Abstract
BackgroundPantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. By analysing the pan-genome of eight sequenced P. ananatis strains isolated from different sources we identified factors potentially underlying its ability to colonize and interact with hosts in both the plant and animal Kingdoms.ResultsThe pan-genome of the eight compared P. ananatis strains consisted of a core genome comprised of 3,876 protein coding sequences (CDSs) and a sizeable accessory genome consisting of 1,690 CDSs. We estimate that ~106 unique CDSs would be added to the pan-genome with each additional P. ananatis genome sequenced in the future. The accessory fraction is derived mainly from integrated prophages and codes mostly for proteins of unknown function. Comparison of the translated CDSs on the P. ananatis pan-genome with the proteins encoded on all sequenced bacterial genomes currently available revealed that P. ananatis carries a number of CDSs with orthologs restricted to bacteria associated with distinct hosts, namely plant-, animal- and insect-associated bacteria. These CDSs encode proteins with putative roles in transport and metabolism of carbohydrate and amino acid substrates, adherence to host tissues, protection against plant and animal defense mechanisms and the biosynthesis of potential pathogenicity determinants including insecticidal peptides, phytotoxins and type VI secretion system effectors.ConclusionsP. ananatis has an ‘open’ pan-genome typical of bacterial species that colonize several different environments. The pan-genome incorporates a large number of genes encoding proteins that may enable P. ananatis to colonize, persist in and potentially cause disease symptoms in a wide range of plant and animal hosts.Electronic supplementary materialThe online version of this article (doi: 10.1186/1471-2164-15-404) contains supplementary material, which is available to authorized users.
Highlights
Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut
The pan-genome of a bacterial species can be defined as the global gene repertoire of the species, and consists of a core genome, representing the genes present in all strains of the species, and an accessory genome composed of genes that are unique to particular strains as well as those genes that are absent from one or more of the sequenced strains [12,13]
This analysis indicated that between 89.3 and 95.7% of the proteins encoded on the genome of one strain have orthologs encoded on the genomes of the other strains, with an average amino acid identity of 99.4% (Figure 1, Additional file 1: Tables S1 and Additional file 2: Tables S2). These results suggested that an extensive, highly-conserved core genome, encompassing the majority of proteins encoded on each individual genome, exists among P. ananatis strains
Summary
Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. By analysing the pan-genome of eight sequenced P. ananatis strains isolated from different sources we identified factors potentially underlying its ability to colonize and interact with hosts in both the plant and animal Kingdoms. Pantoea ananatis is a member of the family Enterobacteriaceae and is characterised by its ubiquity in nature and its frequent association with both plant and animal hosts. It has been found in a wide array of environments including rivers, soil samples, refrigerated beef and aviation fuel tanks [1,2]. The ubiquity of P. ananatis suggests that it has adapted to proliferate in a wide range of environments, and its isolation from both plant and animal hosts indicate it has adapted for cross-Kingdom colonization and pathogenesis. We have determined and characterized the open P. ananatis pan-genome and show its adaptive capacity to interact with hosts of both the animal and plant Kingdoms
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