Genome-Based Analysis of the Potential Bioactivity of the Terrestrial Streptomyces vinaceusdrappus Strain AC-40

Biology · 8 authors, 6 centres

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AGENT 01 · STRUCTURED SUMMARY

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TL;DR

Streptomyces vinaceusdrappus strain AC-40 was isolated from the rhizosphere of Pelargonium graveolens.

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993 CHARS

Streptomyces vinaceusdrappus strain AC-40 was isolated from the rhizosphere of Pelargonium graveolens. Its total metabolic extract exhibited antibacterial and antifungal activity against all tested pathogens. Whole genome sequencing and genome mining using AntiSMASH identified numerous secondary metabolite biosynthetic gene clusters (BGCs), with NRPS and terpene types most abundant. At least three clusters were homologs of known antimicrobials: streptothricin, candicidin, and albaflavenone, which may explain the observed broad-spectrum antimicrobial activity. Additional BGCs were related to isorenieratene (antioxidant), ectoine (osmoprotectant), siderophores (coelichelin and coelibactin), and lanthipeptides including a novel class I lanthipeptide and two class III clusters. At least five BGCs were highly conserved among rochei group genomes. The study identified gene clusters with little or no relation to known metabolites, suggesting potential for novel antimicrobial compounds.

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other

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preclinical research

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AI pipeline

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ORIGINAL PAPER

PMC10044865

Genome-Based Analysis of the Potential Bioactivity of the Terrestrial Streptomyces vinaceusdrappus Strain AC-40

Biology

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ABSTRACT

Simple Summary The problem of antimicrobial resistance represents a real danger to mankind. There is a crucial necessity to search for new antibiotics. The current advances in sequencing techniques and bioinformatics represent a critical tool for finding out the hidden biosynthetic capabilities within bacterial genomes and finding out novel active secondary metabolites. In this work, we managed to recover the Streptomyces vinaceusdrappus strain AC-40, a rhizobacterium with potent and broad-spectrum antimicrobial activity. We made whole genome sequencing and genome mining for the genes and gene clusters related to beneficial traits such as the production of secondary metabolites and plant growth promotion. Abstract Streptomyces are factories of antimicrobial secondary metabolites. We isolated a Streptomyces species associated with the Pelargonium graveolens rhizosphere. Its total metabolic extract exhibited potent antibacterial and antifungal properties against all the tested pathogenic microbes. Whole genome sequencing and genome analyses were performed to take a look at its main characteristics and to reconstruct the metabolic pathways that can be associated with biotechnologically useful traits. AntiSMASH was used to identify the secondary metabolite gene clusters. In addition, we searched for known genes associated with plant growth-promoting characteristics. Finally, a comparative and pan-genome analysis with three closely related genomes was conducted. It was identified as Streptomyces vinaceusdrappus strain AC-40. Genome mining indicated the presence of several secondary metabolite gene clusters. Some of them are identical or homologs to gene clusters of known metabolites with antimicrobial, antioxidant, and other bioactivities. It also showed the presence of several genes related to plant growth promotion traits. The comparative genome analysis indicated that at least five of these gene clusters are highly conserved through rochei group genomes. The genotypic and phenotypic characteristics of S. vinaceusdrappus strain AC-40 indicate that it is a promising source of beneficial secondary metabolites with pharmaceutical and biotechnological applications.

CITATION EXPORT

Abdelrahman M. Sedeek, Israa Salah, Hasnaa L. Kamel et al.. Genome-Based Analysis of the Potential Bioactivity of the Terrestrial Streptomyces vinaceusdrappus Strain AC-40. Biology. (2023). https://doi.org/10.3390/biology12030345

AUTHORS

8 · 6 CENTRES

Abdelrahman M. Sedeek, Israa Salah, Hasnaa L. Kamel, Mohamed A. Soltan, Eman Nour, Abdulrahman Alshammari, Muhammad Shahid Riaz Rajoka, Tarek R. Elsayed

1Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University—Kantara Branch, Ismailia 41522, Egypt
2Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo 11585, Egypt
3Faculty of Organic Agriculture, Heliopolis University for Sustainable Development, Cairo 11785, Egypt
4Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
5School of Dentistry, University of Maryland, Baltimore, MD 21201, USA
6Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza 12613, Egypt

EDITOR / REVIEWER

Fengli Zhang, Michel Denis