Genomic and phenotypic analyses of chitin degradation and secondary metabolite production in Pseudoalteromonas

Abstract

The continuous emergence and spread of antibiotic resistant bacteria is a huge threat to modern society. We need to find and develop novel antimicrobial compounds to enable treatment of infectious diseases in the future. Bacteria have for decades provided antimicrobial compounds, and along with the genomic sequencing era it has become evident that only a minority of the potential antibiotic compounds encoded in the genomes of bacteria are yet discovered. In the past decades, the marine environment has gained attention because of its rich biodiversity being unexplored from a pharma- and biotech point of view. Marine bacteria are a prolific resource of novel antimicrobials, and in particular those of the genus Pseudoalteromonas. The purpose of this PhD project was to investigate the genus Pseudoalteromonas for its potential to produce novel antimicrobial compounds using in silico and in vitro methods. A global in silico analysis of 157 strains from the genus Pseudoalteromonas confirmed that pigmented species of the genus are potent producers of antimicrobial compounds, dedicating as much as 15% of their genomic content for this purpose. The global analysis also revealed many taxonomic discrepancies within the genus, and led us to pursue the description of a novel species Pseudoalteromonas galatheae. This subsequently contributed to the expansion of phylogeny within the genus and highlighted the importance of incorporating genomic information when describing novel species. Many antimicrobial compounds are encoded in so-called cryptic or silent (or orphan) biosynthetic gene clusters within the genomes, meaning that the chemistry of the compounds produced is not known. Previous studies have shown that using carbon sources mimicking the natural environment of bacteria can induce production of antimicrobial compounds in marine vibrios. In silico analysis of carbohydrate-active enzymes in genomes of Pseudoalteromonas showed that chitin was likely a preferred substrate for the bioactive pigmented species and we thus hypothesized that chitin degradation and production of antimicrobial compounds could be interconnected within the genus Pseudoalteromonas. Using a metabolomics approach as well as constructing chitinase gene deletion mutants it was found that the marine carbon sources did alter the metabolome of two strains, but that chitin was not convincingly inducing production of antimicrobial compounds. Concluding, this work has contributed to the understanding of the genus Pseudoalteromonas, highlighting their immense genetic capacity to produce novel antimicrobial compounds, which is similar to that of our most famous antibiotic producers, the Actinomycetes. This knowledge can be used to target the discovery of novel drugs towards culturable bacteria with a huge unknown bioactivity potential.