Species-Wide Genome Mining of Pseudomonas putida for Potential Secondary Metabolites and Drug-Like Natural Products Characterization

Abstract

The gram negative bacteria species of Pseudomonas putida (P. putida) are important for heterologous expression of diverse biosynthetic pathways and numerous secondary metabolites biosynthesis. The genes code for such secondary metabolites biosynthetic proteins are organized in microbial genomes as clusters to bring the concerted expression of entire biosynthetic machinery. The complete and whole genome sequences of more than fifty different strains available in public DNA sequences databases provide an excellent opportunity to investigate the genetically encoded secondary metabolites potential of ecologically diverse P. putida strains. We implement the advance bioinformatics resources to annotate the so far available P. putida strains genomes for biosynthetic gene clusters (BGCs) and underlie secondary metabolites chemical scaffolds. The P. puida strains are found to harbor genomic signatures coding the molecular machinery for diverse secondary metabolites biosynthesis. The corresponding BGCs of these metabolites are found to be uniquely distributed across different P. putida strains speculate their role toward strain's ecological competency acquirement. The chemoinformatics dereplication and DrugBank database searching revealed the chemical mimicry of one putative metabolite with 2, 3, Dihydroxybenzoylserine, that mediates an antibiotic iron depletion along with human neutrophil lipocalin during innate immune response.