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Open AccessArticle

Isolation, Genomic and Metabolomic Characterization of Streptomyces tendae VITAKN with Quorum Sensing Inhibitory Activity from Southern India

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Department of Biomedical Sciences, School of Biosciences and Technology, VIT University, Vellore 632014, India
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Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 31905, Israel
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Department of Ocean Science, Division of Life Science and Hong Kong, Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
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Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Opatovickýmlýn, Novohradská 237, 37981 Třeboň, Czech Republic
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The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
*
Authors to whom correspondence should be addressed.
Microorganisms 2020, 8(1), 121; https://doi.org/10.3390/microorganisms8010121
Received: 30 December 2019 / Revised: 12 January 2020 / Accepted: 13 January 2020 / Published: 16 January 2020
(This article belongs to the Collection Feature Papers in Environmental Microbiology)
Streptomyces are among the most promising genera in terms of production ability to biosynthesize a variety of bioactive secondary metabolites with pharmaceutical interest. Coinciding with the increase in genomic sequencing of these bacteria, mining of their genomes for biosynthetic gene clusters (BGCs) has become a routine component of natural product discovery. Herein, we describe the isolation and characterization of a Streptomyces tendae VITAKN with quorum sensing inhibitory (QSI) activity that was isolated from southern coastal part of India. The nearly complete genome consists of 8,621,231bp with a GC content of 72.2%. Sequence similarity networks of the BGCs detected from this strain against the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) database and 3365 BGCs predicted by antiSMASH analysis of publicly available complete Streptomyces genomes were generated through the BiG-SCAPE-CORASON platform to evaluate its biosynthetic novelty. Crude extract analysis using high-performance liquid chromatography connected to high resolution tandem mass spectrometry (HPLC-HRMS/MS) and dereplication through the Global Natural Product Social Molecular Networking (GNPS) online workflow resulted in the identification of cyclic dipeptides (2, 5-diketopiperazines, DKPs) in the extract, which are known to possess QSI activity. Our results highlight the potential of genome mining coupled with LC-HRMS/MS and in silico tools (GNPS) as a valid approach for the discovery of novel QSI lead compounds. This study also provides the biosynthetic diversity of BGCs and an assessment of the predicted chemical space yet to be discovered. View Full-Text
Keywords: natural product; actinobacteria; quorum sensing inhibition (QSI); biosynthetic gene clusters (BGCs); global natural product social networking (GNPS); cyclic dipeptides (2,5-diketopiperazines, DKPs); LC-HRMS natural product; actinobacteria; quorum sensing inhibition (QSI); biosynthetic gene clusters (BGCs); global natural product social networking (GNPS); cyclic dipeptides (2,5-diketopiperazines, DKPs); LC-HRMS
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MDPI and ACS Style

Ishaque, N.M.; Burgsdorf, I.; Limlingan Malit, J.J.; Saha, S.; Teta, R.; Ewe, D.; Kannabiran, K.; Hrouzek, P.; Steindler, L.; Costantino, V.; Saurav, K. Isolation, Genomic and Metabolomic Characterization of Streptomyces tendae VITAKN with Quorum Sensing Inhibitory Activity from Southern India. Microorganisms 2020, 8, 121.

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