The diversity of conjugative relaxases and its application in plasmid classification
María Pilar Garcillán-Barcia 1 , María Victoria Francia 2 & Fernando de la Cruz 1
1 Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, Santander, Spain; and 2 Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla e Instituto de Formación e Investigación Marqués de Valdecilla (IFIMAV), Santander, Spain
Correspondence: Fernando de la Cruz, Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, C. Herrera Oria s/n, 39011 Santander, Spain. Tel.: +34 942201942; fax: +34 942201945; e-mail: delacruz@unican.es
Editor: Eduardo Rocha
Copyright © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved
KEYWORDS
plasmid classification • relaxase • bacterial conjugation • type IV secretion system • coupling protein
ABSTRACT
Bacterial conjugation is an efficient and sophisticated mechanism of DNA transfer among bacteria. While mobilizable plasmids only encode a minimal MOB machinery that allows them to be transported by other plasmids, conjugative plasmids encode a complete set of transfer genes (MOB+T4SS). The only essential ingredient of the MOB machinery is the relaxase, the protein that initiates and terminates conjugative DNA processing. In this review we compared the sequences and properties of the relaxase proteins contained in gene sequence databases. Proteins were arranged in families and phylogenetic trees constructed from the family alignments. This allowed the classification of conjugative transfer systems in six MOB families: MOBF, MOBH, MOBQ, MOBC, MOBP and MOBV . The main characteristics of each family were reviewed. The phylogenetic relationships of the coupling proteins were also analysed and resulted in phylogenies congruent to those of the cognate relaxases. We propose that the sequences of plasmid relaxases can be used for plasmid classification. We hope our effort will provide researchers with a useful tool for further mining and analysing the plasmid universe both experimentally and in silico.
María Pilar Garcillán-Barcia 1 , María Victoria Francia 2 & Fernando de la Cruz 1
1 Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, Santander, Spain; and 2 Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla e Instituto de Formación e Investigación Marqués de Valdecilla (IFIMAV), Santander, Spain
Correspondence: Fernando de la Cruz, Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, C. Herrera Oria s/n, 39011 Santander, Spain. Tel.: +34 942201942; fax: +34 942201945; e-mail: delacruz@unican.es
Editor: Eduardo Rocha
Copyright © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved
KEYWORDS
plasmid classification • relaxase • bacterial conjugation • type IV secretion system • coupling protein
ABSTRACT
Bacterial conjugation is an efficient and sophisticated mechanism of DNA transfer among bacteria. While mobilizable plasmids only encode a minimal MOB machinery that allows them to be transported by other plasmids, conjugative plasmids encode a complete set of transfer genes (MOB+T4SS). The only essential ingredient of the MOB machinery is the relaxase, the protein that initiates and terminates conjugative DNA processing. In this review we compared the sequences and properties of the relaxase proteins contained in gene sequence databases. Proteins were arranged in families and phylogenetic trees constructed from the family alignments. This allowed the classification of conjugative transfer systems in six MOB families: MOBF, MOBH, MOBQ, MOBC, MOBP and MOBV . The main characteristics of each family were reviewed. The phylogenetic relationships of the coupling proteins were also analysed and resulted in phylogenies congruent to those of the cognate relaxases. We propose that the sequences of plasmid relaxases can be used for plasmid classification. We hope our effort will provide researchers with a useful tool for further mining and analysing the plasmid universe both experimentally and in silico.
