Structure and evolution of gene regulatory networks in microbial genomes

Abstract

With the availability of genome sequences for hundreds of microbial genomes, it has become possible to address several questions from a comparative perspective to understand the structure and function of regulatory systems, at least in model organisms. Recent studies have focused on topological properties and the evolution of regulatory networks and their components. Our understanding of natural networks is paving the way to embedding synthetic regulatory systems into organisms, allowing us to expand the natural diversity of living systems to an extent we had never before anticipated.

Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?

“…The set of motifs that can bind to a particular DNA subsequence is randomly determined once and for all at the beginning of the evolutionary run. Like in most bacteria, the sign of the regulation depends on whether the binding occurs up or downstream from the first transcribed nucleotide (J an g a an d Collado-Vides, 2007). The resulting transcription level is used to scale up or down both the metabolic activity (height of the triangle) and the regulatory activities of the protein.…”

“…This value of affinity is used to determine the strength of the protein's influence on the transcriptional activity of the promoter it binds to. Like in most bacterial promoters, the nature of the regulation (activation or inhibition) depends on whether the binding occurs before (upstream) or after (downstream) the position of the first transcribed nucleotide (janga and Collado-Vides, 2007). Thus, in RAevol, a promoter is composed of three DNA subsequences: the consensus sequence (where the RNA polymerase starts the transcription process) and its two flanking regions.…”

Mathematical Modelling of Gene Regulatory Networks

“…Genomic view of gene regulatory network. From genomic perspective transcriptional regulation can be presented as an interplay between cis-regulatory elements and different transcription factors (Janga & Collado-Vides, 2007) The activity of functional genes is influenced by few factors: transcriptional factors and cofactor that effects transcription, by degradation of proteins and transcripts and by posttranslational modifications (Hecker et al, 2009). The idea of gene regulatory network is to describe dependence between molecules included in gene activity.…”

“…Although the number of completely sequenced genomes is mounting rapidly, our knowledge of transcription regulation is limited to a few model organisms (Janga & Collado-Vides, 2007). The interactive regulation of genes, working together to create gene networks has been considered the origin of many functions of organism (Mochizuki, 2008).…”

Bacterial Promoter Features Description and Their Application on E. coli in silico Prediction and Recognition Approaches

“…In face of this, the detailing of the principals and the organization of transcriptional process is helpful for understanding the complexity of biological systems involved, for instance, cellular responses to environmental changes or in the molecular bases of many diseases caused by microbes (Janga & Collado-Vides, 2007).…”