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Nucleic Acids Res. 2014 May;42(9):5715-27. doi: 10.1093/nar/gku194. Epub 2014 Mar 12.

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion.

Author information

1
Microbial Evolutionary Genomics, Institut Pasteur, Paris 75015, France UMR3525, CNRS, Paris 75015, France jgugliel@pasteur.fr.
2
Centre d'Informatique pour les Biologistes, Institut Pasteur, Paris 75015, France.
3
Microbial Evolutionary Genomics, Institut Pasteur, Paris 75015, France UMR3525, CNRS, Paris 75015, France.
4
Institute of Biomedicine and Biotechnology of Cantabria (CSIC-Sodercan-University of Cantabria), Santander 39011, Spain.

Abstract

Conjugation of DNA through a type IV secretion system (T4SS) drives horizontal gene transfer. Yet little is known on the diversity of these nanomachines. We previously found that T4SS can be divided in eight classes based on the phylogeny of the only ubiquitous protein of T4SS (VirB4). Here, we use an ab initio approach to identify protein families systematically and specifically associated with VirB4 in each class. We built profiles for these proteins and used them to scan 2262 genomes for the presence of T4SS. Our analysis led to the identification of thousands of occurrences of 116 protein families for a total of 1623 T4SS. Importantly, we could identify almost always in our profiles the essential genes of well-studied T4SS. This allowed us to build a database with the largest number of T4SS described to date. Using profile-profile alignments, we reveal many new cases of homology between components of distant classes of T4SS. We mapped these similarities on the T4SS phylogenetic tree and thus obtained the patterns of acquisition and loss of these protein families in the history of T4SS. The identification of the key VirB4-associated proteins paves the way toward experimental analysis of poorly characterized T4SS classes.

PMID:
24623814
PMCID:
PMC4027160
DOI:
10.1093/nar/gku194
[Indexed for MEDLINE]
Free PMC Article

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