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

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

doi:10.1186/s12864-018-4796-5

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

Ghofran K. Othoum, Salim Bougouffa, Rozaimi Mohamad Razali, Ameerah Bokhari, Soha Alamoudi, André Antunes, Xin Gao, Robert Hoehndorf, Stefan T. Arold, Takashi Gojobori, Heribert Hirt, Ivan Mijakovic, Vladimir B. Bajic, Feras Fawzi Lafi, Magbubah Essack

Research output: Contribution to journal › Article › peer-review

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Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsB. 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.

Original language	English (US)
Journal	BMC Genomics
Volume	19
Issue number	1
DOIs	https://doi.org/10.1186/s12864-018-4796-5
State	Published - May 22 2018

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https://repository.kaust.edu.sa/bitstream/10754/627974/1/s12864-018-4796-5.pdf

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Othoum, G. K., Bougouffa, S., Mohamad Razali, R., Bokhari, A., Alamoudi, S., Antunes, A., Gao, X., Hoehndorf, R., Arold, S. T., Gojobori, T., Hirt, H., Mijakovic, I., Bajic, V. B., Lafi, F. F., & Essack, M. (2018). In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters. BMC Genomics, 19(1). https://doi.org/10.1186/s12864-018-4796-5

@article{24e41b7c3fa54fe5a46a75164966e8bc,

title = "In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters",

abstract = "BackgroundThe 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.ResultsWe 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.ConclusionsB. 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.",

author = "Othoum, {Ghofran K.} and Salim Bougouffa and {Mohamad Razali}, Rozaimi and Ameerah Bokhari and Soha Alamoudi and Andr{\'e} Antunes and Xin Gao and Robert Hoehndorf and Arold, {Stefan T.} and Takashi Gojobori and Heribert Hirt and Ivan Mijakovic and Bajic, {Vladimir B.} and Lafi, {Feras Fawzi} and Magbubah Essack",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): FCC/1/1976–02-01, FCS/1/2911–01-01, BAS/1/1606–01-01, URF/1/1976–06-01, BAS/1/1624–01-01, BAS/1/1659–01-01, BAS/1/1059–01-01 Acknowledgements: The authors wish to acknowledge the experimental support from the King Abdullah University of Science and Technology (KAUST) Bioscience Core Laboratory. The research reported in this publication was supported by King Abdullah University of Science and Technology (KAUST) through the Awards Nos. FCC/1/1976–02-01, FCS/1/2911–01-01, BAS/1/1606–01-01, URF/1/1976–06-01, BAS/1/1624–01-01, BAS/1/1659–01-01, BAS/1/1059–01-01 from the Office of Sponsored Research (OSR).",

year = "2018",

month = may,

day = "22",

doi = "10.1186/s12864-018-4796-5",

language = "English (US)",

volume = "19",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central Ltd.",

number = "1",

}

TY - JOUR

T1 - In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

AU - Othoum, Ghofran K.

AU - Bougouffa, Salim

AU - Mohamad Razali, Rozaimi

AU - Bokhari, Ameerah

AU - Alamoudi, Soha

AU - Antunes, André

AU - Gao, Xin

AU - Hoehndorf, Robert

AU - Arold, Stefan T.

AU - Gojobori, Takashi

AU - Hirt, Heribert

AU - Mijakovic, Ivan

AU - Bajic, Vladimir B.

AU - Lafi, Feras Fawzi

AU - Essack, Magbubah

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): FCC/1/1976–02-01, FCS/1/2911–01-01, BAS/1/1606–01-01, URF/1/1976–06-01, BAS/1/1624–01-01, BAS/1/1659–01-01, BAS/1/1059–01-01 Acknowledgements: The authors wish to acknowledge the experimental support from the King Abdullah University of Science and Technology (KAUST) Bioscience Core Laboratory. The research reported in this publication was supported by King Abdullah University of Science and Technology (KAUST) through the Awards Nos. FCC/1/1976–02-01, FCS/1/2911–01-01, BAS/1/1606–01-01, URF/1/1976–06-01, BAS/1/1624–01-01, BAS/1/1659–01-01, BAS/1/1059–01-01 from the Office of Sponsored Research (OSR).

PY - 2018/5/22

Y1 - 2018/5/22

N2 - BackgroundThe 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.ResultsWe 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.ConclusionsB. 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.

AB - BackgroundThe 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.ResultsWe 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.ConclusionsB. 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.

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UR - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4796-5

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SN - 1471-2164

VL - 19

JO - BMC Genomics

JF - BMC Genomics

IS - 1

ER -

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

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