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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 104.
Published online Mar 12, 2009. doi:  10.1186/1471-2164-10-104
PMCID: PMC2660368
Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?
Frédéric Boyer,1 Gwennaële Fichant,2,3 Jérémie Berthod,1 Yves Vandenbrouck,corresponding author1 and Ina Attreecorresponding author4,5
1CEA, iRTSV, Laboratoire Biologie, Informatique et Mathématiques, F-38054 Grenoble, France
2Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
3Centre National de la Recherche Scientifique, LMGM, F-31000 Toulouse, France
4CEA, iRTSV, Laboratoire Biochimie et Biophysique des Systèmes Intégrés, F-38054 Grenoble, France
5UMR5092, Centre National de la Recherche Scientifique/CEA/Université Joseph Fourier, F-38000 Grenoble, France
corresponding authorCorresponding author.
Frédéric Boyer: frederic.boyer/at/cea.fr; Gwennaële Fichant: gwennaele.fichant/at/ibcg.biotoul.fr; Jérémie Berthod: jeremie.berthod/at/cea.fr; Yves Vandenbrouck: yves.vandenbrouck/at/cea.fr; Ina Attree: ina.attree-delic/at/cea.fr
Received November 25, 2008; Accepted March 12, 2009.
Abstract
Background
The availability of hundreds of bacterial genomes allowed a comparative genomic study of the Type VI Secretion System (T6SS), recently discovered as being involved in pathogenesis. By combining comparative and phylogenetic approaches using more than 500 prokaryotic genomes, we characterized the global T6SS genetic structure in terms of conservation, evolution and genomic organization.
Results
This genome wide analysis allowed the identification of a set of 13 proteins constituting the T6SS protein core and a set of conserved accessory proteins. 176 T6SS loci (encompassing 92 different bacteria) were identified and their comparison revealed that T6SS-encoded genes have a specific conserved genetic organization. Phylogenetic reconstruction based on the core genes showed that lateral transfer of the T6SS is probably its major way of dissemination among pathogenic and non-pathogenic bacteria. Furthermore, the sequence analysis of the VgrG proteins, proposed to be exported in a T6SS-dependent way, confirmed that some C-terminal regions possess domains showing similarities with adhesins or proteins with enzymatic functions.
Conclusion
The core of T6SS is composed of 13 proteins, conserved in both pathogenic and non-pathogenic bacteria. Subclasses of T6SS differ in regulatory and accessory protein content suggesting that T6SS has evolved to adapt to various microenvironments and specialized functions. Based on these results, new functional hypotheses concerning the assembly and function of T6SS proteins are proposed.
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