Reconstructing and analyzing the experimentally-supported binary protein-protein interaction network of Moorella thermoacetica, an anaerobe of industrial interest

Abstract

There has been a rapidly increasing industrial interest in developing optimized engineering solutions for CO2 capture and subsequent conversion into biofuels and useful chemicals. The investigation of the non-photosynthetic CO2 bioconversion has gained momentum in the field of metabolic engineering and industrial biotechnology in recent years, as an alternative to the biomass-based microbial processes. Acetogens are bacteria, which possess the particular ability, using catabolically the relevant Wood – Ljungdahl (W-L) pathway. The thermophilic obligatory anaerobe, Moorella thermoacetica, has been the model acetogen due to its small fully-sequenced genome. Furthermore, its metabolic network has been reconstructed and relevant metabolic boundaries have been determined. However, its protein-protein interaction (PPI) network remains unexplored. In fact, PPI networks have not been studied extensively in bacteria. However, multi-omic analyses are crucial to further our understanding of bacterial molecular physiology and regulation and the integrated interpretation of omic datasets in the context of multi-level biomolecular networks is of great value and should be increasingly used in microbial research too. In this study, we extend the biomolecular analysis toolbox of M. thermoacetica by reconstructing a high-confidence experimentally-supported protein-protein interaction (PPI) network, based on (a) systematic literature curation, (b) comparative genomic analysis of the experimental binary PPI networks of Bacillus subtilis, an evolutionary adjacent microorganism, and the model bacterium Escherichia coli, and (c) the functional PPI resource STRING. The PPI network was further analyzed for its topology and pathway enrichment, including links to the metabolic network. The acquired results supported the need to pay better attention to the elucidation of the microbial PPI networks, especially of the extremophiles that have gained industrial interest.