Draft genome sequence of Actinomadura sp. K4S16 and elucidation of the nonthmicin biosynthetic pathway

Hisayuki Komaki^1✉, Enjuro Harunari², Natsuko Ichikawa³, Akira Hosoyama³, Moriyuki Hamada¹, Kannika Duangmal⁴, Arinthip Thamchaipenet⁴, Yasuhiro Igarashi²

1. Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Kisarazu, Chiba 292-0818, Japan.
2. Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan.
3. NBRC, Shibuya-ku, Tokyo 151-0066, Japan.
4. Faculty of Science, Kasetsart University, Bangkok, Thailand.

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Citation:
Komaki H, Harunari E, Ichikawa N, Hosoyama A, Hamada M, Duangmal K, Thamchaipenet A, Igarashi Y. Draft genome sequence of Actinomadura sp. K4S16 and elucidation of the nonthmicin biosynthetic pathway. J Genomics 2020; 8:53-61. doi:10.7150/jgen.44650. Available from https://www.jgenomics.com/v08p0053.htm

Abstract

Actinomadura sp. K4S16 (=NBRC 110471) is a producer of a novel tetronate polyether compound nonthmicin. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation and analysis of the genome sequence. The 9.6 Mb genome of Actinomadura sp. K4S16 encoded 9,004 putative ORFs, of which 7,701 were assigned with COG categories. The genome contained four type-I polyketide synthase (PKS) gene clusters, two type-II PKS gene clusters, and three nonribosomal peptide synthetase (NRPS) gene clusters. Among the type-I PKS gene (t1pks) clusters, a large t1pks cluster was annotated to be responsible for nonthmicin synthesis based on bioinformatic analyses. We also performed feeding experiments using labeled precursors and propose the biosynthetic pathway of nonthmicin.

Keywords: Actinomadura, biosynthesis, nonthmicin, polyether, polyketide, tetronate