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 - PubMed (original) (raw)

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

Pieter De Maayer et al. BMC Genomics. 2011.

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.

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Figures

Figure 1

Figure 1

Distribution of T6SS loci among Pantoea and Erwinia species. The presence (+) or absence (-) of ortholgous T6SS loci for the various Pantoea and Erwinia strains are shown. A neighbor-joining tree (bootstrap n = 1,000) based on a ClustalW alignment of GyrB amino acid sequences indicates the phylogenetic relationship of the strains.

Figure 2

Figure 2

The T6SS-1 loci of P. ananatis LMG 20103 and E. amylovora CFBP 1430. The conserved regions (block I and III) are shaded in gray, while the non-conserved hcp and vgrG islands are not shaded. Genes encoding conserved domain proteins are represented by green arrows while the grey arrows indicate other genes conserved among the Pantoea and Erwinia T6SS-1 loci which were not identified as part of the conserved core described by Boyer et al. [15]. Red arrows represent the hcp and vgrG genes while genes not conserved among the Pantoea and Erwinia species are colored in white. Graphs show the G+C content (%) (window size = 50 bp, step = 10 bp) in the respective T6SS-1 loci.

Figure 3

Figure 3

The orthologous T6SS-1 loci in Pantoea and Erwinia species. The conserved regions (block I and III) are shaded in gray, while the non-conserved hcp and vgrG islands are not shaded. Genes encoding conserved domain proteins identified by Boyer et al. [15] are represented by green arrows, and grey arrows indicate other genes conserved among the Pantoea and Erwinia T6SS-1 loci which were not identified as part of the conserved core described by Boyer et al. [15]. Red arrows represent the hcp and vgrG genes while genes not conserved among the Pantoea and Erwinia species are colored in white.

Figure 4

Figure 4

The orthologous T6SS-2 loci in Pantoea and Erwinia species. Genes encoding proteins with the conserved domains identified by Boyer et al. [15] are represented by green arrows while the grey arrows indicate other genes conserved among the Pantoea and Erwinia T6SS-2 loci which were not identified as part of the conserved core. White arrows represent the genes not conserved among the Pantoea and Erwinia species.

Figure 5

Figure 5

Phylogenetic relationships between the T6SS loci among the Pantoea and Erwinia species. A neighbor-joining tree (bootstrap n = 1,000; Poisson correction; Complete gap deletion) was constructed based on a ClustalW alignment of the IcmF (COG3523) amino acid sequences from the Pantoea and Erwinia T6SS loci and orthologous loci in several closely related Enterobacteriaceae.

Figure 6

Figure 6

The T6SS-3 loci of P. ananatis LMG 20103 and E. amylovora CFBP 1430. The conserved regions (block I, III and V) are shaded in gray, while non-conserved regions are not shaded. Genes encoding conserved domain proteins identified by Boyer et al. [15] represented by green arrows while the grey arrow indicates a gene conserved among the Pantoea and Erwinia T6SS-3 loci which was not identified as part of the conserved core. Red arrows represent the hcp and vgrG genes while genes not conserved among the Pantoea and Erwinia species are colored in white. The graphs show the G+C content (%) (window size = 50 bp, step = 10 bp) in the respective T6SS-3 loci.

Figure 7

Figure 7

The orthologous T6SS-3 loci in Pantoea and Erwinia species. The conserved regions (block I, III and V) are shaded in gray, while non-conserved regions are not shaded. Genes encoding conserved core proteins identified by Boyer et al. [15] are represented by green arrows while the grey arrows indicate other genes conserved among the Pantoea and Erwinia T6SS-3 loci which were not identified as part of the conserved core. Red arrows represent the hcp and vgrG genes while genes not conserved among the Pantoea and Erwinia species are colored in white.

Figure 8

Figure 8

Additional T6SS loci in Pantoea sp. aB-valens and Erwinia billingiae Eb661. Genes encoding proteins with the conserved domains identified by Boyer et al. [15] are indicated by green arrows. Red arrows represent the hcp and vgrG genes while genes not conserved among the Pantoea and Erwinia species are colored in white.

Figure 9

Figure 9

Conserved and non-conserved domains in the VgrG proteins of P. ananatis LMG 20103 and E. amylovora CFBP 1430. The conserved VgrG domains are colored in blue, Gp5 domains are in black, COG4253 domains in the T6SS-3 VgrG proteins in yellow and the non-conserved C-terminal extensions are colored in red. The amino acid locations of each domain are shown. The graphs show G+C contents (window size = 50 bp, step = 10 bp) in the respective vgrG genes.

Figure 10

Figure 10

Phylogeny of the Pantoea and Erwinia VgrG proteins. Neighbor-joining tree showing the phylogenetic relationship between the VgrG proteins among the various Pantoea and Erwinia species. The tree (bootstrap n = 1,000; Poisson correction; Complete gap deletion) was constructed based on a ClustalW alignment of the VgrG amino acid sequences. "Evolved" VgrG proteins are indicated in brackets.

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