from Sarath Chandra Janga and Gabriel Moreno-Hagelsieb writing in Bacterial Gene Regulation and Transcriptional Networks:

An average of 60% of prokaryotic genes are organized into operons-polycistronic transcription units, making them a very important feature of their genomic organization. Operons most commonly contain genes whose products have functional associations and are abundant because they constitute an easy means for coregulation and the associated genes can act as a functional unit with a higher success rate in horizontal gene transfer events than single genes. Operons are transcribed from a single promoter, thus rarely needing genomic features between their constituting genes, naturally resulting in shorter distances between genes in operons than between adjacent genes in different transcription units. Thus, operons can be predicted based on distances between adjacent genes in the same DNA strand. This feature, intergenic distance, is the most informative criterion for predicting operons. However, predictions based on conservation of gene order followed by phylogenetic profiles, provide cleaner predictions, albeit with much lower coverage. Transcriptional terminators and other sequence features might add quality to operon predictions, but the gain is minimal for most prokaryotes. Operon organization is not well conserved with evolutionary divergence. However, operons rearrange in a functionally coherent manner. Thus, the combination of operon predictions with operon rearrangements constitutes the most powerful source for the prediction of functional associations by genomic context in prokaryotes.

Further reading: Bacterial Gene Regulation and Transcriptional Networks

from Agustino Martínez-Antonio writing in Bacterial Gene Regulation and Transcriptional Networks:

Transcription factors function as sensory systems acting at the core of genetic regulatory switches. The transcriptional regulatory network in Escherichia coli can be studied as the integration of the whole of these genetic sensory systems. The operation of this regulatory system affect the expression of genes by interacting with the DNA at the promoter regions of transcription units. In this review I present the advances of what we know about the mechanistic logic for the operation of the regulatory program in E. coli. It is proposed that for a better understanding on the operation of the regulatory network it should be considered the globalism of transcription factors, the signal perceived by each, their co-regulating activity, the genome position of regulatory and target genes, and cellular concentration of the regulatory proteins, among others.

Further reading: Bacterial Gene Regulation and Transcriptional Networks

from Alberto Danielli and Vincenzo Scarlato writing in Bacterial Gene Regulation and Transcriptional Networks:

The human gastric pathogen Helicobacter pylori appears to enroll only 17 transcriptional regulators to transduce environmental signals into coordinated output expression of the genome. We show that the low number of transcriptional regulators, together with the large body of molecular tools, set H. pylori as appealing model organism to characterize transcriptional network structures involved in virulence regulation and host-pathogen interactions. In particular we provide evidence that the regulators are wired in a shallow transcriptional regulatory network (TRN), which orchestrates the key physiological responses needed to colonize the gastric niche: heat and stress response, motility and chemotaxis, acid acclimation and metal ion homeostasis. Interestingly, long regulatory cascades are absent, and rather than having a plethora of specialized regulators, the TRN of H. pylori appears to transduce separate environmental inputs by using different combinations of a small set of regulators. It is not tailored to adapt to many environmental stimuli, and apparently not flexible to react to metabolic signals encountered outside of the gastric niche. On the other hand, the predominance of negative regulatory interactions suggests that this architecture of the TRN evolved to quickly respond to changing conditions in the gastric niche in order to maintain homeostasis. Metal-responsive regulators such as NikR and Fur appear to have a very important role in this TRN, forming a central regulatory hub, with regulatory interaction feeding into all other sub-network circuits.

Further reading: Bacterial Gene Regulation and Transcriptional Networks

from Stephen J. W. Busby and Stephen D. Minchin writing in Bacterial Gene Regulation and Transcriptional Networks:

The traditional methods for discovering transcriptional regulatory networks in bacteria, based on genetics and biochemistry, are now being replaced by high throughput pan-genome methods. Experimental approaches include methods involving RNA or methods based on the direct observation of transcription factors. This review places the new methods in context and discusses their potential benefits and drawbacks.

Further reading: Bacterial Gene Regulation and Transcriptional Networks

from Georgi Muskhelishvili and Andrew Travers writing in Bacterial Gene Regulation and Transcriptional Networks:

In the bacterial nucleoid different configurations of negatively supercoiled DNA are constrained by different NAPs. Thus while H-NS can constrain, by bridging, the interwindings of plectonemic structure, HU induces a left-handed coiled configuration while FIS can bind within DNA loops. The topological and dynamic interconvertibility of these structures contributes substantially to the regulation of gene expression in bacteria. We review here some of the mechanisms involved and argue that they form the basis for a coordination of gene transcription which results in the establishment of a single interconnected heterarchical control system that is responsible both for maintaining, when appropriate, a homoeostatic control of growth and also for mediating transitions between different cellular physiological states.

Further reading: Bacterial Gene Regulation and Transcriptional Networks

from Yuko Makita and Kenta Nakai writing in Bacterial Gene Regulation and Transcriptional Networks:

Bacillus subtilis is a soil living bacterium, long known as a representative of the low G+C group of Gram-positive bacteria in contrast to Escherichia coli, a representative of Gram-negative bacteria. Its genome contains about 4,176 protein-coding genes and 178 RNA genes. The number of sigma factors is 18, which is much larger than 7 in E. coli. Although there are very few theoretical studies of its global transcriptional network, our preliminary analysis based on experimentally validated data stored in the DBTBS database suggests that it is a typical scale-free network largely governed by a small number of hub transcription factors like that of many other model organisms. However, some of the results of the network motif analysis in E. coli were not confirmed in B. subtilis. Although this is likely to be due to the small sample size in B. subtilis, a more cautious approach might be necessary to perform network motif analyses of bacterial gene regulatory networks, which are not so large, in general. As a specific sub-network, the gene regulatory network for sporulation, which is regarded as a model of eukaryotic differentiation process, is described. In the description of the network, not only transcriptional regulation but also post-translational regulation as well as genome recombination are necessary.

Further reading: Bacterial Gene Regulation and Transcriptional Networks