Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis


Kutnu M., İşlerel E. T. , TUNÇBAĞ N., ÖZCENGİZ G.

Integrative biology : quantitative biosciences from nano to macro, vol.14, no.5, pp.99-110, 2022 (Peer-Reviewed Journal) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 14 Issue: 5
  • Publication Date: 2022
  • Doi Number: 10.1093/intbio/zyac010
  • Journal Name: Integrative biology : quantitative biosciences from nano to macro
  • Journal Indexes: Science Citation Index Expanded, Scopus, BIOSIS, Biotechnology Research Abstracts, CAB Abstracts, EMBASE, INSPEC, MEDLINE, Veterinary Science Database
  • Page Numbers: pp.99-110
  • Keywords: Bacillus subtilis, bacilysin, proteomics, network modeling, clustering, pathway analysis, GLOBAL REGULATOR CODY, INSERTIONAL MUTATIONS, CCPA PROTEIN, MECHANISM, GENES, CELL, ACTIVATION, STRESS, GROWTH

Abstract

© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.The Gram-positive bacterium Bacillus subtilis produces a diverse range of secondary metabolites with different structures and activities. Among them, bacilysin is an enzymatically synthesized dipeptide that consists of L-alanine and L-anticapsin. Previous research by our group has suggested bacilysin's role as a pleiotropic molecule in its producer, B. subtilis PY79. However, the nature of protein interactions in the absence of bacilysin has not been defined. In the present work, we constructed a protein-protein interaction subnetwork by using Omics Integrator based on our recent comparative proteomics data obtained from a bacilysin-silenced strain, OGU1. Functional enrichment analyses on the resulting networks pointed to certain putatively perturbed pathways such as citrate cycle, quorum sensing and secondary metabolite biosynthesis. Various molecules, which were absent from the experimental data, were included in the final network. We believe that this study can guide further experiments in the identification and confirmation of protein-protein interactions in B. subtilis.