Research articles
ScienceAsia 49 (2023):ID 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
|
