Bacteria were the first forms of life on Earth and are the most prevalent biomass on the planet; their success is perhaps unsurprising given their rapid evolutionary rates and remarkable adaptive ability. One such bacteria, Pantoea ananatis, has been the focus of a recent study published in BMC Genomics, by Pieter De Maayer from the Centre for Microbial Ecology and Genomics at the University of Pretoria, South Africa, and colleagues. This ubiquitous bacteria has been implicated in a number of plant diseases, including those of economically important crops such as pineapple, maize and onion. It is found across a broad range of environments, from soils and rivers to refrigerated beef and aviation fuel tanks, and its hosts include not only plants but also insects and even humans.
De Maayer and colleagues analysed the pan-genome of eight individual strains of P. ananatis; a pan-genome referring to the entire gene pool of all strains of a species, including genes not shared by all strains. It may be characterised as open or closed, depending on the relative presence of core (present in all strains) versus accessory (unique to or absent from particular strains) elements in the genome. They found that 69.65 percent of coding DNA sequences (CDSs) were core to all eight genomes and a sizeable 30.36 per cent were accessory. Extrapolating from this, they predicted that, with the addition of each sequenced strain, the core genome would change little but the accessory genome would increase by approximately 106 unique CDSs. Such an open pan-genome has similarly been found in other bacterial species that occupy a wide range of environments, have a diverse range of lifestyles and/or possess efficient means of horizontal transfer.
The nature of the open pan-genome of P. ananatis was investigated further by classifying the CDSs on the basis of orthology. Maayer found that the accessory part of the genome encodes mainly for proteins of unknown function and that 41.4 per cent of strain-unique CDSs are derived from prophages (that is, viral genomes integrated into the bacterial genomes). The translated protein products of the pan-genome CDSs were then compared against a database to identify those that may be involved in host-microbe interactions. The shared orthology with other microorganisms revealed the presence of a large number of proteins encoding for colonisation of distinct hosts, including animals, as well as for interactions with insect hosts, plant-microbe interactions and plant- and animal-pathogenesis.
During their evolutionary arms race, many bacteria have overcome host defences or colonised new hosts by accessorising their genomes with DNA from bacteria outside their species. These results suggest that horizontal transfer is likewise significant in the diversification of P. ananatis and indeed may have helped in its cross-Kingdom leap. As reports increase of P. ananatis-caused diseases in previously unrecorded environments and hosts, and with the potential to infect humans, such insights into the evolution and ecological success of this species are crucial.
Analysis of the
Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts
BMC Genomics 2014, 15:404
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