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Research articles

ScienceAsia 49 (2023): 661-669 |doi: 10.2306/scienceasia1513-1874.2023.067


Genomic analysis and physicochemical screening of ikarugamycin, fumaquinone, and a new compound, pudicin from Streptomyces sp. 3MP-14


Nattaporn Klykleunga,†, Hirotaka Matsuob,c,†, Masato Iwatsukic, Yoko Takahashic, Satoshi Omurac, Masahiro Yukid, Takuji Kudod, Moriya Ohkumad, Rataya Luechapudiporne, Somboon Tanasupawata,*, Takuji Nakashimac,f

 
ABSTRACT:     An endophytic actinomycete, strain 3MP-14 isolated from the root of Mimosa pudica belonged to the genus Streptomyces and was closely related to Streptomyces mimosae JCM 33328T (100%) based on 16S rRNA gene sequences. The strain had genome sizes of 7.2 Mb with genomic G+C contents of 73.4 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of strain 3MP-14 were 100% when compared with S. mimosae JCM 33328T . Based on the polyphasic approach, dDDH, and ANI, strain 3MP-14 was identified as Streptomyces mimosae. Twenty-four putative secondary metabolite biosynthetic gene clusters (BGCs) were identified from the draft genome analysis of strain 3MP-14. In the course of chemical investigation for the products of the strain, a physicochemical (PC) screening was conducted, and a new compound, designated as pudicin, and two known antimicrobials, ikarugamycin and fumaquinone, were identified. The structure elucidation of pudicin revealed a unique structurally new compound with N-acetylcysteine moiety using one-dimensional and two-dimensional nuclear magnetic resonance (1D and 2D NMR spectroscopy) and Electrospray Ionization Mass Spectrometry (ESI-MS). Pudicin showed slight antioxidative activity based on 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging method with the IC50 value of 394.89 ? 3.88 ?g/ml.

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a Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330 Thailand
b Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, 1-2 Hachimandai, Tsukuba 305-0843 Japan
c Omura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641 Japan
d Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
e Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330 Thailand
f Research Organization for Nano and Life Innovation, Waseda University, 513 Waseda, Tsurumaki-cho, Shin-juku-ku, Tokyo 162-0041 Japan

* Corresponding author, E-mail: Somboon.T@chula.ac.th

Received 16 Jan 2023, Accepted 4 Jun 2023