Mining biosynthetic gene clusters in Virgibacillus genomes
Artikel i vetenskaplig tidskrift, 2019

BACKGROUND: Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobial activities against multidrug-resistant bacteria that have become a global health threat. Genera of the phylum Firmicutes are frequently identified as sources of such metabolites, but the biosynthetic potential of its Virgibacillus genus is not known. Here, we used comparative genomic analysis to determine whether Virgibacillus strains isolated from the Red Sea mangrove mud in Rabigh Harbor Lagoon, Saudi Arabia, may be an attractive source of such novel antimicrobial agents.

RESULTS: A comparative genomics analysis based on Virgibacillus dokdonensis Bac330, Virgibacillus sp. Bac332 and Virgibacillus halodenitrificans Bac324 (isolated from the Red Sea) and six other previously reported Virgibacillus strains was performed. Orthology analysis was used to determine the core genomes as well as the accessory genome of the nine Virgibacillus strains. The analysis shows that the Red Sea strain Virgibacillus sp. Bac332 has the highest number of unique genes and genomic islands compared to other genomes included in this study. Focusing on biosynthetic gene clusters, we show how marine isolates, including those from the Red Sea, are more enriched with nonribosomal peptides compared to the other Virgibacillus species. We also found that most nonribosomal peptide synthases identified in the Virgibacillus strains are part of genomic regions that are potentially horizontally transferred.

CONCLUSIONS: The Red Sea Virgibacillus strains have a large number of biosynthetic genes in clusters that are not assigned to known products, indicating significant potential for the discovery of novel bioactive compounds. Also, having more modular synthetase units suggests that these strains are good candidates for experimental characterization of previously identified bioactive compounds as well. Future efforts will be directed towards establishing the properties of the potentially novel compounds encoded by the Red Sea specific trans-AT PKS/NRPS cluster and the type III PKS/NRPS cluster.

Bacteriocins

Nonribosomal peptides

Lanthipeptides

Genome-mining

Biosynthetic gene clusters

Polyketides

Antimicrobial

Virgibacillus

Bioinformatics

Författare

Ghofran Othoum

King Abdullah University of Science and Technology (KAUST)

Washington University in St. Louis

Salim Bougouffa

King Abdullah University of Science and Technology (KAUST)

Ameerah Bokhari

King Abdullah University of Science and Technology (KAUST)

Feras F. Lafi

King Abdullah University of Science and Technology (KAUST)

Zayed University

T. Gojobori

King Abdullah University of Science and Technology (KAUST)

Heribert Hirt

King Abdullah University of Science and Technology (KAUST)

Ivan Mijakovic

Chalmers, Biologi och bioteknik, Systembiologi

Danmarks Tekniske Universitet (DTU)

Vladimir B. Bajic

King Abdullah University of Science and Technology (KAUST)

M. Essack

King Abdullah University of Science and Technology (KAUST)

BMC Genomics

1471-2164 (ISSN)

Vol. 20 1 696-

Ämneskategorier

Mikrobiologi

Mikrobiologi inom det medicinska området

Genetik

DOI

10.1186/s12864-019-6065-7

PubMed

31481022

Mer information

Senast uppdaterat

2019-11-08