Abstract
BackgroundPseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.ResultsHere, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.ConclusionsThis study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.
Highlights
Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions
Pseudoalteromonas dataset For the analysis of the Pseudoalteromonas pangenome, a dataset comprising 38 genomes present in GenBank, 13 of which belonging to strains isolated from different Antarctic sea ecological niches was assembled
Since the results of the pangenome analyses, i.e. the open pangenomes and the high proportion of L genes, appear to suggest that the Horizontal Gene Transfer (HGT) had a role in the evolution of this genus, we investigated more in details these events, by searching the presence of genes involved in the exchange of genes and trying to estimate the events of gene losses and gains that have occurred during the evolution of Pseudoalteromonas
Summary
Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. Bosi et al BMC Genomics (2017) 18:93 display aerobic and chemoheterotrophic metabolism, and they are motile due to sheathed polar and/or unsheathed lateral flagella Members of this genus have been isolated from almost all marine habitats, such as coastal, open and deep-sea waters, sediments, or in association with higher organisms, such as algae, invertebrates and fishes [3,4,5]. Other signatures of cold adaptation are the psychrophilesspecific codon usage bias, that is involved in resistance to protein aging features involving asparagine cyclization and deamidation [10], and the high number of rRNA and tRNA genes, which might explain its translational efficiency even in cold condition [7] This latter observation justifies an increasing use of PhTAC125 in biotechnological applications, such as for the high quality production of recombinant eukaryotic proteins [11,12,13]. The integration of genomic and expression data together with detailed physiological data allowed for the formulation of a genome scale metabolic model [16], that can be used to predict phenotypes and design experiments aimed at the optimization of PhTAC125 metabolic capabilities
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