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

Abstract

Abstract: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.

Insertion site and distribution of a genomic island conferring DNA phosphorothioation in the Mycobacterium abscessus complex

“…S1). tRNA genes are preferred integration sites for mobile elements (Liu & Zhu, 2010;Reiter et al, 1989;Williams, 2002), and as we reported in this study, sequences surrounding these integration sites are often highly conserved (Ou et al, 2006). GIs are also frequently flanked by DRs (Hacker et al, 1997;Ou et al, 2006), and a 22 bp DR flanks the Dnd-GI in ATCC 19977…”

“…3a). Direct repeats (DRs) Dnd genomic island in the M. abscessus complex and tRNA genes are frequently associated with GIs (Hacker et al, 1997;Liu & Zhu, 2010;Ou et al, 2006;Reiter et al, 1989;Williams, 2002). The Dnd-GI insertion site (Fig.…”

A Distinct and Divergent Lineage of Genomic Island-Associated Type IV Secretion Systems in Legionella

“…Flanking the LGI-T4SS clusters within each of the LGIs are variable genomic regions that indicate multiple insertion, deletion and translocation events, typical of genomic islands and other mobile genetic elements ( Figures S1 and S2 ). The LGIs are all found within hypervariable regions of the genome, adjacent to tRNA genes, which are typical recognition sites for site-specific recombinases such as integrases and transposases [55] , suggesting that these regions are hotspots for the acquisition of horizontally acquired DNA. Indeed there are several direct repeats flanking the LGIs, which correspond to the last 37 to 48 bp at the 3′ end of the tRNA genes adjacent to the LGIs ( Table 1 , Figures S1 and S2 ).…”

Identifying Genomic Islands with Deep Neural Networks

“…A Genomic Island (GI) then is a cluster of genes that is typically between 10-200kb in length and has been transferred horizontally 11 . HGT may contribute to anywhere between 1.6% to 32.6% of the genomes [12][13][14][15][16][17][18][19][20] . This naturally implies that a major factor in the variability across bacterial species and clades can be attributed to GIs 21 .…”