Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution.
Biosynthetic gene clusters
Brevibacterium
Comparative genomics
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
19 Oct 2023
19 Oct 2023
Historique:
received:
11
06
2023
accepted:
21
09
2023
medline:
23
10
2023
pubmed:
20
10
2023
entrez:
19
10
2023
Statut:
epublish
Résumé
Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.
Identifiants
pubmed: 37858045
doi: 10.1186/s12864-023-09694-7
pii: 10.1186/s12864-023-09694-7
pmc: PMC10588199
doi:
Substances chimiques
Anti-Bacterial Agents
0
Phenazines
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
622Subventions
Organisme : Agencia Nacional de Investigación y Desarrollo
ID : 21191625
Organisme : Agencia Nacional de Investigación y Desarrollo
ID : 1221264
Informations de copyright
© 2023. BioMed Central Ltd., part of Springer Nature.
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