Comparative genomics of type VI secretion systems in strains of Pantoea ananatisfrom different environments

Abstract

BackgroundThe Type VI secretion system (T6SS) has been identified in several different bacteria, including the plant pathogenPantoea 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.ResultsThree 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.ConclusionOur 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.

Pantoea ananatis: genomic insights into a versatile pathogen

“…Recent genetic and mutagenic analyses have also contributed to our understanding of the mechanisms underlying P. ananatis phytopathogenesis. For example, P. ananatis strains encode up to three T6SSs, which may play a role in pathogenesis in both plant and animal hosts (De Maayer et al ., ; Shyntum et al ., ). The first and second T6SSs appear to be universal among P. ananatis strains and are hypothesized to play a role in antibiosis, fitness and niche adaptation (Shyntum et al ., ).…”

“…For example, P. ananatis strains encode up to three T6SSs, which may play a role in pathogenesis in both plant and animal hosts (De Maayer et al ., ; Shyntum et al ., ). The first and second T6SSs appear to be universal among P. ananatis strains and are hypothesized to play a role in antibiosis, fitness and niche adaptation (Shyntum et al ., ). It is likely that the second T6SS locus, which is incomplete, arose through the duplication of the first locus, whereas the third locus, which is plasmid borne, was acquired through horizontal gene transfer (De Maayer et al ., ).…”

Pantoea ananatis Utilizes a Type VI Secretion System for Pathogenesis and Bacterial Competition

“…Previous sequence analyses demonstrated the presence of two gene clusters in the genome of P. ananatis LMG 2665 T that contain genes homologous to those present in T6SSs (Shyntum et al 2014). The 40.6-kb T6SS-1 gene cluster contains genes that are predicted to encode the 13 core T6SS proteins (TssA-M), five proteins associated with T6SSs in other bacteria ( Tag) and 18 proteins that are present in very few or no other systems.…”

“…Although the truncated T6SS-3 gene cluster, which lacks 11 of the core T6SS genes, appears not to play a role in either pathogenicity or antibacterial competition, and therefore may not encode a functional T6SS, it is intriguing to understand why this cluster is maintained. Its 100% prevalence amongst P. ananatis strains (Shyntum et al 2014) suggests that this seemingly stable gene cluster may be advantageous to the bacteria for an as yet unknown function.…”

“…Comparative genomic analysis of Pantoea species have demonstrated the presence of up to three gene clusters, designated T6SS-1 through T6SS-3, encoding components of the T6SS (De Maayer et al 2011). Subsequent comparative genomics of sequenced P. ananatis strains indicated that the T6SS-1 and T6SS-3 gene clusters are present in all strains analyzed, whereas the T6SS-2 gene cluster is present in some but not all of these strains (Shyntum et al 2014). It is currently not known whether these gene clusters are functionally redundant or are required for a specific activity.…”