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CLC number: Q78

On-line Access: 2010-09-08

Received: 2009-12-28

Revision Accepted: 2010-06-21

Crosschecked: 2010-08-09

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Journal of Zhejiang University SCIENCE B 2010 Vol.11 No.9 P.708-718


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

Author(s):  Hai-lan Liu, Jun Zhu

Affiliation(s):  Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China, Institute of Maize Research, College of Agriculture, Sichuan Agricultural University, Ya’an 625014, China

Corresponding email(s):   jzhu@zju.edu.cn

Key Words:  Genomic islands, Prochlorococcus, Transfer RNA (tRNA), Palindromic structure, Codon usage

Hai-lan Liu, Jun Zhu. Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus[J]. Journal of Zhejiang University Science B, 2010, 11(9): 708-718.

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author="Hai-lan Liu, Jun Zhu",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus
%A Hai-lan Liu
%A Jun Zhu
%J Journal of Zhejiang University SCIENCE B
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%N 9
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%D 2010
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B0900417

T1 - Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus
A1 - Hai-lan Liu
A1 - Jun Zhu
J0 - Journal of Zhejiang University Science B
VL - 11
IS - 9
SP - 708
EP - 718
%@ 1673-1581
Y1 - 2010
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B0900417

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 strains. Both 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 P. marinus MIT9515, 8 in P. marinus MED4, 6 in P. marinus MIT9301, and 6 in P. marinus MIT9312. Monte Carlo simulation showed that tRNA genes are hotspots for the integration of genomic islands in Prochlorococcus strains. The 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 ends. These findings contradict previous hypotheses concerning the molecular basis for the frequent use of tRNA as the insertion site for foreign genetic materials. The analysis of a genomic island associated with a tRNA-Asn gene in P. marinus 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 island. Through 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.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


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