In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

Ghofran Othoum; Salim Bougouffa; Rozaimi Razali; Ameerah Bokhari; Soha Alamoudi; André Antunes; Xin Gao; Robert Hoehndorf; Stefan T. Arold; T. Gojobori; Heribert Hirt; Ivan Mijakovic; Vladimir B. Bajic; Feras F. Lafi; M. Essack

doi:10.1186/s12864-018-4796-5

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters
Artikel i vetenskaplig tidskrift, 2018

Background: The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions. Results: We report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species. Conclusions:B. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.

Bioinformatics

Bacteriocins

Genome-mining

Bacillus licheniformis

Nonribosomal peptides

Bacillus paralicheniformis

Biosynthetic gene clusters

Antimicrobials

Lanthipeptides

Polyketides