Insights into the Transposable Mobilome of Paracoccus spp. (Alphaproteobacteria)

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.

Autonomous and non-autonomous Tn3-family transposons and their role in the evolution of mobile genetic elements

“…5 We have analyzed functional TEs of the Tn3-family in a pool of environmental strains of the genera Paracoccus (Alphaproteobacteria) 9 and Pseudomonas (Gammaproteobacteria). 10 These elements were identified using trap plasmids which enable positive selection of transposition events and therefore the direct "capture" of even phenotypically silent elements.…”

“…10 These elements were identified using trap plasmids which enable positive selection of transposition events and therefore the direct "capture" of even phenotypically silent elements. 11 This approach permitted the characterization of several typical non-composite transposons: (i-ii) Tn3434 and Tn6122 -cryptic elements 9,12 , (iii) Tn5393 -conferring streptomycin resistance 9,12,13 (iv) Tn4662a -containing a predicted toxin-antitoxin module, and (v) Tn5563a -carrying part of the mer mercury resistance operon. 10 Interestingly, we also identified several TEs of unusual structure, which significantly broaden our knowledge on the diversity and evolution of Tn3 family transposons.…”

“…TnPpa1 (44,286 bp) is composed of 2 divergently oriented copies of cryptic transposon Tn3434 (Tn3 family), which border a large DNA region of chromosomal origin, containing genes encoding enzymes involved in the central intermediary metabolism, plus transporters, transcriptional regulators and conserved proteins of unknown function 9,14 . This element may be considered a composite transposon whose transposition is mediated by 2 copies of the non-composite Tn3434.…”

“…Interestingly, this transposition phenomenon was dependent on the nature of the incoming replicon. 9 The second group of atypical "captured" TEs are non-autonomous Tn3-family elements, named TIMEs (Tn3-derived Inverted-repeat Mobile Elements), identified in several Pseudomonas spp. strains.…”

“…Examples of such elements are Tn6122 (3792 bp) of Paracoccus halophilus JCM 14014 and the aforementioned Tn3434 (3659 bp), responsible for mobility of TnPpa1. 9 Both elements encode related transposases, but their resolvases are more divergent, suggesting that different RES modules might have been independently acquired in the course of evolution. This was confirmed by the identification of Tn3-family transposons (e.g.…”