Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes
Open Access
- 13 April 2012
- journal article
- research article
- Published by Springer Science and Business Media LLC in Mobile DNA
- Vol. 3 (1), 6-11
- https://doi.org/10.1186/1759-8753-3-6
Abstract
Background: Tyrosine-based site-specific recombinases (TBSSRs) are DNA breaking-rejoining enzymes. In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), such as temperate phage genomes, integrated conjugative elements (ICEs) or integron cassettes. TBSSRs are also involved in the segregation of plasmids and chromosomes, the resolution of plasmid dimers and of co-integrates resulting from the replicative transposition of transposons. With the aim of improving the annotation of TBSSR genes in genomic sequences and databases, which so far is far from robust, we built a set of over 1,300 TBSSR protein sequences tagged with their genome of origin. We organized them in families to investigate: i) whether TBSSRs tend to be more conserved within than between classes of MGE types and ii) whether the (sub)families may help in understanding more about the function of TBSSRs associated in tandem or trios on plasmids and chromosomes. Results: A total of 67% of the TBSSRs in our set are MGE type specific. We define a new class of actinobacterial transposons, related to Tn554, containing one abnormally long TBSSR and one of typical size, and we further characterize numerous TBSSRs trios present in plasmids and chromosomes of α- and β-proteobacteria. Conclusions: The simple in silico procedure described here, which uses a set of reference TBSSRs from defined MGE types, could contribute to greatly improve the annotation of tyrosine-based site-specific recombinases in plasmid, (pro)phage and other integrated MGE genomes. It also reveals TBSSRs families whose distribution among bacterial taxa suggests they mediate lateral gene transfer.Keywords
This publication has 46 references indexed in Scilit:
- Cytoscape 2.8: new features for data integration and network visualizationBioinformatics, 2010
- Novel Tn4371-ICE like element in Ralstonia pickettiiand Genome mining for comparative elementsBMC Microbiology, 2009
- ACLAME: A CLAssification of Mobile genetic Elements, update 2010Nucleic Acids Research, 2009
- In Vitro Recombination Catalyzed by Bacterial Class 1 Integron Integrase IntI1 Involves Cooperative Binding and Specific Oligomeric IntermediatesPLOS ONE, 2009
- Jalview Version 2—a multiple sequence alignment editor and analysis workbenchBioinformatics, 2009
- IslandViewer: an integrated interface for computational identification and visualization of genomic islandsBioinformatics, 2009
- The National Center for Biotechnology Information's Protein Clusters DatabaseNucleic Acids Research, 2008
- NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathwaysNucleic Acids Research, 2008
- A New In Vitro Strand Transfer Assay for Monitoring Bacterial Class 1 Integron Recombinase IntI1 ActivityPLOS ONE, 2007
- Unlinking chromosome catenanes in vivo by site-specific recombinationThe EMBO Journal, 2007