Abstract
BackgroundMobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. The insertion of some specific Insertion Sequences had been associated with repetitive extragenic palindromic (REP) elements. Considering that there are a sufficient number of available genomes with described REPs, and exploiting the advantage of the traceability of transposition events in genomes, we decided to exhaustively analyze the relationship between REP sequences and mobile elements.ResultsThis global multigenome study highlights the importance of repetitive extragenic palindromic elements as target sequences for transposases. The study is based on the analysis of the DNA regions surrounding the 981 instances of Insertion Sequence elements with respect to the positioning of REP sequences in the 19 available annotated microbial genomes corresponding to species of bacteria with reported REP sequences. This analysis has allowed the detection of the specific insertion into REP sequences for ISPsy8 in Pseudomonas syringae DC3000, ISPa11 in P. aeruginosa PA01, ISPpu9 and ISPpu10 in P. putida KT2440, and ISRm22 and ISRm19 in Sinorhizobium meliloti 1021 genome. Preference for insertion in extragenic spaces with REP sequences has also been detected for ISPsy7 in P. syringae DC3000, ISRm5 in S. meliloti and ISNm1106 in Neisseria meningitidis MC58 and Z2491 genomes. Probably, the association with REP elements that we have detected analyzing genomes is only the tip of the iceberg, and this association could be even more frequent in natural isolates.ConclusionOur findings characterize REP elements as hot spots for transposition and reinforce the relationship between REP sequences and genomic plasticity mediated by mobile elements. In addition, this study defines a subset of REP-recognizer transposases with high target selectivity that can be useful in the development of new tools for genome manipulation.
Highlights
Mobile elements are involved in genomic rearrangements and virulence acquisition, and are important elements in bacterial genome evolution
It was proposed that repetitive extragenic palindromic (REP) sequences play a role as transcriptional attenuators [2] it was later stated that REP sequences are not specific terminators [3]
Analyzing the results obtained in our study of the association between REP sequences and mobile elements, we have distinguished two types of associations: (i) type 1 association, in which the percentage of association is 100% and each IS copy is inserted in the same position of a REP sequence, making it possible to define the DNA target consensus sequence (Tables 1 and 2 and Figure 2) and (ii) type 2 association, in which the IS elements are near to, or adjacent to REP sequences, but fragments of broken REP sequences just flanking IS elements are not detected (Tables 1 and 2)
Summary
Mobile elements are involved in genomic rearrangements and virulence acquisition, and are important elements in bacterial genome evolution. It was proposed that REP sequences play a role as transcriptional attenuators [2] it was later stated that REP sequences are not specific terminators [3]. Based on their role as mRNA sta-. There are some cases in which REP sequences appear as targets for transposition and recombination events In this sense, it has been shown that IS1397 and IS621 insert within REP sequences of Escherichia coli and that ISKpn insert into REP sequences of Klebsiella pneumoniae [9,10,11,12]. REP sequences appear at the recombination junctions of lambda bio phages [13] and amplification of plasmid F_128 is initiated by REP-REP recombination [14]
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