摘要
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.
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.
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)
