adv,2009,29:849-856.
[8]Zhao XQ,Li Q,He L,et al.Exploration of a natural reservoir of flocculating genes from various Saccharomyces cerevisiae strains and improved ethanol fermentation using stable genetical-ly engineered flocculating yeast strains[J].Process Biochem,2012,47(11):1612-1619.
[9]He LY,Zhao XQ,Bai FW.Engineering industrial Saccharomyces cerevisiae strain with the FLO1-derivative gene isolated from the flocculating yeast SPSC01 for constitutive flocculation and fuel ethanol production[J].Appl Energy,2012,100:33-40.
[10]Li Q,Zhao XQ,Chang AK,et al.Ethanol-induced yeast flocculation directed by the promoter of TPS1encoding trehalose-6-phosphate synthase 1 for efficient ethanol production[J].Met Eng,2012,14:1-8.
[11]Schüller C,Brewster JL,Alexander MR,et al.The HOG pathway controls osmotic regulation of transcription via the stress response element(STRE)of the Saccharomyces cerevisiae CTT1gene[J].EMBO J,1994,13(18):4382-4389.
[12]彭炳银,陈晓,沈煜,等.不同启动子控制下木酮糖激酶的差异表达及其对酿酒酵母木糖代谢的影响[J].微生物学报,2011,51(7):914-922.
[13]刘秀颖,何秀萍,卢莹,等.基于基因组DNA诱变的遗传重组改造乙醇工业酵母的耐热性及发酵性能[J].生物工程学报,2011,21(7):1049-1056.
[14]张晓阳,杜风光,池小琴,等.代谢工程与全基因组重组构建酿酒酵母抗逆高产乙醇菌[J].中国生物工程杂志,2011,31(7):91-97.
[15]赵心清,姜如娇,李宁,等.利用SPT3的定向进化提高工业酿酒酵母乙醇耐受性[J].生物工程学报,2010,26:159-164.
[16]李倩,赵心清,Kim J.,等.三种选育高乙醇耐受性工业酿酒酵母方法的比较[J].生物工程学报,2013,29:1672-1675.
[17]赵心清,白凤武,李寅.系统生物学和合成生物学研究在生物燃料生产菌株改造中的应用[J].生物工程学报,2010,26:880-887.
[18]Ma C,Wei XW,Sun CH,et al.Improvement of acetic acid tolerance of Saccharomyces cerevisiae using a zinc-finger-based artificial transcription factor and identification of novel genes involved in acetic acid tolerance[J].Appl Microbiol Biotechnol,2015.In press.
[19]魏小文,马翠,熊亮,等.过表达液泡蛋白酶B基因提高酿酒酵母高温乙醇发酵效率[J].微生物学通报,2015,出版中.
[20]Wolf DH,Ehmann C.Studies on a proteinase B mutant of yeast[J].European J Biochem,1979,98:375-384.
[21]Hirsch HH,Schiffer HH,Wolf DH.Biogenesis of the yeast vacuole(lysosome)Proteinase yscB contributes molecularly and kinetically to vacuolar hydrolase-precursor maturation[J].European J Biochem,1992,207(3):867-876.
[22]Chiang HL,Schekman R,Hamamoto S.Selective uptake of cytosolic,peroxisomal,and plasma membrane proteins into the yeast lysosome for degradation[J].J Biol Chem,1996,271(17):9934-9941.
[23]Van Den Hazel HB,Kielland-Brandt MC,Winther JR.Review:biosynthesis and function of yeast vacuolar proteases[J].Yeast,1996,12(1):1-16.
[24]Wan C,Zhang MM,Fang Q,et al.Impact of zinc sulfate addition on dynamic metabolic profiling of Saccharomyces cerevisiae subjected to long term acetic acid stress treatment and identification of key metabolites involved in antioxidant effect of zinc[J].Metallomics,2015,7:322-332.
[25]陈亮宇,王玉梅,赵心清.基因组挖掘技术在海洋放线菌天然产物研究开发中的应用及展望[J].微生物学通报,2013,40:1896-1908.
[26]Zhao XQ,Li WJ,Jiao WC,et al.Streptomyces xinghaiensis sp.nov.,a new marine actinomycete derived from a marine sediment sample[J].Int J Syst Evol Microbiol,2009,59:2870-2874.
[27]Chen C,Feng WW,Qin S,et al.Streptomyces xiaopingdaonensis sp.nov.,a novel marine actinomycete isolated from the sediment of Xiaopingdao in Dalian,China[J].Antonie van Leeuwenhoek,2015,107(2):511-518.
[28]Zhao XQ,Yang TH.Draft genome sequence of the marine derived actinomycete Streptomyces xinghaiensis NRRL B24674T[J].J Bacteriol,2011,193:5543.
[29]Zhao XQ,Geng X,Chen C,et al.Draft genome sequence of the marine actinomycete Streptomyces sulphureus L180,isolated from marine sediment[J].J Bacteriol,2012,194:4482.
[30]Chen C,Zhao XQ,Jin YY,et al.Effect of overexpression of endogenous and exogenous Streptomyces antibiotic regulatory proteins on tacrolimus(FK506)production in Streptomyces sp.KCCM 11116P[J].RSC Adv,2015,5:15756-15762.