Analysis of modularity in proteome-wide protein interaction networks of Methanothermobacter thermautotrophicus strain ΔH and metal-loving bacteria

Abstract

The proteins perform their functions independently and control all biological systems through protein–protein interaction (PPI) networks. The majority of proteins interact with others for proper biological activity in complex cellular and metabolic processes. A proteome-scale study affords the importance to reveal the function of molecular complexes and modularity of network architectures in microorganisms. In the present study, a PPI network has been developed for Methanothermobacter thermautotrophicus ΔH (MTH). The modular structure and hubs of the resulted network have been compared with PPI networks of metal-loving bacteria including Geobacter metallireducens and Geobacter sulfurreducens. Network quality and robustness were assessed with gene ontology terms. The predicted network of MTH consisted of 2450 edges and 256 nodes interacting with 564 metabolic genes. The metabolic link of interacting proteins was evaluated with efforts to mine experimental PPI data from the literature. The topological properties of each network model were robust and consistent for studying the network modularity. Besides, 172 different protein complexes were identified from the PPI network model of MTH in which 87 poorly characterized proteins characterized with certain functions. Core PPI networks in MTH and metal-loving bacteria were separately evolved and established for the organism-specific functions. Results of our study revealed that both MTH and metal-loving bacteria have a specialized PPI network module for electrical interplay systems in the geothermal environment.