Comparative Analysis of the Core Proteomes among thePseudomonasMajor Evolutionary Groups Reveals Species-Specific Adaptations forPseudomonas aeruginosaandPseudomonas chlororaphis

ThePseudomonasgenus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 completePseudomonasproteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosaandPseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens,Pseudomonas stutzeri,Pseudomonas syringae,Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39-70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, withP. aeruginosahaving the highest number of these andP. fluorescenshaving none. We identified severalP. aeruginosa-specific core proteins (such asCntL,CntM,PlcB,Acp1,MucE,SrfA,Tse1,Tsi2,Tse3, andEsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific forP. cholororaphisand we hypothesize that these proteins may confer a competitive advantage against other root-colonizers.