Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization

Corynebacterium Glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small Rna and Protein-Protein Interactions

“…There are three types of nodes in the C. glutamicum networks that we study here: genes, heteromeric protein complexes, and sRNAs. Heteromeric protein complexes are conformed by two or more regulatory proteins transcribed by different genes and are included in the network to reduce redundancy and improve the accuracy of the representation [1]. The effect of the sRNAs regulatory interactions is carried out at the post-transcriptional level.…”

“…C. glutamicum is an industrially relevant organism due to its amino acids production proficiency. It is also a model organism in the study of the regulatory networks [1], along with other organisms such as Escherichia coli, Bacillus subtilis, and Streptomyces coelicolor; which are usually used for comparison purposes. C. glutamicum grows by apical elongation, unlike B. subtilis and E. coli that grow by lateral elongation [2].…”

“…Despite being model organisms, their global regulatory networks still incomplete [1] and the scenario is worst for non-model organisms. Even though high-throughput technologies speed up the reconstruction of regulatory networks, it results in biased structural properties of the networks when compared with other reconstructions performed mainly by conventional approaches [6].…”

“…Prove of that is their modest performance for model organisms in the DREAM5 challenge [7] and the inconsistency between gene expression data and the model used for regulatory networks [8]. Although a re-assessment is required with more complete networks and a larger number of model organisms [1]. An integrative approach of expression data and regulatory binding sites have shown to improve the prediction, although most of that improvement is by the binding site's approach, which provides more biological information (e.g., [8])…”

“…After this update, C. glutamicum moved from the fourth to the second position as the organism with the most complete regulatory network in Abasy, according to our recently published model of the total number of interactions a complete regulatory network has. We discuss the global structural properties of the three network models in the context of the previous versions for the transcriptional regulatory models and more than 40 other bacterial networks from Abasy Atlas, the most complete collection of experimentally-validated regulatory networks [1]. We analyzed the organizing principles and the system-level components of the three networks to identify the effects of the inclusion of interactions supported by non-strong experiments, protein-protein interactions, and the post-transcriptional layer regulation by sRNAs.…”