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Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences
Bao Ton-Hoang1, Patricia Siguier, Yves Quentin
1Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, 118, Route de Narbonne, 31062 Toulouse Cedex, France. tonhoang@ibcg.biotoul.fr
Nucleic Acids Research
|December 27, 2011
Summary
Repetitive palindromic sequences (REPs) and their associated transposase (TnpA(REP)) drive genome evolution in E. coli and Shigella. TnpA(REP) activity demonstrates potential transposase domestication in prokaryotes.
Area of Science:
- Genomics
- Molecular Biology
- Microbial Genetics
Background:
- Repetitive palindromic sequences (REPs) are intergenic elements often found in clustered structures known as BIMEs.
- REPs share similarities with insertion sequences (IS200/605) encoding Y1 transposases (TnpA(IS200/IS605)), known for single-strand transposition.
- A novel clade, TnpA(REP) transposases, has been identified associated with REP/BIME structures called REPtrons, potentially mediating REP/BIME proliferation.
Purpose of the Study:
- To analyze REP distribution and REPtron structure across E. coli and Shigella strains.
- To investigate the in vitro activity and characteristics of E. coli K12 TnpA(REP).
- To understand the role of TnpA(REP) in REP/BIME amplification and variability.
Main Methods:
- Comparative analysis of REP distribution and REPtron structure in E. coli and Shigella.
- Phylogenetic analysis of tnpA(REP) acquisition and loss.
- In vitro biochemical assays to study TnpA(REP) cleavage and recombination activity on BIMEs.
Main Results:
- Phylogenetic analysis revealed early acquisition and subsequent loss of tnpA(REP) in some strains.
- In vitro studies demonstrated that TnpA(REP) catalyzes cleavage and recombination of BIMEs.
- TnpA(REP) exhibits distinct properties compared to TnpA(IS200/605), influencing BIME variability and amplification.
Conclusions:
- TnpA(REP) plays a significant role in the proliferation and diversification of REP/BIME elements within bacterial genomes.
- The findings suggest TnpA(REP) may represent an early instance of transposase domestication in prokaryotes.
- This study enhances understanding of mobile genetic element dynamics and genome evolution in bacteria.
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