转移-信使RNA(transfer-message RNA,tmRNA)是细菌中普遍存在的稳定非编码sRNA,同时具备tRNA和mRNA双重特性,主要介导反式翻译核糖体拯救机制,对病原菌致病性和胁迫响应具有重要影响。【目的】从tmRNA功能研究入手,揭示对水产养殖和人...转移-信使RNA(transfer-message RNA,tmRNA)是细菌中普遍存在的稳定非编码sRNA,同时具备tRNA和mRNA双重特性,主要介导反式翻译核糖体拯救机制,对病原菌致病性和胁迫响应具有重要影响。【目的】从tmRNA功能研究入手,揭示对水产养殖和人类公共安全造成严重危害的维氏气单胞菌(Aeromonas veronii)的致病分子机制。【方法】采用生物学信息学工具IntaRNA2.0对维氏气单胞菌tmRNA可能结合的下游靶标进行预测,通过基因本体论(geneontology,GO)和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)富集分析,鉴定预测靶标参与的生物学过程及信号通路,并使用qPCR技术验证候选靶标基因在维氏气单胞菌野生型、tmRNA敲除株和smpB敲除株中的表达情况,以初步鉴定维氏气单胞菌tmRNA以sRNA形式调控的潜在下游靶标。【结果】tmRNA可以sRNA形式与下游100个潜在特异性靶标结合,这些靶标基因主要结合于tmRNA的3′端tRNA样结构域(tRNA-likedomain,TLD)、H2域及PK3、PK4域,参与细菌基本代谢过程。qPCR结果表明,在特异性结合的靶标基因中,基因WP_201994931.1以SmpB非依赖的方式受到tmRNA调节;WP_201954220.1、WP_005335875.1、WP_265062582.1、WP_265061484.1和WP_265061494.1等基因的表达则受到SmpB蛋白调控。【结论】本研究初步鉴定基因WP_201994931.1有可能是tmRNA作为sRNA调控的下游靶标,对拓展tmRNA功能研究领域有一定指导作用,有助于后续进一步探究维氏气单胞菌的致病和环境适应等重要生命活动的分子机制。展开更多
tmRNA,a combination of a tRNA-related fragment and a small mRNA fragment,was confirmed as the integration site of genomic islands(GIs).Using sequence alignment and comparative genomics,68 GIs associated with tmRNA gen...tmRNA,a combination of a tRNA-related fragment and a small mRNA fragment,was confirmed as the integration site of genomic islands(GIs).Using sequence alignment and comparative genomics,68 GIs associated with tmRNA genes were identified among 13 genera of Enterobacteriaceae.Among them,53 GIs were found in Escherichia coli and Salmonella enterica.Among these 53 GIs,tandem GIs were verified in eight S.enterica and two E.coli chromosomes.The downstream regions of the tmRNA genes in most of the E.coli and S.enterica chromosomes include one GI or tandem GIs region and a remnant variable region distal to the tmRNA.The chronology of integration of tandem GIs into the genome indicated that GIs farther from the tmRNA were incorporated into the genome earlier than those nearer from the tmRNA.The integrases of the tmRNA gene-associated GIs can be further categorized into three subtypes:HP1 integrases,PhiCTX integrases,and P4 integrases,which are the most predominant.The GIs were first integrated into the chromosome by the P4 integrase,subsequently by the PhiCTX integrase,and finally by the HP1 integrase.Thus,the tmRNA gene is an important site for investigating the genetics and evolution of tandem GIs.展开更多
文摘转移-信使RNA(transfer-message RNA,tmRNA)是细菌中普遍存在的稳定非编码sRNA,同时具备tRNA和mRNA双重特性,主要介导反式翻译核糖体拯救机制,对病原菌致病性和胁迫响应具有重要影响。【目的】从tmRNA功能研究入手,揭示对水产养殖和人类公共安全造成严重危害的维氏气单胞菌(Aeromonas veronii)的致病分子机制。【方法】采用生物学信息学工具IntaRNA2.0对维氏气单胞菌tmRNA可能结合的下游靶标进行预测,通过基因本体论(geneontology,GO)和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)富集分析,鉴定预测靶标参与的生物学过程及信号通路,并使用qPCR技术验证候选靶标基因在维氏气单胞菌野生型、tmRNA敲除株和smpB敲除株中的表达情况,以初步鉴定维氏气单胞菌tmRNA以sRNA形式调控的潜在下游靶标。【结果】tmRNA可以sRNA形式与下游100个潜在特异性靶标结合,这些靶标基因主要结合于tmRNA的3′端tRNA样结构域(tRNA-likedomain,TLD)、H2域及PK3、PK4域,参与细菌基本代谢过程。qPCR结果表明,在特异性结合的靶标基因中,基因WP_201994931.1以SmpB非依赖的方式受到tmRNA调节;WP_201954220.1、WP_005335875.1、WP_265062582.1、WP_265061484.1和WP_265061494.1等基因的表达则受到SmpB蛋白调控。【结论】本研究初步鉴定基因WP_201994931.1有可能是tmRNA作为sRNA调控的下游靶标,对拓展tmRNA功能研究领域有一定指导作用,有助于后续进一步探究维氏气单胞菌的致病和环境适应等重要生命活动的分子机制。
基金supported by the National Natural Science Foundation of China (30821005 and 30870075)the National Basic Research Program of China (2009CB118906)the Shanghai Leading Academic Discipline Project (B203)
文摘tmRNA,a combination of a tRNA-related fragment and a small mRNA fragment,was confirmed as the integration site of genomic islands(GIs).Using sequence alignment and comparative genomics,68 GIs associated with tmRNA genes were identified among 13 genera of Enterobacteriaceae.Among them,53 GIs were found in Escherichia coli and Salmonella enterica.Among these 53 GIs,tandem GIs were verified in eight S.enterica and two E.coli chromosomes.The downstream regions of the tmRNA genes in most of the E.coli and S.enterica chromosomes include one GI or tandem GIs region and a remnant variable region distal to the tmRNA.The chronology of integration of tandem GIs into the genome indicated that GIs farther from the tmRNA were incorporated into the genome earlier than those nearer from the tmRNA.The integrases of the tmRNA gene-associated GIs can be further categorized into three subtypes:HP1 integrases,PhiCTX integrases,and P4 integrases,which are the most predominant.The GIs were first integrated into the chromosome by the P4 integrase,subsequently by the PhiCTX integrase,and finally by the HP1 integrase.Thus,the tmRNA gene is an important site for investigating the genetics and evolution of tandem GIs.
