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

Malik, Adeel; Kim, Yu Ri; Jang, In Hee; Hwang, Sunghoon; Oh, Dong-Chan; Kim, Seung Bum

doi:10.1186/s12864-020-6468-5

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

Journal Article · Mon Feb 03 00:00:00 EST 2020 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-020-6468-5· OSTI ID:1626827

Malik, Adeel ^[1]; Kim, Yu Ri ^[1]; Jang, In Hee ^[1]; Hwang, Sunghoon ^[2]; Oh, Dong-Chan ^[2];

^[1]

Chungnam National Univ., Daejeon (Korea, Republic of)
Seoul National Univ. (Korea, Republic of)

Background: 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. Results: A high quality draft genome (7.8Mb) 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. Conclusions: 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); Joint Genome Institute (JGI)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626827

Journal Information:: BMC Genomics, Vol. 21, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 11 works

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Additional file 1 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797566 The current record is supplemented by this image	image	January 2020
Additional file 1 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797566.v1 The current record is supplemented by this image	image	January 2020
Additional file 2 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797572 The current record is supplemented by this text	text	January 2020
Additional file 2 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797572.v1 The current record is supplemented by this text	text	January 2020
Additional file 3 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797578 The current record is supplemented by this image	image	January 2020
Additional file 3 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797578.v1 The current record is supplemented by this image	image	January 2020
Additional file 4 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797581 The current record is supplemented by this image	image	January 2020
Additional file 4 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797581.v1 The current record is supplemented by this image	image	January 2020
Additional file 5 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797584 The current record is supplemented by this image	image	January 2020
Additional file 5 of Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.11797584.v1 The current record is supplemented by this image	image	January 2020
Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.c.4841772 The current record is supplemented by this collection	collection	January 2020
Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium Malik, Adeel; Kim, Yu; Jang, In https://doi.org/10.6084/m9.figshare.c.4841772.v1 The current record is supplemented by this collection	collection	January 2020