基因组重排技术在微生物菌种改良中的应用
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摘要
基因组重排作为一种快速改良细胞表型的方法,不仅能有效提高微生物合成活性产物的能力,也能提高微生物的耐受性和对底物的利用率,还能激活沉默基因的表达产生新的化合物.本文综合论述了基因组重排的概况和基因组重排的过程,并讨论了基因组重排对微生物表型改良的应用以及对基因组重排的展望.
Genome shuffling is a rapid method to improve cell phenotypes.This technology can effectively enhance the biosynthesis capacity of active compounds by microorganisms,improve the tolerance and substrate uptake,and even activate silent gene expression and produce new compounds.In this review,we summarize the process of genome shuffling,discuss the application of genome shuffling for phenotype improvement and give its development trends in the future.
Genome shuffling is a rapid method to improve cell phenotypes.This technology can effectively enhance the biosynthesis capacity of active compounds by microorganisms,improve the tolerance and substrate uptake,and even activate silent gene expression and produce new compounds.In this review,we summarize the process of genome shuffling,discuss the application of genome shuffling for phenotype improvement and give its development trends in the future.
引文
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[32]YU L,PEI X L,LEI T,et al.Genome shuffling enhanced L-lactic acid production by improving glucose tolerance of Lactobacillus rhamnosus[J].Journal of Biotechnology,2008,134(12):154-159.
[33]DEGERANDO H M,GUICHARD F F,RUDANT L,et al.Improving isopropanol tolerance and production of Clostridium beijerinckii DSM 6423by random mutagenesis and genome shuffling[J].Applied Genetics and Molecular Biotechnology,2016,100:5427-5436.
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[35]郑连宝,裘娟萍.基因组重排技术在开发新代谢产物中的应用[J].中国生物工程杂志,2012,32(3):100-105.ZHEN L B,QIU J P.The application of genome shuffling in developing new metabolites[J].China Biotechnology,2012,32(3):100-105.
[36]WANG M Z,LIU S S,LI Y Y,et al.Protoplast mutation and genome shuffling induce the endophytic fungus Tuberculariasp.TF5to produce new compounds[J].Current Microbiology,2010,61:254-260.
[37]DAI M H,COPLEY S D.Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723[J].Applied and Environmental Microbiology,2004,70:2391-2397.
[38]KUMAR M.Improving polycyclic aromatic hydrocarbons degradation by genome shuffling[J].Asian Journal of Microbiology Biotechnology and Environmental Science,2007,9(1):145-149.
[39]LYU X A,JIN Y Y,LI Y D,et al.Genome shuffling of Streptomyces viridochromogenes for improved production of avilamycin[J].Applied and Environmental Microbiology,2013,97:641-648.
[40]WANG L,CHEN X S,WU G Y,et al.Genome shuffling and gentamicin-resistance to improveε-Poly-L-lysine productivity of Streptomyces albulus W-156[J].Applied Biochemistry Biotechnology,2016,180:1601-1617.
[41]WANG Y H,LI Y,PEI X L,et al.Genome-shuffling improved acid tolerance and L-lactic acid volumetric productivity in Lactobacillus rhamnosus[J].Journal of Biotechnology,2007,129:510-515.
[42]周扬,薛正莲,夏俊邢,等.常压室温等离子体(ARTP)诱变及高通量筛选那西肽高产菌株[J].工业微生物,2015,45(2):7-12.ZHOU Y,XUE Z L,XIA J X,et al.Screening strains of high-yield nosiheptide production by Atmospheric and Room Temperature Plasma(ARTP)and high throughput screening[J].Industrial Microbiology,2015,45(2):7-12.
[43]HARNER N K,WEN X,BAJWA P K.Genetic improvement of native xylose-fermenting yeasts for ethanol production[J].Journal of Industrial Microbiology&Biotechnology,2015,42:1-20.
[2]STEMMER W P C.Rapid evolution of a protein in vitro by DNA shuffling[J].Nature,1994,370(6488):389-391.
[3]STEMMER W P C,CRAMERI A,MINSHULL I.Molecular evolution of genes and pathways by DNA shuffling[J].The Faseb Journal,1997,11(9):1559.
[4]CRAMERI A,RAILLARD S A,BERMUDEZ E,et al.DNA shuffling of a family of genes from diverse species accelerates directed evolution[J].Nature,1998,391(6664):288-291.
[5]CRAMERI A,DAWES G,RODRIGUEZ J,et al.Molecular evolution of an arsenate detoxification pathway by DNA shuffling[J].Nature Biotechnology,1997,15(5):4436-4438.
[6]CHRISTIANS F C,SCAPOZZA L,CRAMERI A,et al.Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling[J].Nature Biotechnology,1999,17(3):259-264.
[7]CHANG C J,CHEN T T,COX B W,et al.Evolution of a cytokine using DNA family shuffling[J].Nature Biotechnology,1999,17(8):793-797.
[8]POWELL S K,KALOSS M A,PINKSTAFF A,et al.Breeding of retroviruses by DNA shuffling for improved stability and processing yields[J].Nature Biotechnology,2000,18(12):1279-1282.
[9]STEPHANOPOULOS G.Metabolic engineering by genome shuffling[J].Nature Biotechnology,2002,20:666-668.
[10]BAOLEY J E.Toward a science of metabolic engineering[J].Science,1991,252:1668-1675.
[11]STEPHANOPOULOS G,VALLINO J J.Network rigidity and metabolic engineering in metabolite overproduction[J].Science,1991,252(5013):1675-1681.
[12]李丹婷,袁小枫,申屠旭萍,等.淀粉酶产色链霉菌1628发酵培养基及发酵条件的优化[J].中国计量学院学报,2015,26(1):99-104.LI D T,YUAN X F,SHENTU X P,et al.Optimization of medium and fermentation conditions of Streptomyces distatochromogenes[J].Journal of China University of Metrology,2015,26(1):99-104.
[13]DELCARDAYRE S,TOBIN M B,STEMMER W P C,et al.Evolution of whole cells and organisms by recursive sequence recombination:US,US 6335198B1[P].(2004-04-06)[2018-02-09].
[14]WANG Z G,WU X H,FRIENDBERG E C.Nucleotide excision repair of DNA by human cell extracts is suppressed in reconstituted nucleosomes[J].Journal of Biological Chemistry,1991,266:22472-22478.
[15]CROOK N,ALPER H S.Classical Strain Improvement[M].Hoboken:Wiley,2013:1-33.
[16]CUPPLES C G,MILLER J H.A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions[J].Proceedings of the National Academy of Sciences of the United States of America,1989,86:5345-5349.
[17]HAMPSEY M.A tester system for detecting each of the six base-pair substitutions in Saccharomyces cerevisiae by selecting for an essential cysteine in iso-1-cytochrome-c[J].Genetics,1991,128(1):59-67.
[18]LI S,CHEN X,DONG C,et al.Combining genome shuffling and interspecific hybridization among Streptomyces improvedε-poly-L-lysine production[J].Applied Biochemistry and Biotechnology,2013,169:338-350.
[19]WANG Q L,ZHANG D,LI Y D,et al.Genome shuffling and ribosome engineering of Streptomyces actuosus for high-yield nosiheptide production[J].Applied Biochemistry Biotechnology,2014,173:1553-1563.
[20]HOPWOOD D A,WRIGHT H M.Bacterial protoplast fusion:recombination in fused protoplasts of Streptomyces coelicolor[J].Molecular Genetics and Genomics,1978,162:307-317.
[21]ZHAO K,PING W X,ZHANG L N,et al.Screening and breeding of high taxol producing fungi by genome shuffling[J].Science in China Series C-Life Science,2008,51(3):222-231.
[22]JOHN R P,GANGADHARAN D,NAMPOOTHIRI K M.Genome shuffling of Lactobacillus delbrueckii mutant and Bacillus amyloliquefaciens through protoplasmic fusion for L-lactic acid production from starchy wastes[J].Bioresource Technology,2008,99(17):8008-8015.
[23]DAI M H,ZIESMAN S,RATCLIFFE T.Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli[J].Metabolism Engineering,2005,7:45-52.
[24]HIDA H,YAMADA T,YAMADA Y.Genome shuffling of Streptomyces sp.U121for improved production of hydroxycitric acid[J].Applied Microbiology and Biotechnology,2007,73(6):1387-1393.
[25]ZHENG D Q,WU X C,WANG P M,et al.Drug resistance marker-aided genome shuffling to improve acetic acid tolerance in Saccharomyces cerevisiae[J].Journal of Industrial Microbiology&Biotechnology,2011,38:415-422.
[26]GONG J X,ZUHENG H J,W Z J,et al.Genome shuffling:Progress and applications for phenotype improvement[J].Biotechnology Advances,2009,27:996-1005.
[27]THOMPSON G D,DTTON R,SPARKS T C.Spinosad a case study:an example from a natural products discovery programme[J].Pest Management Science,2000,56:696-702.
[28]WANG H,XUE W,HE Y,et al.Improvement of the ability to produce spinosad in Saccharopolyspora spinosa through the acquisition of drug resistance and genome shuffling[J].Annals of Microbiology,2015,65:771-777.
[29]ZHOU P F,WANG Y W,GUO M,et al.Daptomycin:putative new mechanisms of action and resistance evolved from transcriptome data mining[J].Review of Medical Microbiology,2009,20:12-18.
[30]YU G,HU Y,HUI M,et al.Genome shuffling of Streptomyces roseosporus for improving daptomycin production[J].Applied Biochemistey and Biotechnology,2014,172:2661-2669.
[31]SUN J,LI H,NI Y,et al.Genome shuffing of Colletotrichum lini for improving 3β,7α,15α-trihydroxy-5-androsten-17-one production from dehydroepiandrosterone[J].Journal of Industrial Microbiology&Biotechnology,2017,44:937-947.
[32]YU L,PEI X L,LEI T,et al.Genome shuffling enhanced L-lactic acid production by improving glucose tolerance of Lactobacillus rhamnosus[J].Journal of Biotechnology,2008,134(12):154-159.
[33]DEGERANDO H M,GUICHARD F F,RUDANT L,et al.Improving isopropanol tolerance and production of Clostridium beijerinckii DSM 6423by random mutagenesis and genome shuffling[J].Applied Genetics and Molecular Biotechnology,2016,100:5427-5436.
[34]CHENG C,ALMARIO M P,KAO K C.Genome shuffling to generate recombinant yeasts for tolerance to inhibitors present in lignocellulosic hydrolysates[J].Biotechnology Letter,2015,37:2193-2200.
[35]郑连宝,裘娟萍.基因组重排技术在开发新代谢产物中的应用[J].中国生物工程杂志,2012,32(3):100-105.ZHEN L B,QIU J P.The application of genome shuffling in developing new metabolites[J].China Biotechnology,2012,32(3):100-105.
[36]WANG M Z,LIU S S,LI Y Y,et al.Protoplast mutation and genome shuffling induce the endophytic fungus Tuberculariasp.TF5to produce new compounds[J].Current Microbiology,2010,61:254-260.
[37]DAI M H,COPLEY S D.Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723[J].Applied and Environmental Microbiology,2004,70:2391-2397.
[38]KUMAR M.Improving polycyclic aromatic hydrocarbons degradation by genome shuffling[J].Asian Journal of Microbiology Biotechnology and Environmental Science,2007,9(1):145-149.
[39]LYU X A,JIN Y Y,LI Y D,et al.Genome shuffling of Streptomyces viridochromogenes for improved production of avilamycin[J].Applied and Environmental Microbiology,2013,97:641-648.
[40]WANG L,CHEN X S,WU G Y,et al.Genome shuffling and gentamicin-resistance to improveε-Poly-L-lysine productivity of Streptomyces albulus W-156[J].Applied Biochemistry Biotechnology,2016,180:1601-1617.
[41]WANG Y H,LI Y,PEI X L,et al.Genome-shuffling improved acid tolerance and L-lactic acid volumetric productivity in Lactobacillus rhamnosus[J].Journal of Biotechnology,2007,129:510-515.
[42]周扬,薛正莲,夏俊邢,等.常压室温等离子体(ARTP)诱变及高通量筛选那西肽高产菌株[J].工业微生物,2015,45(2):7-12.ZHOU Y,XUE Z L,XIA J X,et al.Screening strains of high-yield nosiheptide production by Atmospheric and Room Temperature Plasma(ARTP)and high throughput screening[J].Industrial Microbiology,2015,45(2):7-12.
[43]HARNER N K,WEN X,BAJWA P K.Genetic improvement of native xylose-fermenting yeasts for ethanol production[J].Journal of Industrial Microbiology&Biotechnology,2015,42:1-20.