细菌基因敲除策略及其在维氏气单胞菌研究中的应用
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摘要
基因敲除技术是20世纪80年代发展起来的一种分子生物学技术,目前已广泛应用于微生物基因功能等相关领域的研究中。维氏气单胞菌(Aeromonas veronii,A. veronii)是气单胞菌科气单胞菌属的一种,近年来,该菌引发疾病的报道逐年增多,因此,对其致病机制的研究显得尤为重要。本文对细菌不同基因敲除策略及其在A. veronii基因功能研究中的应用作一综述,旨在为A. veronii致病机制的深入研究提供参考。
Gene knockout is a molecular biological technique developed in 1980 s,which has been widely used for the studies in relevant fields such as gene function of microorganism. The diseases caused by Aeromonas veronii increased year by year,thus it is important to study the pathogenic mechanism. This paper reviews the application of various gene knockout strategies in the study on gene function of A. veronii in order to provide a reference for further study on pathogenic mechanism of the bacterium.
Gene knockout is a molecular biological technique developed in 1980 s,which has been widely used for the studies in relevant fields such as gene function of microorganism. The diseases caused by Aeromonas veronii increased year by year,thus it is important to study the pathogenic mechanism. This paper reviews the application of various gene knockout strategies in the study on gene function of A. veronii in order to provide a reference for further study on pathogenic mechanism of the bacterium.
引文
[1] YANG Y, YANG Y M, HU T. Research progress on the knockout techniques of prokaryotic microorganisms[J]. Int J Stomatol, 2016, 43(5):578-583.(in Chinese)阳燕,杨英明,胡涛.原核微生物基因敲除策略的研究进展[J].国际口腔科学杂志,2016, 43(5):578-583.
[2] NAWAZ M, SUNG K, KHAN S A, et al. Biochemical and molecular characterization of tetracycline-resistant Aeromonas veronii isolates from catfish[J]. Appl Environ Microbiol, 2006,72(10):6461-6466.
[3] YU J H, HAN J J, KIM H J, et al. First report of Aeromonas veronii infection in farmed Israeli carp Cyprinus carpio in Korea[J]. J Fish Pathol, 2010, 23(2):165-176.
[4] AUSTIN B, AUSTIN D A. Aeromonadaceae representatives(Motile Aeromonads)//Bacterial fish pathogens[M]. 2016:161-214.
[5] KAMILYA D,BARUAH A. Epizootic ulcerative syndrome(EUS)in fish:history and current status of understanding[J].Rev Fish Biol Fisheries, 2014, 24(1):369-380.
[6] LOCH T P, FAISAL M. Infection of lake whitefish(Coregonus clupeaformis)with motile Aeromonas spp. in the Laurentian Great Lakes[J]. J Great Lakes Res, 2010, 36(1):6-12.
[7] WANG X, YAN Q,LEI Y, et al. Isolation and identification on pathogenic bacteria of"rotten skin"disease in Chinese giant salamander(Andrias davidianus)[J]. Chin J Zoon, 2010,26(10):944-948.(in Chinese)王旭,颜其贵,雷燕,等.中国大鲵腐皮病病原菌的分离与鉴定[J].中国人兽共患病学报,2010, 26(10):944-948.
[8] XU Y, LIN L Y, YAO J Y, et al. Pathogen isolation, identification and susceptibility test of ulcerative disease syndrome on Pelteobagrus fulvidraco[J]. Freshwater Fisheries, 2015, 45(5):100-104.(in Chinese)徐洋,蔺凌云,姚嘉赟,等.黄颡鱼“溃疡综合征”病原的分离鉴定及药敏试验[J].淡水渔业,2015, 45(5):10-104.
[9] PAN X Y, SHEN J Y, LI J Y, et al. Identification and biological characteristics of the pathogen causing Macrobrachium nipponense soft-shell syndrome[J]. Microbiol Chin,2009,36(10):1571-1576.(in Chinese)潘晓艺,沈锦玉,李建应,等.青虾“软壳综合症”病原及其特性[J].微生物学通报,2009, 36(10):1571-1576.
[10] WANG L,DUO L B. Research progress on the knockout techniques of gene function of Klebsiella pneumonia[J]. Chin J Clin Lab Sci, 2015, 33(5):376-377.(in Chinese)王丽,多丽波.基因敲除技术在肺炎克雷伯菌基因功能研究中的应用进展[J].临床检验杂志,2015, 33(5):376-377.
[11] AN D J, KANG Y H, CH L, et al. Advance and application of CRISPR/Cas9 mediated genome editing technique on pathogenic microorganism[J]. Chin J Zoon, 2017,33(3):280-286.(in Chinese)安鼎杰,康元环,陈龙,等.CRISPR/Cas9基因编辑技术在病原微生物中的应用[J].中国人兽共患病学报,2017, 33(3):280-286.
[12] HAN H J, TAKI T, KONDO H, et al. Pathogenic potential of a collagenase gene from Aeromonas veronii[J]. Can J Microbiol, 2008, 54(1):1-10.
[13] ZHANG K, WANG H, GUO F, et al. OMP31 of Brucella melitensis 16M impairs the apoptosis of macrophages triggered by TNF-alpha[J]. Exp Ther Med, 2016, 12(4):2783-2789.
[14] LAU P C, SUNG C K, LEE J H, et al. PCR ligation mutagenesis in transformable streptococci:application and efficiency[J]. J Microbiol Methods, 2002, 49(2):193-205.
[15] POTEETE A R, FENTON A C. Genetic requirements of phage lambda red-mediated gene replacement in Escherichia coli K-12[J]. J Bacteriol, 2000, 182(8):2336-2340.
[16] MURPHY K C, CAMPELLONE K G. Lambda red-mediated recombinogenic engineering of enterohemorrhagic and entero-pathogenic E. coli[J]. BMC Mol Biol, 2003, 4:11.
[17] KARLINSEY J E. Lambda-red genetic engineering in Salmonella enterica serovar Typhimurium[J]. Methods Enzymol, 2007,421:199-209.
[18] LESIC B, RAHME L G. Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa[J]. BMC Mol Biol, 2008, 9(1):20..
[19] ZHOU W, FU X A, ZHANG D X, et al. Research progress on the gene knockout techniques[J]. Chin J Vet Med, 2015,51(3):67-69.(in Chinese)周维,付喜爱,张德显,等.基因敲除技术的研究进展[J].中国兽医杂志,2015, 51(3):67-69.
[20] WENG L, BISWAS I, MORRISON D A. A self-deleting Crelox-ermAM cassette, Cheshire,for marker-less gene deletion in Streptococcus pneumonia[J]. J Microbiol Methods, 2009, 79(3):353-357.
[21] BANERJEE A, BISWAS I. Markerless multiple-gene-deletion system for Streptococcus mutants[J]. Appl Environ Microbiol,2008, 74(7):2037-2042.
[22] YAN X, YU H J, HONG Q, et al. Cre/lox system and PCRbased genome engineering in Bacillus subtilis[J]. Appl Environ Microbiol, 2008, 74(17):5556-5562.
[23] POMERANTSEV A P, SITARAMAN R, GALLOWAY C R, et al. Genome engineering in Bacillus anthracis using Crerecombinase[J]. Infect Immun,2006,74(1):682-693.
[24] SIMON R, PRIIEFER U, PEHLER A. A broad host range mobilization system for in vivo genetic engineering:transposon mutagenesis in Gram negative bacteria[J]. Nat Biotechnol,1983, 1(9):784-791.
[25] ROSSIGNOL M, BASSET A, ESPELI O, et al. NKBOR, a miniTn10-based transposon for random insertion in the chro-mosome of Gram-negative bacteria and the rapid recovery of sequences flanking the insertion sites in Escherichia coli[J]. Res Microbiol, 2001, 152(5):481-485.
[26] ZHANG J,GUO F, CHEN C, et al. Brucella melitensis 16M-△hfq attenuation confers protection against wild-type challenge in BALB/c mice[J]. Microbiol Immunol, 2013, 57(7):502-510.
[27] SHEN J, HU Z L, LI S F,et al. Studies on the screening for Klebsiella peneumoniae VBNC mutants and its transformation characteristics[J]. Acta Hydrobiologica Sinica, 2009,33(1):28-33.(in Chinese)沈菊,胡章立,黎双飞.肺炎克雷伯氏菌VBNC状态转化突变株的筛选与特性研究[J].水生生物学报,2009, 33(1):28-33.
[28] PANG M, XIE X, DONG Y, et al. Identification of novel virulence-related genes in Aeromonas hydrophila by screening transposon mutants in a Tetrahymena infection model[J]. Vet Microbiol, 2017, 199(1):36-46.
[29] SILVER A C, RABINOWITZ N M, KUFFER S, et al. Identification of Aeromonas veronii genes required for colonization of the medicinal leech,Hirudoverbana[J]. J Bacteriol,2007,189(19):6763-6772.
[30] JIANG W, BIKARD D, COX D, et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems[J]. Nat Biotechnol, 2013, 31(3):233-239.
[31] GARNEAU J E, DUPUIS M E, VILLION M, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA[J]. Nature, 2010, 468(7320):67-71.
[32] PYNE M E, MOO-YOUNG M, CHUNG D A, et al. Coupling the CRISPR/Cas9 system with lambda red recombineering enables simplified chromosomal gene replacement in Escherichia coli[J]. Appl Environ Microbiol,2015, 81(15):5103-5114.
[33] JIANG Y, CHEN B, DU AN C, et al. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system[J]. Appl Environ Microbiol, 2015, 81(7):2506-2514.
[34] LIU Z, LIU P, LIU S, et al. Small protein B upregulates sensor kinase bvgS expression in Aeronwnas veronii[J]. Front Microbiol,2015,6:579.
[35] HADI N, YANG Q, BARNETT T C, et al. Bundle-forming pilus locus of Aeromonas veronii bv. Sobria[J]. Infect Immun,2012, 80(4):1351-1360.
[36] MCCOY A J, KOIZUMI Y, HIGA N, et al. Differential regulation of caspase-1 activation via NLRP3/NLRC4 inflammasomes mediated by aerolysin and typeⅢsecretion system during Aeromonas veronii biovar sobria[J]. J Immunol, 2010, 185(11):7077-7084.
[37] SONG T, TOMA C, NAKASONE N, et al. Aerolysin is activated by metalloprotease in Aeromonas veronii biovar sobria[J]. J Med Microbiol, 2004, 53(Pt 6):477-482.
[38] MALTZ M, GRAF J. The typeⅡsecretion system is essential for erythrocyte lysis and gut colonization by the leech digestive tract symbiont Aeromonas veronii[J]. Appl Environ Microbiol,2011,77(2):597-603.
[39] SILVER A C, KIKUCHI Y, FADL A A, et al. Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations[J]. Proc Natl Acad Sci USA, 2007, 104(22):9481-9486.
[40] MALTZ M, LEVARGE B L, GRAF J. Identification of iron and heme utilization genes in Aeromonas and their role in the colonization of the leech digestive tract[J]. Front Microbiol, 2015,6:763.
[2] NAWAZ M, SUNG K, KHAN S A, et al. Biochemical and molecular characterization of tetracycline-resistant Aeromonas veronii isolates from catfish[J]. Appl Environ Microbiol, 2006,72(10):6461-6466.
[3] YU J H, HAN J J, KIM H J, et al. First report of Aeromonas veronii infection in farmed Israeli carp Cyprinus carpio in Korea[J]. J Fish Pathol, 2010, 23(2):165-176.
[4] AUSTIN B, AUSTIN D A. Aeromonadaceae representatives(Motile Aeromonads)//Bacterial fish pathogens[M]. 2016:161-214.
[5] KAMILYA D,BARUAH A. Epizootic ulcerative syndrome(EUS)in fish:history and current status of understanding[J].Rev Fish Biol Fisheries, 2014, 24(1):369-380.
[6] LOCH T P, FAISAL M. Infection of lake whitefish(Coregonus clupeaformis)with motile Aeromonas spp. in the Laurentian Great Lakes[J]. J Great Lakes Res, 2010, 36(1):6-12.
[7] WANG X, YAN Q,LEI Y, et al. Isolation and identification on pathogenic bacteria of"rotten skin"disease in Chinese giant salamander(Andrias davidianus)[J]. Chin J Zoon, 2010,26(10):944-948.(in Chinese)王旭,颜其贵,雷燕,等.中国大鲵腐皮病病原菌的分离与鉴定[J].中国人兽共患病学报,2010, 26(10):944-948.
[8] XU Y, LIN L Y, YAO J Y, et al. Pathogen isolation, identification and susceptibility test of ulcerative disease syndrome on Pelteobagrus fulvidraco[J]. Freshwater Fisheries, 2015, 45(5):100-104.(in Chinese)徐洋,蔺凌云,姚嘉赟,等.黄颡鱼“溃疡综合征”病原的分离鉴定及药敏试验[J].淡水渔业,2015, 45(5):10-104.
[9] PAN X Y, SHEN J Y, LI J Y, et al. Identification and biological characteristics of the pathogen causing Macrobrachium nipponense soft-shell syndrome[J]. Microbiol Chin,2009,36(10):1571-1576.(in Chinese)潘晓艺,沈锦玉,李建应,等.青虾“软壳综合症”病原及其特性[J].微生物学通报,2009, 36(10):1571-1576.
[10] WANG L,DUO L B. Research progress on the knockout techniques of gene function of Klebsiella pneumonia[J]. Chin J Clin Lab Sci, 2015, 33(5):376-377.(in Chinese)王丽,多丽波.基因敲除技术在肺炎克雷伯菌基因功能研究中的应用进展[J].临床检验杂志,2015, 33(5):376-377.
[11] AN D J, KANG Y H, CH L, et al. Advance and application of CRISPR/Cas9 mediated genome editing technique on pathogenic microorganism[J]. Chin J Zoon, 2017,33(3):280-286.(in Chinese)安鼎杰,康元环,陈龙,等.CRISPR/Cas9基因编辑技术在病原微生物中的应用[J].中国人兽共患病学报,2017, 33(3):280-286.
[12] HAN H J, TAKI T, KONDO H, et al. Pathogenic potential of a collagenase gene from Aeromonas veronii[J]. Can J Microbiol, 2008, 54(1):1-10.
[13] ZHANG K, WANG H, GUO F, et al. OMP31 of Brucella melitensis 16M impairs the apoptosis of macrophages triggered by TNF-alpha[J]. Exp Ther Med, 2016, 12(4):2783-2789.
[14] LAU P C, SUNG C K, LEE J H, et al. PCR ligation mutagenesis in transformable streptococci:application and efficiency[J]. J Microbiol Methods, 2002, 49(2):193-205.
[15] POTEETE A R, FENTON A C. Genetic requirements of phage lambda red-mediated gene replacement in Escherichia coli K-12[J]. J Bacteriol, 2000, 182(8):2336-2340.
[16] MURPHY K C, CAMPELLONE K G. Lambda red-mediated recombinogenic engineering of enterohemorrhagic and entero-pathogenic E. coli[J]. BMC Mol Biol, 2003, 4:11.
[17] KARLINSEY J E. Lambda-red genetic engineering in Salmonella enterica serovar Typhimurium[J]. Methods Enzymol, 2007,421:199-209.
[18] LESIC B, RAHME L G. Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa[J]. BMC Mol Biol, 2008, 9(1):20..
[19] ZHOU W, FU X A, ZHANG D X, et al. Research progress on the gene knockout techniques[J]. Chin J Vet Med, 2015,51(3):67-69.(in Chinese)周维,付喜爱,张德显,等.基因敲除技术的研究进展[J].中国兽医杂志,2015, 51(3):67-69.
[20] WENG L, BISWAS I, MORRISON D A. A self-deleting Crelox-ermAM cassette, Cheshire,for marker-less gene deletion in Streptococcus pneumonia[J]. J Microbiol Methods, 2009, 79(3):353-357.
[21] BANERJEE A, BISWAS I. Markerless multiple-gene-deletion system for Streptococcus mutants[J]. Appl Environ Microbiol,2008, 74(7):2037-2042.
[22] YAN X, YU H J, HONG Q, et al. Cre/lox system and PCRbased genome engineering in Bacillus subtilis[J]. Appl Environ Microbiol, 2008, 74(17):5556-5562.
[23] POMERANTSEV A P, SITARAMAN R, GALLOWAY C R, et al. Genome engineering in Bacillus anthracis using Crerecombinase[J]. Infect Immun,2006,74(1):682-693.
[24] SIMON R, PRIIEFER U, PEHLER A. A broad host range mobilization system for in vivo genetic engineering:transposon mutagenesis in Gram negative bacteria[J]. Nat Biotechnol,1983, 1(9):784-791.
[25] ROSSIGNOL M, BASSET A, ESPELI O, et al. NKBOR, a miniTn10-based transposon for random insertion in the chro-mosome of Gram-negative bacteria and the rapid recovery of sequences flanking the insertion sites in Escherichia coli[J]. Res Microbiol, 2001, 152(5):481-485.
[26] ZHANG J,GUO F, CHEN C, et al. Brucella melitensis 16M-△hfq attenuation confers protection against wild-type challenge in BALB/c mice[J]. Microbiol Immunol, 2013, 57(7):502-510.
[27] SHEN J, HU Z L, LI S F,et al. Studies on the screening for Klebsiella peneumoniae VBNC mutants and its transformation characteristics[J]. Acta Hydrobiologica Sinica, 2009,33(1):28-33.(in Chinese)沈菊,胡章立,黎双飞.肺炎克雷伯氏菌VBNC状态转化突变株的筛选与特性研究[J].水生生物学报,2009, 33(1):28-33.
[28] PANG M, XIE X, DONG Y, et al. Identification of novel virulence-related genes in Aeromonas hydrophila by screening transposon mutants in a Tetrahymena infection model[J]. Vet Microbiol, 2017, 199(1):36-46.
[29] SILVER A C, RABINOWITZ N M, KUFFER S, et al. Identification of Aeromonas veronii genes required for colonization of the medicinal leech,Hirudoverbana[J]. J Bacteriol,2007,189(19):6763-6772.
[30] JIANG W, BIKARD D, COX D, et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems[J]. Nat Biotechnol, 2013, 31(3):233-239.
[31] GARNEAU J E, DUPUIS M E, VILLION M, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA[J]. Nature, 2010, 468(7320):67-71.
[32] PYNE M E, MOO-YOUNG M, CHUNG D A, et al. Coupling the CRISPR/Cas9 system with lambda red recombineering enables simplified chromosomal gene replacement in Escherichia coli[J]. Appl Environ Microbiol,2015, 81(15):5103-5114.
[33] JIANG Y, CHEN B, DU AN C, et al. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system[J]. Appl Environ Microbiol, 2015, 81(7):2506-2514.
[34] LIU Z, LIU P, LIU S, et al. Small protein B upregulates sensor kinase bvgS expression in Aeronwnas veronii[J]. Front Microbiol,2015,6:579.
[35] HADI N, YANG Q, BARNETT T C, et al. Bundle-forming pilus locus of Aeromonas veronii bv. Sobria[J]. Infect Immun,2012, 80(4):1351-1360.
[36] MCCOY A J, KOIZUMI Y, HIGA N, et al. Differential regulation of caspase-1 activation via NLRP3/NLRC4 inflammasomes mediated by aerolysin and typeⅢsecretion system during Aeromonas veronii biovar sobria[J]. J Immunol, 2010, 185(11):7077-7084.
[37] SONG T, TOMA C, NAKASONE N, et al. Aerolysin is activated by metalloprotease in Aeromonas veronii biovar sobria[J]. J Med Microbiol, 2004, 53(Pt 6):477-482.
[38] MALTZ M, GRAF J. The typeⅡsecretion system is essential for erythrocyte lysis and gut colonization by the leech digestive tract symbiont Aeromonas veronii[J]. Appl Environ Microbiol,2011,77(2):597-603.
[39] SILVER A C, KIKUCHI Y, FADL A A, et al. Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations[J]. Proc Natl Acad Sci USA, 2007, 104(22):9481-9486.
[40] MALTZ M, LEVARGE B L, GRAF J. Identification of iron and heme utilization genes in Aeromonas and their role in the colonization of the leech digestive tract[J]. Front Microbiol, 2015,6:763.