Genome Mining Revealed a High Biosynthetic Potential for Antifungal Streptomyces sp. S-2 Isolated from Black Soot.

Piotr Siupka,Dagmara Babicka,Artur Piński,Zofia Piotrowska-Seget

doi:10.3390/ijms21072558

Piotr Siupka, Dagmara Babicka + Show 2 more

Open Access

https://doi.org/10.3390/ijms21072558

Copy DOI

Abstract

The increasing resistance of fungal pathogens has heightened the necessity of searching for new organisms and compounds to combat their spread. Streptomyces are bacteria that are well-known for the production of many antibiotics. To find novel antibiotic agents, researchers have turned to previously neglected and extreme environments. Here, we isolated a new strain, Streptomyces sp. S-2, for the first time, from black soot after hard coal combustion (collected from an in-use household chimney). We examined its antifungal properties against plant pathogens and against fungi that potentially pose threat to human health (Fusarium avenaceum, Aspergillus niger and the environmental isolates Trichoderma citrinoviridae Cin-9, Nigrospora oryzae sp. roseF7, and Curvularia coatesieae sp. junF9). Furthermore, we obtained the genome sequence of S-2 and examined its potential for secondary metabolites production using anti-SMASH software. The S-2 strain shows activity against all of the tested fungi. Genome mining elucidated a vast number of biosynthetic gene clusters (55), which distinguish this strain from closely related strains. The majority of the predicted clusters were assigned to non-ribosomal peptide synthetases or type 1 polyketide synthetases, groups known to produce compounds with antimicrobial activity. A high number of the gene clusters showed no, or low similarity to those in the database, raising the possibility that S-2 could be a producer of novel antibiotics. Future studies on Streptomyces sp. S-2 will elucidate its full biotechnological potential.

Highlights

Streptomyces, a genus of Actinobacteria, includes over 800 species described so far [1]
Streptomyces are a major source for antibiotics used by humans, as they produce over two-thirds of the clinically useful antibiotics that are of natural origin [1,5,6,7,8,9]
Advancements in sequencing and genome mining methods have shown that Streptomyces have greater than previously predicted potential to produce secondary metabolites, as a large number of biosynthetic gene clusters (BGCs) have been revealed [5,16,17,18,19]

Summary

Introduction

Streptomyces, a genus of Actinobacteria, includes over 800 species described so far [1] These bacteria are Gram-positive, have a large genome (8–10 Mbp) with high GC content, have a complex morphology, and are widespread in soil, where they play important roles in the degradation of organic matter and nutrient circulation (for a review, see [2]). The members of this genus are known producers of a wide variety of secondary metabolites that are important in medicine and industry [2,3,4]. The activation of BGCs from Streptomyces sclerotialus NRLP ISP-5269 using genetic engineering has led to the discovery of scleric acid, a new compound that is active against Mycobacterium tuberculosis [23]

Methods

Results

Conclusion