烟草青枯菌FQY_4基因组中原噬菌体生物信息学分析
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摘要
为了解青枯菌(ralstonia solanacearum)基因组中原噬菌体和噬菌体元件的信息,在烟草青枯菌FQY_4全基因组序列的基础上,分析了FQY_4染色体上的原噬菌体,结果显示FQY_4染色体上有1个具有完整噬菌体特征的原噬菌体,3个噬菌体元件。比较青枯菌GMI1000和FQY_4中的原噬菌体的序列信息,结果显示它们具有一定的相似性,其中青枯菌FQY_4的原噬菌体-2与噬菌体φRSA1的相似度为82%,它们有40个编码基因高度同源,相似度为99%以上。这些信息可为青枯菌原噬菌体的多样性分析,噬菌体和青枯菌的协同进化研究奠定基础。
In order to know prophage and its elements in the genome of ralstonia solanacearum, prophages in the chromosome of FQY-4 was analyzed on the basis of its complete genomic sequence. Results showed that there was one prophage which contained the typical characteristics of phage, and three incomplete prophage elements. Compared with the Ralstonia Solanacearum strain GMI1000, FQY_4 shared similarity in prophage, and homology between the prophage-2 in FQY_4 and prophage ?RSA1 was 82%and there were 40 coding sequences with highly significant homology level of more than 99%, which laid solid foundation for diversity analysis of prophage of Ralstonia Solanacearum, and for co-evolution of Ralstonia Solanacearum and phages.
In order to know prophage and its elements in the genome of ralstonia solanacearum, prophages in the chromosome of FQY-4 was analyzed on the basis of its complete genomic sequence. Results showed that there was one prophage which contained the typical characteristics of phage, and three incomplete prophage elements. Compared with the Ralstonia Solanacearum strain GMI1000, FQY_4 shared similarity in prophage, and homology between the prophage-2 in FQY_4 and prophage ?RSA1 was 82%and there were 40 coding sequences with highly significant homology level of more than 99%, which laid solid foundation for diversity analysis of prophage of Ralstonia Solanacearum, and for co-evolution of Ralstonia Solanacearum and phages.
引文
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[27]Ronning CM,Losada L,Brinkac L,et al.Genetic and phenotypic diversity in Burkholderia:contributions by prophage and phage-like elements[J].BMC Microbiol,2010(10):202.
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[29]Varani AM,Monteiro-Vitorello CB,Nakaya H I,et al.The Role of Prophage in Plant-Pathogenic Bacteria[J].Annual review of phytopathology,2013(51):429-451.
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[31]Addy H S,Askora A,Kawasaki T,et al.Loss of virulence of the phytopathogen Ralstonia solanacearum through infection byRSM filamentous phages[J].Phytopathology,2012,102(5):469-477.
[32]Addy H S,Askora A,Kawasaki T,et al.The filamentous phageφRSS1 enhances virulence of phytopathogenic Ralstonia solanacearum on tomato[J].Phytopathology,2012,102(3):244-251.
[33]Gabriel DW,Allen C,Schell M,et al.Identification of open reading frames unique to a select agent:Ralstonia solanacearum race 3 biovar 2[J].Mol.Plant-Microbe Interact,2006(19):69-79.
[34]Guidot A,Elbaz M,Carrere S,et al.Specific genes from the potato brown rot strains of Ralstonia solanacearum and their potential use for strain detection[J].Phytopathology,2009(99):1105-1112.
[35]谭锦,王雪峰,苏华楠,等.中国柑橘黄龙病病原菌两个原噬菌体超变异基因遗传多样性[J].中国农业科学,2013,46(18):3784-3792.
[36]阮萃才,梁远,刘锦玲,等.原噬菌体诱导法在环境诱变剂研究中的应用[J].环境科学,1990,11(3):41-43.
[37]张子千,刘莹,陈向东.Natrinema属极端嗜盐古生菌溶原性噬菌体SNJ1的相关研究[C]//2012年湖北生物产业发展高端论坛暨湖北省生物工程学会2012年度学术交流会论文汇编,2012.
[2]徐凤宇,苏胜兵,马红霞,等.不同类型土壤中分枝杆菌噬菌体分离率的比较[J].生态学报,2013,33(15):4616-4622.
[3]Wommack KE,Colwell RR.Virioplankton:viruses in aquatic ecosystems.Microbiol[J].Mol Biol Rev,2000,64(1):69-114.
[4]Kidambi SP,Ripp S,Miller RV.Evidence for phagemediated gene transfer among Pseudomonas aeruginosa strains on the phylloplane[J].Appl.Environ.Microbiol.,1994,60(2):496-500.
[5]Killiny N,Almeida RPP.Host structural carbohydrate induces vector transmission of a bacterial plant pathogen[J].Proc.Natl.Acad.Sci.USA.,2009,106(52):22416-22420.
[6]蔡刘体,汪汉成,袁赛飞,等.青枯菌特异性噬菌体的研究进展与应用[J].生物技术通讯,2012,11:145-148.
[7]Kawasaki T.,Shimizu M.,Satsuma H,et al.Genomic Ralstonia solanacearum p h a g eФRSB1,a T7-like wide-host-range phage[J].J.Bacteriol.,2009,191(1):422-427.
[8]Yamada T,Satoh S.,Ishikawa H,et al.A jumbo phage infecting the phytopathogen Ralstonia solanacearumdefines a new lineage of the Myoviridae family[J].Virology,2010,398(1):135-147.
[9]Kawasaki T.,Nagata S.,Fujiwara A.,et al.Genomic characterization of the filamentous integrative bacteriophageФRSS1 andФRSM1,which infect Ralstonia solanacearum[J].J.Bacteriol.,2007,189(16):5792-5802.
[10]Brussow H,Canchaya C,Hardt W D.Phages and the evolution of bacterial pathogens:from genomic rearrangements to lysogenic conversion[J].Microbiol.Mol.Biol.Rev.,2004,68(3):560-602.
[11]Koide T,Zaini PA,Moreira LM,et al.DNA microarray nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence[J].J.Bacteriol.,2004,186(16):5442-5449.
[12]Nunes LR,Rosato YB,Muto NH,et al.Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements[J].Genome Res.,2003,13(4):570-578.
[13]Canchaya C,Fournous G,Brussow H.The impact of prophages on bacterial chromosomes[J].Mol.Microbiol.,2004,53(1):9-18.
[14]Casjens S.Prophages and bacterial genomics:What have we learned so far[J].Mol.Microbiol.,2003,49(2):277-300.
[15]Salanoubat M,Genin S,Artiguenave F,et al.Genome sequence of the plant pathogen Ralstonia solanacearum[J].Nature,2002,415:497-502.
[16]Genin and Denny.Pathogenomics of the Ralstonia solanacearum species complex[J].Annu.Rev.Phytopathol.,2012,50(4):1-23.
[17]Li Zefeng,Wu Sanling,Bai Xuefei,et al.Genome Sequence of the Tobacco Bacterial Wilt Pathogen Ralstonia solanacearum[J].J Bacteriol.,2011,139(21):6088-6089.
[18]Cao Yi,Tian Bao yu,Liu Yanxi a,et al.Gequencing of Ralstonia solanacearum FQY_4,Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance[J].Genome announcements,2013,(1)3:1-2.
[19]Askora A.,Kawasaki T.,Usami S.,et al.Host recognition phytopathogen Rolstonia Solanacearum[J].Virology,2009,(384):69-76.
[20]Askora A,Kawasaki T,Fujie,et al.Resolvase-like serine recombinase mediates integration/excision in the bacteriophageφRSM[J].J Biosci Bioeng,2011,111(2):109-116.
[21]Fujiwara A.,Kawasaki T.Usami S.,et al.Genomic characterization of Ralstonia solanacearum phageФRSA1and its related prophage(ФRSX)in strain GMI1000[J].J.Bacteriol.,2008,190(1):143-150.
[22]Kawasaki T.,Nagata S.,Fujiwara A.et al.Genomic characterization of the filamentous integrative bacteriophageФRSS1 andФRSM1,which infect Ralstonia solanacearum[J].J.Bacteriol.,2007,189(16):5792-5802.
[23]Effantin G,Hamasaki R,Kawasaki T,et al.Cryo-Electron Microscopy Three-Dimensional Structure of the Jumbo PhageΦRSL1 Infecting the Phytopathogen Ralstonia solanacearum[J].Structure,2013,21(2):298-305.
[24]Clokie MR,Millard AD,Letarov AV,et al.Phages in nature[J].Bacteriophage,2011;1:31-45.
[25]Remenant B,de Cambiaire JC,Cellier G,et al.Ralstonia syzygii,the blood disease bacterium and some asian R.solanacearum strains form a single genomic species despite divergent lifestyles[J].PLo S ONE,2011.6:e24356.
[26]Gomez P and Buckling A.Bacteria-phage antagonistic coevolution in soil[J].Science,2011,(332):106-109.
[27]Ronning CM,Losada L,Brinkac L,et al.Genetic and phenotypic diversity in Burkholderia:contributions by prophage and phage-like elements[J].BMC Microbiol,2010(10):202.
[28]Kenzaka T,Tani K,Nasu M.High-frequency phagemediated gene transfer in freshwater environments determined at single-cell level[J].ISME J,2010(4):648-659.
[29]Varani AM,Monteiro-Vitorello CB,Nakaya H I,et al.The Role of Prophage in Plant-Pathogenic Bacteria[J].Annual review of phytopathology,2013(51):429-451.
[30]Tyler JS,Beeri K,Reynolds J L,et al.Prophage Induction Is Enhanced and Required for Renal Disease and Lethality in an EHEC Mouse Model[J].PLo S pathogens,2013,9(3):e1003236.
[31]Addy H S,Askora A,Kawasaki T,et al.Loss of virulence of the phytopathogen Ralstonia solanacearum through infection byRSM filamentous phages[J].Phytopathology,2012,102(5):469-477.
[32]Addy H S,Askora A,Kawasaki T,et al.The filamentous phageφRSS1 enhances virulence of phytopathogenic Ralstonia solanacearum on tomato[J].Phytopathology,2012,102(3):244-251.
[33]Gabriel DW,Allen C,Schell M,et al.Identification of open reading frames unique to a select agent:Ralstonia solanacearum race 3 biovar 2[J].Mol.Plant-Microbe Interact,2006(19):69-79.
[34]Guidot A,Elbaz M,Carrere S,et al.Specific genes from the potato brown rot strains of Ralstonia solanacearum and their potential use for strain detection[J].Phytopathology,2009(99):1105-1112.
[35]谭锦,王雪峰,苏华楠,等.中国柑橘黄龙病病原菌两个原噬菌体超变异基因遗传多样性[J].中国农业科学,2013,46(18):3784-3792.
[36]阮萃才,梁远,刘锦玲,等.原噬菌体诱导法在环境诱变剂研究中的应用[J].环境科学,1990,11(3):41-43.
[37]张子千,刘莹,陈向东.Natrinema属极端嗜盐古生菌溶原性噬菌体SNJ1的相关研究[C]//2012年湖北生物产业发展高端论坛暨湖北省生物工程学会2012年度学术交流会论文汇编,2012.