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Front. Microbiol. | doi: 10.3389/fmicb.2018.03139

Genome Mining of Streptomyces sp. YIM 130001 Isolated from Lichen Affords new Thiopeptide Antibiotic

 Olha Schneider1,  Nebojsa Simic1, Finn L. Aachmann1,  Christian Rückert2, Kåre A. Kristiansen1,  Joern Kalinowski2, Yi Jiang3, Lisong Wang4, Cheng-lin Jiang3,  Rahmi Lale1 and  Sergey B. Zotchev5*
  • 1Norwegian University of Science and Technology, Norway
  • 2Bielefeld University, Germany
  • 3Yunnan University, China
  • 4Kunming Institute of Botany (CAS), China
  • 5Department of Pharmacognosy, Universität Wien, 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.

Keywords: Streptomyces sp. from lichen, genome mining, Antibacterial activity, new thiopeptide antibiotic, berninamycins

Received: 18 Sep 2018; Accepted: 04 Dec 2018.

Edited by:

Learn-Han Lee, Novel Bacteria and Drug Discovery Research Group (NBDD), Monash University Malaysia, Malaysia

Reviewed by:

Kelle C. Freel, University of Hawaii at Manoa, United States
Dipesh Dhakal, Sun Moon University, South Korea
Wei Li Thong, University of Manchester, United Kingdom  

Copyright: © 2018 Schneider, Simic, Aachmann, Rückert, Kristiansen, Kalinowski, Jiang, Wang, Jiang, Lale and Zotchev. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Sergey B. Zotchev, Universität Wien, Department of Pharmacognosy, Vienna, 7491, Austria, sergey.zotchev@univie.ac.at