Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions

  title={Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions},
  author={Juan M. Escorcia-Rodr'iguez and Andreas Tauch and Julio A. Freyre-Gonz{\'a}lez},
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… 
3 Citations

Reconstruction of a global gene regulatory network for Streptomyces coelicolor: Curation, inference, and assessment

A low level of direct experimental validation is found for the regulatory interactions reported in the literature and curated in this work, and the structural properties and functional architecture of the networks are contrasted to assess the predictions’ reliability, finding the inference from DNA sequence data to be the most trustworthy.

Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor

This work manually curated 29 years of literature and databases to assemble a meta-curated experimentally-validated gene regulatory network (GRN) with 5386 genes and 9707 regulatory interactions that provides the most extensive and up-to-date reconstruction available for the regulatory circuitry of this organism.

System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks

A new layer is proposed, the concilion, which is the group of structural genes and their local regulators responsible for a single function that, organized hierarchically, coordinate a response in a way reminiscent of the deliberation and negotiation that take place in a council.



CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

  • J. Baumbach
  • Biology, Computer Science
    BMC Bioinformatics
  • 2007
The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks and is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms.

CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks

CoryneRegNet 7 is the largest TRN database for the Corynebacterium genus and aids in elucidating transcriptional mechanisms enabling adaptation, survival and infection.

Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus.

Regulogger is described, a novel computational method that uses comparative genomics to eliminate spurious members of predicted gene regulons and increases the specificity of predictions up to 25-fold over methods that use cis-element detection in isolation.

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

This work significantly expanded a reference collection of manually curated regulons, giving access to the transcriptional regulons reconstructed in bacterial genomes, and provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties.

Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

Reconstruction of TRNs helps to better understand the metabolism and functions of prokaryotic organisms and presents a level of control above the operons and permits coordinated control of operons that each have their own unique control.

From Corynebacterium glutamicum to Mycobacterium tuberculosis—towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet

A bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates a prediction of orthologous genes and the prediction of transcription factor binding sites is designed, and 460 regulatory interactions were identified for M. tuberculosis using the comparative approach.

The TetR Family of Regulators

The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.