Corynebacterium glutamicum regulation beyond transcription: Organizing principles and reconstruction of an extended regulatory network incorporating regulations mediated by small RNA and protein-protein interactions

TL;DR

This study constructs and compares comprehensive regulatory network models for Corynebacterium glutamicum, integrating transcriptional, post-transcriptional, and protein-protein interactions to better understand its complex regulation.

Contribution

It presents three extended regulatory network models incorporating various evidence types, including sRNA and protein interactions, significantly expanding previous models.

Findings

Increased network interactions by up to 1225 compared to 2018

Inclusion of sRNA regulations altered network modularity

C. glutamicum's regulatory structure differs from other bacteria

Abstract

Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here, we report three regulatory network models for C. glutamicum: strong (3040 interactions) constructed solely with regulations previously supported by directed experiments; all evidence (4665 interactions) containing the strong network, regulations previously supported by non-directed experiments, and protein-protein interactions with a direct effect on gene transcription; and sRNA (5222 interactions) containing the all evidence network and sRNA-mediated regulations. Compared to the previous version (2018), the strong and all evidence networks increased by 75 and 1225 interactions, respectively. We analyzed the system-level components of the three networks to identify how they differ and compared their structures against those for the networks of more than 40 species. The inclusion of the sRNAs regulations changed the proportions of the system-level components and increased the number of modules but decreased their size. The C. glutamicum regulatory structure contrasted with other bacterial regulatory networks. Finally, we used the strong networks of three model organisms to provide insights and future directions of the C. glutamicum regulatory network characterization.