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Diversity of PKS and NRPS gene clusters between Streptomyces abyssomicinicus sp. nov. and its taxonomic neighbor

The Journal of Antibiotics volume 73, pages 141–151 (2020)Cite this article

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Abstract

Streptomyces sp. CHI39, isolated from a rock soil sample, is a producer of abyssomicin I. The taxonomic status was clarified by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to Streptomyces fragilis, with similarity of 99.9%. Strain CHI39 comprised LL-diaminopimelic acid, glutamic acid, glycine, and alanine in its peptidoglycan. The predominant menaquinones were MK-9(H6), and major fatty acids were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The chemotaxonomic features matched those described for the genus Streptomyces. Genome sequencing was conducted for strain CHI39 and S. fragilis NBRC 12862T. The results of digital DNA–DNA hybridization along with differences in phenotypic characteristics between the strains suggested strain CHI39 to be a novel species, for which Streptomyces abyssomicinicus sp. nov. is proposed; the type strain is CHI39T (=NBRC 110469T). Next, we surveyed polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters in genomes of S. abyssomicinicus CHI39T and S. fragilis NBRC 12862T. These strains encoded 9 and 12 clusters, respectively, among which only four clusters were shared between them while the others are specific in each strain. This suggests that strains classified to distinct species each harbor many specific secondary metabolite-biosynthetic pathways even if the strains are taxonomically close.

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Acknowledgements

This study was supported in part by the commissioned project from the Japan Patent Office. We are grateful to Ms Satomi Saitou for assistance of taxonomic experiments. We thank Mr Munemitsu Yuasa, Ms Satomi Miura, and Ms Maiko Hashimoto for sequencing the genomes. We also thank Ms Yuko Kitahashi and Ms Aya Uohara for finishing the genome sequences, annotating the NRPS and PKS genes and registering the genome sequences in the DDBJ.

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Authors and Affiliations

  1. Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Chiba, 292-0818, Japan

    Hisayuki Komaki & Tomohiko Tamura

  2. NBRC, Tokyo, 151-0066, Japan

    Kenta Sakurai, Akira Hosoyama & Akane Kimura

  3. Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain

    Martha E. Trujilo

  4. Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, 939-0398, Japan

    Yasuhiro Igarashi

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  1. Hisayuki Komaki
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Correspondence to Hisayuki Komaki.

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Komaki, H., Sakurai, K., Hosoyama, A. et al. Diversity of PKS and NRPS gene clusters between Streptomyces abyssomicinicus sp. nov. and its taxonomic neighbor. J Antibiot 73, 141–151 (2020). https://doi.org/10.1038/s41429-019-0261-1

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