Identifying global regulators in transcriptional regulatory networks in bacteria.

By Agustino Martínez-Antonio, Julio Collado-Vides. Current Opinion in Microbiology, 2003

541 citations recorded by the source corpus.

The machinery for cells to take decisions, when environmental conditions change, includes protein-DNA interactions defined by transcriptional factors and their targets around promoters. Properties of global regulators are revised attempting to reach diagnostic explicit criteria for their definition and eventual future computational identification. These include among others, the number of regulated genes, the number and type of co-regulators, the different sigma-classes of promoters and the number of transcriptional factors they regulate, the size of the evolutionary family they belong to, and the variety of conditions where they exert their control. As a consequence, global versus local regulation can be identified, as shown for Escherichia coli and eventually in other genomes.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/38d33e0c7fb0ac91b434c140399f164f4153bd36

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Citations in the corpus

The regulation of bacterial transcription initiation (2004, background): “cgi?CB=CB006311">Lrp ; see Box 2 ) control 50% of all regulated genes, whereas ∼60 transcription factors control only a single promote”
Centrality Analysis Methods for Biological Networks and Their Application to Gene Regulatory Networks (2008, background): “%) identi ﬁ ed by Martínez-Antonio and Collado-Vides (2003) and outperforms the other centralities used.”
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein (2009, background): “T Escherichia coli catabolite activator protein (CAP) (1) is a transcriptional activator known to regulate hundreds of transcription units by responding to fluctuations of the cellular concentration of cAMP (2).”
Structure and evolution of transcriptional regulatory networks. (2004, unknown): “Martinez-Antonio and Collado-Vides [18 ] defined global regulators by taking into account additional factors, such as the number of co-regulators and the number of conditions.”
Genomic analysis of regulatory network dynamics reveals large topological changes (2004, background): “They are thought to target a broad spectrum of gene function”
Regulation of transcription from the fusion promoters generated by transposition of Tn4652 into the upstream region of pheBA operon in Pseudomonas putida (2005, unknown): “…in regulation of the transcription: 1) the global ones such as sigma factors affect many regulons (stimulons) and have the major role in transcriptional regulation; 2) specific regulators ensure the precise gene (operon) expression (Ishihama, 2000; Martinez-Antonio and Collado-Vides, 2003).”
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions (2005, background): “The definition of global regulators is obtained from (3).”
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond (2015, background): “0 hosts a GENSOR unit for each local TF (6) for which there is experimental evidence in the database.”