Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens  

作　　者：SONG Lei ZHANG XueHong 

机构地区：[1]Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China [2]College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China

出　　处：《Chinese Science Bulletin》2011年第10期987-995,共9页

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)

摘　　要：Mobile genomic islands (GIs) can be excised from the chromosome,then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase.Some mobile GIs can also be transferred into a new receptor cell by transformation,conjugation,or transduction.The action sites of the integrase are usually flanked direct repeats (DRs) of the GIs.Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI.Mobile GIs are generally associated with transfer RNAs (tRNAs).Based on the correlation between flanking sequences and tRNA sequences,the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1,P.aeruginosa PA14,P.fluorescens Pf-5 and P.fluorescens Pf0-1 were identified.Among the 11 GIs,Pf0-1GI-1 is responsible for benzoate degradation.PAO1GI-1,Pf5GI-2,Pf5GI-3,and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate.The action sites of the integrases are these GIs direct repeats.Due to distinct DRs,cutting sites for the internal integrase of PAO1GI-1,Pf5GI-2,Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNA Gly gene,outside the anticodon loop of the tRNA Ser gene and tRNALys gene,and at the asymmetric 3'-end of the tRNA Leu gene,respectively.PAO1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences.This study describes basic information about the action sites of the integrases,assesses the mobility of GIs,and can help design and transfer mobile GIs to candidate strains.Mobile genomic islands （GIs） can be excised from the chromosome, then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase. Some mobile GIs can also be transferred into a new receptor cell by transformation, conjugation, or transduction. The action sites of the integrase are usually flanked direct repeats （DRs） of the GIs. Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI. Mobile GIs are generally associated with transfer RNAs （tRNAs）. Based on the correlation between flanking sequences and tRNA sequences, the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1, P. aeruginosa PAl4, P. fluorescens Pf-5 and P. fluorescens Pf0-1 were identified. Among the 11 GIs, Pf0-1GI-1 is responsible for benzoate degradation. PAO1GI-1, Pf5GI-2, Pf5GI-3, and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate. The action sites of the integrases are these GIs direct repeats. Due to distinct DRs, cutting sites for the internal integrase of PAO1GI-1, Pf5GI-2, Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNAGly gene, outside the anticodon loop of the tRNAser gene and tRNALys gene, and at the asymmetric 3＇-end of the tRNALeu gene, respectively. PAO 1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences. This study describes basic information about the action sites of the integrases, assesses the mobility of GIs, and can help design and transfer mobile GIs to candidate strains.

关 键 词：荧光假单胞菌 铜绿假单胞菌 准确定位 基因组 移动GIS 地理信息系统 侧翼序列 地理标志 

分 类 号：Q78[生物学—分子生物学]