DOI: 10.5061/dryad.vd7k7
title: Data from: Comparative genomics of type VI secretion systems in strains of Pantoea ananatis from different environments

description: Background: The Type VI secretion system (T6SS) has been identified in
 several different bacteria, including the plant pathogen Pantoea ananatis.
 Previous in silico analyses described three different T6SS loci present in
 the pathogenic strain of P. ananatis LMG 20103. This initial investigation
 has been extended to include an additional seven sequenced strains of P.
 ananatis together with 39 strains from different ecological niches.
 Comparative and phylogenetic analyses were used to investigate the
 distribution, evolution, intra-strain variability and operon structure of
 the T6SS in the sequenced strains. Results: Three different T6SS loci were
 identified in P. ananatis strain LMG 20103 and designated PA T6SS 1-3. PA
 T6SS-1 was present in all sequenced strains of P. ananatis and in all 39
 additional strains examined in this study. In addition, PA T6SS-1 included
 all 13 core T6SS genes required for synthesis of a functional T6SS. The
 plasmid-borne PA T6SS-2 also included all 13 core T6SS genes but was
 restricted to only 33% (15/46) of the strains examined. In addition, PA
 T6SS-2 was restricted to strains of P. ananatis isolated from symptomatic
 plant material. This finding raises the possibility of an association
 between PA T6SS-2 and either pathogenicity or host specificity. The third
 cluster PA T6SS-3 was present in all strains analyzed in this study but
 lacked 11 of the 13 core T6SS genes suggesting it may not encoded a
 functional T6SS. Inter-strain variability was also associated with hcp and
 vgrG islands, which are associated with the T6SS and encode a variable
 number of proteins usually of unknown function. These proteins may play a
 role in the fitness of different strains in a variety of ecological niches
 or as candidate T6SS effectors. Phylogenetic analysis indicated that PA
 T6SS-1 and PA T6SS-2 are evolutionarily distinct. Conclusion: Our analysis
 indicates that the three T6SSs of P. ananatis appear to have been
 independently acquired and may play different roles relating to
 pathogenicity, host range determination and/or niche adaptation. Future
 work will be directed toward understanding the roles that these T6SSs play
 in the biology of P. ananatis.
description: Figure 11a. Alignment of
 representative Hcp proteins of Pantoea ananatisAlignment of all
 representative Hcp proteins encoded by strains of Pantoea ananatis. Hcp
 amino acid sequences were aligned in MEGA5 using ClustalW with default
 settings.hcp
 alignment.megAdditional file 12.
 Phylogenetic analysis of orphan Hcp proteins found in the genome sequence
 of sequenced strains of Pantoea ananatisThis figure shows the
 evolutionary history of the Hcp proteins of Pantoea ananatis. Evolutionary
 history was inferred using the Maximum likelihood method based on the
 rtRev amino acid substitution model. The analysis includes mostly “orphan”
 Hcp proteins and some T6SS-related Hcp proteins from strains shown in the
 above figure. The different Hcp Groups (1 to 4) are shown in rectangles.
 The green and blue rectangles correspond to orphan Hcp proteins and type
 VI secretion system - associated Hcp proteins of Pantoea ananatis,
 respectively.Additional file 12. Hcp
 phylogenetic tree.docAlignment of
 concatenated TssB and TssC sequences from different bacteria
 speciesTssBC alignment file
 contains alignments of the concatenated amino acid sequences of TssB and
 TssC proteins of bacteria whose genome sequences contain at least one type
 six secretion system gene cluster. The alignments were done in Mega5 using
 ClastalW.TssBC
 alignment.megFigure 6. Evolutionary
 relationships of the different type VI secretion systems of Pantoea
 ananatis using concatenated TssB and TssC amino acid
 sequences.This figure shows the
 evolutionary history of the type VI secretion systems (T6SS) found in
 strains of Pantoea ananatis. Evolutionary history was inferred by using
 the Maximum Likelihood Method using the LG amino acid substitution model.
 The TssB/C homologs used in this study are indicated next to the name of
 the bacteria. Blue octagons represent T6SS phylogenetic Groups A-D
 proposed by Bingle et al. (2008). Representative position of PA T6SS-1 and
 PA T6SS-2 are shown in blue and green rectangles,
 respectively.Fig 6. TssBC phylogenetic
 tree_2.docAdditional file 8a.
 Alignment of the C-terminal amino acid sequences of RhsD proteins of
 Pantoea ananatisAdditional file 8a
 contains an alignment of the amino acid sequences found on the C-terminal
 domain of RhsD proteins of Pantoea ananatis. The rhsD genes are found in
 the viscinity of vgrG genes located in the type VI secretion system-1 gene
 cluster of different strains of Pantoea ananatis. The Amino acid sequences
 from the DPIGL peptide motif which is conserved in Rhs homologs of other
 bacteria was used for the alignment. Alignments were done in MEGA5 using
 ClastalW with the default settings.RhsD
 alignment.megAdditional file 8b.
 Alignment of RhsI amino acid sequence of Pantoea
 ananatis.Additional file 8b:
 Alignment of the amino acid sequences of RhsI proteins located downstream
 of the the rhsD genes found in the viscinity of the type VI secretion
 system-1 gene cluster of different strains of Pantoea
 ananatis.RhsI
 aligment.meg