Analysis of the 3' ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

作     者：Hai-lan LIU Jun ZHU 

作者机构：Institute of Bioinformaties College of Agriculture and Biotechnology Zhejiang University Hangzhou 310029 China Institute of Maize Research College of Agriculture Sichuan Agricultural University Ya'an 625014 China 

出 版 物：《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 (浙江大学学报（英文版）B辑（生物医学与生物技术）)

年 卷 期：2010年第11卷第9期

页      面：708-718页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种] 

基　　金：(No. 2006AA10A102) supported by the National High-Tech R & D Program (863) of China 

主　　题：Genomic islands Prochlorococcus Transfer RNA(tRNA) Palindromic structure Codon usage 

摘      要：The purpose of this study was to investigate the characteristics of transfer RNA(tRNA) responsible for the association between tRNA genes and genes of apparently foreign origin(genomic islands) in five high-light adapted Prochlorococcus *** bidirectional best BLASTP(basic local alignment search tool for proteins) search and the conservation of gene order against each other were utilized to identify genomic islands,and 7 genomic islands were found to be immediately adjacent to tRNAs in Prochlorococcus marinus AS9601,11 in *** MIT9515,8 in *** MED4,6 in *** MIT9301,and 6 in *** *** Carlo simulation showed that tRNA genes are hotspots for the integration of genomic islands in Prochlorococcus *** tRNA genes associated with genomic islands showed the following characteristics:(1) the association was biased towards a specific subset of all iso-accepting tRNA genes;(2) the codon usages of genes within genomic islands appear to be unrelated to the codons recognized by associated tRNAs;and,(3) the majority of the 3 ends of associated tRNAs lack CCA *** findings contradict previous hypotheses concerning the molecular basis for the frequent use of tRNA as the insertion site for foreign genetic *** analysis of a genomic island associated with a tRNA-Asn gene in *** MIT9301 suggests that foreign genetic material is inserted into the host genomes by means of site-specific recombination,with the 3 end of the tRNA as the target,and during the process,a direct repeat of the 3 end sequence of a boundary tRNA(namely,a scar from the process of insertion) is formed elsewhere in the genomic *** the analysis of the sequences of these targets,it can be concluded that a region characterized by both high GC content and a palindromic structure is the preferred insertion site.