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Front Microbiol. 2018 Dec 19;9:3139. doi: 10.3389/fmicb.2018.03139. eCollection 2018.

Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic.

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Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway.
Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
Yunnan Institute of Microbiology, Yunnan University, Kunming, China.
Key Lab for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
Department of Pharmacognosy, University of Vienna, Vienna, Austria.


Streptomyces bacteria are recognized as an important source for antibiotics with broad applications in human medicine and animal health. Here, we report the isolation of a new lichen-associating Streptomyces sp. YIM 130001 from the tropical rainforest in Xishuangbanna (Yunnan, China), which displayed antibacterial activity against Bacillus subtilis. The draft genome sequence of this isolate strain revealed 18 putative biosynthetic gene clusters (BGCs) for secondary metabolites, which is an unusually low number compared to a typical streptomycete. Inactivation of a lantibiotic dehydrogenase-encoding gene from the BGC presumed to govern biosynthesis of a thiopeptide resulted in the loss of bioactivity. Using comparative HPLC analysis, two peaks in the chromatogram were identified in the extract from the wild-type strain, which were missing in the extract from the mutant. The compounds corresponding to the identified peaks were purified, and structure of one compound was elucidated using NMR. The compound, designated geninthiocin B, showed high similarity to several 35-membered macrocyclic thiopeptides geninthiocin, Val-geninthiocin and berninamycin A. Bioinformatics analysis of the geninthiocin B BGC revealed its close homology to that of berninamycins.


antibacterial activity; berninamycins; genome mining; new Streptomyces sp. from lichen; new thiopeptide antibiotic

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