title: Comparative genomics of the Type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins.
abstract: BACKGROUND
  The Type VI secretion apparatus is assembled by a conserved set of proteins encoded within a distinct locus. The putative effector proteins Hcp and VgrG are also encoded within these loci. We have identified numerous distinct Type VI secretion system (T6SS) loci in the genomes of several ecologically diverse Pantoea and Erwinia species and detected the presence of putative effector islands associated with the hcp and vgrG genes.
  
  
  RESULTS
  Between two and four T6SS loci occur among the Pantoea and Erwinia species. While two of the loci (T6SS-1 and T6SS-2) are well conserved among the various strains, the third (T6SS-3) locus is not universally distributed. Additional orthologous loci are present in Pantoea sp. aB-valens and Erwinia billingiae Eb661. Comparative analysis of the T6SS-1 and T6SS-3 loci showed non-conserved islands associated with the vgrG and hcp, and vgrG genes, respectively. These regions had a G+C content far lower than the conserved portions of the loci. Many of the proteins encoded within the hcp and vgrG islands carry conserved domains, which suggests they may serve as effector proteins for the T6SS. A number of the proteins also show homology to the C-terminal extensions of evolved VgrG proteins.
  
  
  CONCLUSIONS
  Extensive diversity was observed in the number and content of the T6SS loci among the Pantoea and Erwinia species. Genomic islands could be observed within some of T6SS loci, which are associated with the hcp and vgrG proteins and carry putative effector domain proteins. We propose new hypotheses concerning a role for these islands in the acquisition of T6SS effectors and the development of novel evolved VgrG and Hcp proteins.
authors: Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa. pieter.demaayer@fabi.up.ac.za
authors: Pieter
authors: P
authors: De Maayer
authors: Stephanus N
authors: SN
authors: Venter
authors: Tim
authors: T
authors: Kamber
authors: Brion
authors: B
authors: Duffy
authors: Teresa A
authors: TA
authors: Coutinho
authors: Theo H M
authors: TH
authors: Smits
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D058947:Bacterial Secretion Systems; D001482:Base Composition; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D004885:Erwinia / Q000235:genetics*; D056426:Genetic Loci; D044404:Genomic Islands; D020636:Pantoea / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems; D004269:DNA, Bacterial