Isolation, genomic and metabolomic characterization of Streptomyces tendae VITAKN with quorum sensing inhibitory activity from Southern India

Nabila Mohammed Ishaque, Ilia Burgsdorf, Jessie James Limlingan Malit, Subhasish Saha, Roberta Teta, Daniela Ewe, Krishnan Kannabiran, Pavel Hrouzek, Laura Steindler, Valeria Costantino, Kumar Saurav

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article number121
JournalMicroorganisms
Volume8
Issue number1
DOIs
StatePublished - Jan 2020

Bibliographical note

Funding Information:
This study was supported by the Ministry of Education, Youth and Sports of the Czech Republic MSCA IF II project (CZ.02.2.69/0.0/0.0/18_070/0010493) and Czech Science foundation (GA?R)?Project No.19-17868Y). This research was also funded by Project ?Campania Oncoterapie? No. B61G18000470007. Finally, the study was supported by Cross-Border cooperation Czech?Bavaria?Project No. 41.

Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

  • Actinobacteria
  • Biosynthetic gene clusters (BGCs)
  • Cyclic dipeptides (2,5-diketopiperazines, DKPs)
  • Global natural product social networking (GNPS)
  • LC-HRMS
  • Natural product
  • Quorum sensing inhibition (QSI)

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)
  • Virology

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