Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis

• Published in: Diversity (Basel) 2020-08, Vol.12 (8), p.289
• Main Authors: Nikolaidis, Marios, Mossialos, Dimitris, Oliver, Stephen G., Amoutzias, Grigorios D.
• Format: Article
• Language: English
• Subjects: Adaptation; Bacteria; Bacteriocins; Classification; Comparative analysis; comparative genomics; core-proteome; Genes; Genomes; Holin; Mitomycin; Nosocomial infections; Pathogenicity; Pathogens; Phylogenetics; phylogenomics; Phylogeny; Proteins; Proteomes; Proteomics; Pseudomonas; Pseudomonas aeruginosa; Pseudomonas chlororaphis; Pseudomonas fluorescens; Pseudomonas putida; Scripts; Species; species-specific adaptations; Standard deviation; Taxonomy; Transcription
• ISSN: 1424-2818; 1424-2818
• DOI: 10.3390/d12080289

The Pseudomonas genus 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 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas 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, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) 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 for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers.