TY - JOUR
T1 - Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes
AU - Van Houdt, Rob
AU - Leplae, Raphael
AU - Lima-Mendez, Gipsi
AU - Mergeay, Max
AU - Toussaint, Ariane
N1 - Funding Information:
This work was partly supported by the European Space Agency (ESA-PRODEX) and the Belgian Science Policy (Belspo) through the MISSEX and COMICS projects, and by collaboration agreement between SCKCEN and Université Libre de Bruxelles. GLM holds a postdoctoral fellowship from FWO (Fonds Wetenschappelijk Onderzoek).
PY - 2012
Y1 - 2012
N2 - 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 - and -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.
AB - 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 - and -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.
UR - http://www.scopus.com/inward/record.url?scp=84864644262&partnerID=8YFLogxK
U2 - 10.1186/1759-8753-3-6
DO - 10.1186/1759-8753-3-6
M3 - Article
AN - SCOPUS:84864644262
SN - 1759-8753
VL - 3
JO - Mobile DNA
JF - Mobile DNA
IS - 1
M1 - 6
ER -