Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium

• Published in: BMC genomics Vol. 21; no. 1; p. 118
• Main Authors: Malik, Adeel, Kim, Yu Ri, Jang, In Hee, Hwang, Sunghoon, Oh, Dong-Chan, Kim, Seung Bum
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 03.02.2020; BioMed Central; Springer; BMC
• Subjects: Acidic soils; Adaptation; Antibiotics; Antiparasitic agents; Bacteria; BASIC BIOLOGICAL SCIENCES; Biodegradation; Biological activity; Biomass; Biopolymers; Biosynthesis; Biotechnology & Applied Microbiology; Carbohydrates; CAZyme; Cellulose; Chromatography; Composition; Core genome; Cysteine; Cystine; Drug resistance; Enzymes; Gene clusters; Genes; Genetic aspects; Genetic research; Genetics & Heredity; Genomes; Genomics; Gram-positive bacteria; High performance liquid chromatography; Liquid chromatography; Mass spectrometry; Mass spectroscopy; Metabolism; Metabolites; Methods; Microbial enzymes; Microorganisms; Neutrotolerant acidophilic; Novels; Peptides; Physiological aspects; Plant metabolites; Polymers; Secondary metabolite; Secondary metabolites; Similarity; Singletons; Sortase; Species; Spectroscopy; Streptomyces; Streptomyces yeochonensis; South Korea; Secondary metabolite; CAZyme; Neutrotolerant acidophilic; Core genome; Singletons; Sortase; Streptomyces yeochonensis
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-6468-5

Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. A high quality draft genome (7.8 Mb) of S. yeochonensis CN732 was obtained with a G + C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.