Insights from the protein-protein interaction network analysis of Mycobacterium tuberculosis toxin-antitoxin systems.

Zoozeal Thakur,Ajit Kumar,Renu Dharra,Vandana Saini,Promod K Mehta

doi:10.6026/97320630013380

Abstract

Protein-protein interaction (PPI) network analysis is a powerful strategy to understand M. tuberculosis (Mtb) system level physiology in the identification of hub proteins. In the present study, the PPI network of 79 Mtb toxin-antitoxin (TA) systems comprising of 167 nodes and 234 edges was investigated. The topological properties of PPI network were examined by 'Network analyzer' a cytoscape plugin app and STRING database. The key enriched biological processes and the molecular functions of Mtb TA systems were analyzed by STRING. Manual curation of the PPI data identified four proteins (i.e. Rv2762c, VapB14, VapB42 and VapC42) to possess the highest number of interacting partners. The top 15% hub proteins were identified in the PPI network by employing two statistical measures, i.e. betweenness and radiality by employing cytohubba. Insights gained from the molecular protein models of VapC9 and VapC10 are also documented.

Highlights

The ability of Mycobacterium tuberculosis (Mtb) to persist inside the host cells under a variety of adverse conditions including oxidative stress, nutrient starvation and hypoxia helps to understand pathogenesis [1, 2]
We report the topological and functional enrichment analysis of Protein-protein interaction (PPI) network of 79 Mtb TA systems constructed from STRING v10.5 and Cytoscape v3.5.0
PPI network analysis of Mtb TA systems: Protein-protein association data of 79 TA systems of Mtb H37Rv was extracted from STRING v 10.5

Summary

Introduction

The ability of Mycobacterium tuberculosis (Mtb) to persist inside the host cells under a variety of adverse conditions including oxidative stress, nutrient starvation and hypoxia helps to understand pathogenesis [1, 2]. We report the topological and functional enrichment analysis of PPI network of 79 Mtb TA systems constructed from STRING v10.5 and Cytoscape v3.5.0. Functional enrichment of input seed sequences of Mtb TA systems was carried out by STRING to identify significantly enriched GO (Gene Ontology) biological processes and molecular functions. Identification of Hub proteins: Cyto-Hubba [11], a java plugin for Cytoscape software, was employed to determine the hub proteins of PPI network of Mtb TA systems.

Results

Conclusion