Abstract
Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution.
Highlights
Transposable elements (TEs) are components of most prokaryotic genomes
PCM132TC only permits the identification of elements containing strong outwardly oriented promoters or those able to generate hybrid promoters, which drive the transcription of nearby genes
The trap plasmids were introduced by conjugation into 25 strains of Paracoccus spp. and pools of clones carrying mutated plasmids were obtained and analyzed as described in Materials and Methods
Summary
Transposable elements (TEs) are components of most prokaryotic genomes They are mobilized to change their location in DNA by the action of a transposase (TPase), an enzyme which catalyses transposition, i.e. recombination that does not require sequence homology between the TE and the target site. TEs can mobilize chromosomal genes for transposition, which results in shuffling of genetic information among various replicons present in a bacterial cell [4]. These highly recombinogenic elements may be considered as major architects responsible for shaping the structure of prokaryotic genomes. PCR products were analyzed by electrophoresis on 0.8% or 2% agarose gels and where necessary, purified using a Gel Out Kit (A&A Biotechnology)
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