In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters
Journal article, 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
Author
Ghofran Othoum
King Abdullah University of Science and Technology (KAUST)
Salim Bougouffa
King Abdullah University of Science and Technology (KAUST)
Rozaimi Razali
King Abdullah University of Science and Technology (KAUST)
Ameerah Bokhari
King Abdullah University of Science and Technology (KAUST)
Soha Alamoudi
King Abdulaziz University
André Antunes
Edge Hill University
Xin Gao
King Abdullah University of Science and Technology (KAUST)
Robert Hoehndorf
King Abdullah University of Science and Technology (KAUST)
Stefan T. Arold
King Abdullah University of Science and Technology (KAUST)
T. Gojobori
King Abdullah University of Science and Technology (KAUST)
Heribert Hirt
King Abdullah University of Science and Technology (KAUST)
Ivan Mijakovic
Technical University of Denmark (DTU)
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Vladimir B. Bajic
King Abdullah University of Science and Technology (KAUST)
Feras F. Lafi
King Abdullah University of Science and Technology (KAUST)
American University of Madaba
M. Essack
King Abdullah University of Science and Technology (KAUST)
BMC Genomics
14712164 (eISSN)
Vol. 19 1 382Subject Categories
Microbiology
Microbiology in the medical area
Genetics
DOI
10.1186/s12864-018-4796-5