Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama

Abstract

The marine bacterial genus Pseudoalteromonas is known for their ability to produce antimicrobial compounds. The metabolite-producing capacity of Pseudoalteromonas has been associated with strain pigmentation; however, the genomic basis of their antimicrobial capacity remains to be explained. In this study, we sequenced the whole genome of six Pseudoalteromonas strains (three pigmented and three non-pigmented), with the purpose of identifying biosynthetic gene clusters (BGCs) associated to compounds we detected via microbial interactions along through MS-based molecular networking. The genomes were assembled and annotated using the SPAdes and RAST pipelines and mined for the identification of gene clusters involved in secondary metabolism using the antiSMASH database. Nineteen BGCs were detected for each non-pigmented strain, while more than thirty BGCs were found for two of the pigmented strains. Among these, the groups of genes of nonribosomal peptide synthetases (NRPS) that code for bromoalterochromides stand out the most. Our results show that all strains possess BGCs for the production of secondary metabolites, and a considerable number of distinct polyketide synthases (PKS) and NRPS clusters are present in pigmented strains. Furthermore, the molecular networking analyses revealed two new molecules produced during microbial interactions: the dibromoalterochromides D/D’ (11–12).

Integrated Omics Strategy Reveals Cyclic Lipopeptides Empedopeptins from Massilia sp. YMA4 and Their Biosynthetic Pathway

“…Advances in computational science and bioinformatic analysis now provide the possibility of dissecting secondary metabolite biosynthetic pathways from microorganisms [ 2 ]. Comparative genomics analysis and BGC mining have been applied to the natural product studies to discover new sources of bioactive natural products [ 3 ]. In addition, several mass spectrometry based metabolomics analysis approaches, such as Global Natural Products Social Molecular Networking (GNPS), have been utilized to monitor the production of specific molecules [ 4 ].…”

Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin

“…According to the obtained prediction result, total five BGCs were found in the genome of strain NJES-13, including a 44.5 kb long type III polyketide synthase (T3PKS) cluster with 100% similarity, as well as one 47.4 kb long type I polyketide synthase (T1PKS) cluster, two NRPS-like clusters of 43.4 and 42.0 kb, respectively, and one 27.8 kb long beta-lactone cluster. These findings indicate that strain NJES-13 possesses great potential to produce novel bioactive metabolites [ 33 , 34 , 35 , 36 ]. But unlike its closest relative, both T3PKS and T1PKS gene clusters were absent in the type strain of Mobilicoccus pelagius .…”

Antibacterial activity and mechanism of a novel bacteriocin produced by Lactiplantibacillus plantarum against Escherichia coli and Staphylococcus aureus

“…In addition, the bacteriocin was highly susceptible to pepsin and trypsin, and the antibacterial activity of the bacteriocin against the two bacteria was both lost after treatment. The result illustrated that the antibacterial substance in the L. plantarum CFS might be bacteriocin, which was determined as a protein or protein‐like antibacterial substance and could be hydrolyzed by some proteases (Atencio et al ., 2020). The protein content of the crude extracts of the bacteriocin was determined to be 4707 μg/mL.…”