from David E. Whitworth writing in Bacterial Regulatory Networks:

Two-component systems (TCSs) are signalling pathways found abundantly in prokaryotes, and they are the dominant mechanism for stimulus-responsive adaptation in such organisms. An ever-increasing number of physiological phenomena are known to be regulated by TCSs, including cell cycle progression, pathogenesis, motility, and biofilm formation. The basic TCS comprises a receptor protein (sensor kinase) which autophosphorylates in response to a stimulus. The phosphoryl group is then directly transferred to a response regulator protein (the second component) that has a phosphorylation-dependent effector function. While the most basic TCSs are relatively well understood, there are many 'atypical' systems, which exhibit additional mechanistic features (for instance, regulation of sub-cellular location, intrinsic and extrinsic phosphatase activities, and cross-communication between TCSs), adding complexity to their signalling properties. The relatively recent availability of complete prokaryotic genome sequences has also provided new opportunities to appreciate global features of TCS function. For example, analyses have provided insights into TCS evolution, which in turn have yielded computational methods for evaluating TCS protein partnerships. This chapter provides an overview of the common features of TCSs from a historical perspective, and then describes current understanding regarding the mechanisms of TCS function. Finally, outstanding questions regarding TCS function are discussed.

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from Ernesto Perez-Rueda, Nancy Rivera-Gomez, Mario Alberto Martinez-Nuñez and Silvia Tenorio-Salgado writing in Bacterial Regulatory Networks:

The capabilities of organisms to contend with environmental changes depend on their repertoire of genes and their ability to regulate their expression. DNA-binding transcription factors have a fundamental role in this process, because they regulate transcription positively or negatively as a consequence of environmental signals. In this chapter we briefly describe some of the most recent findings on regulatory network evolution from the perspective of DNA-binding transcription factors. We explore diverse elements associated with the evolution of regulatory networks, such as gene duplication, where new interactions can emerge together with their upstream and downstream binding sites. The chapter is divided into sections covering the evolution of transcription factors and their domains, their evolution, and a global analysis. Hypotheses concerning a comprehensive picture of how regulatory networks have evolved in prokaryotes and the role of transcription factors in this organization are discussed.

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from Karlijn C. Bastiaansen, Wilbert Bitter and María A. Llamas writing in Bacterial Regulatory Networks:

Gene expression in bacteria is mainly controlled at the level of transcription initiation. To achieve this process a number of different mechanisms have evolved, one of which is the utilization of alternative sigma factors. Sigma factors are small proteins that associate with the RNA polymerase core enzyme (RNAPc) and direct it to specific promoter sequences, where they initiate gene transcription. Bacteria are able to regulate transcription initiation by synthesizing and activating different sigma factors that recognize different promoter consensus sequences. The largest group of alternative sigma factors consists of the so-called extracytoplasmic function (ECF) sigma factors that regulate gene expression in response to cell envelope stresses or environmental stimuli. The activity of ECF sigma factors is controlled by anti-sigma factors and a complex cascade of regulated (proteolytic) modifications. In gram-negative bacteria, ECF sigma factors are also controlled by cell-surface signalling (CSS), a regulatory system that includes an outer membrane receptor in the signal transduction pathway. In this chapter we will discuss the general composition and function of ECF sigma factors and their role in cell envelope stress responses and CSS.

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from J. Maxwell Dow, Yvonne McCarthy, Karen O'Donovan, Delphine Caly and Robert P. Ryan writing in Bacterial Regulatory Networks:

Cyclic di-GMP is now recognised as an almost universal second messenger in eubacteria that acts to regulate a wide range of functions including developmental transitions, adhesion, biofilm formation, motility and the synthesis of virulence factors. Cyclic di-GMP is synthesised from two GTP molecules by diguanylate cyclases that have a GGDEF domain and degraded by phosphodiesterases with either an EAL or HD-GYP domain. These proteins often have associated signal input domains, suggesting that their enzymatic activity may be modulated by different environmental or cellular cues. Cyclic di-GMP exerts a regulatory action through binding to diverse receptors that include a small protein domain called PilZ, transcription factors, enzymatically-inactive GGDEF, EAL or HD-GYP domains and riboswitches. The multiplicity of GGDEF, EAL and HD-GYP proteins together with a range of receptors within the same bacterial cell indicates the considerable complexity of cyclic di-GMP signalling. This has led to the concept of discrete pools of the nucleotide that are generated locally and act to influence intimately associated targets. A number of signalling proteins may be organised in a regulatory network to control a common function(s). Understanding cyclic di-GMP signalling may afford strategies for inhibition of biofilm formation and virulence factor synthesis in bacterial pathogens.

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from Patricia C. Burrows, Simone C. Wiesler, Zhensheng Pan, Martin Buck and Sivaramesh Wigneshweraraj writing in Bacterial Regulatory Networks:

Amongst the many accessory factors that bind RNA polymerase (RNAp) and serve to control its activities, sigma (σ) factors ubiquitously feature in programming of gene expression in response to abiotic and biotic cues. Here we review the role of the major variant σ factor, σ54, in the expression of gene sets used for establishing the virulence of a wide range of pathogenic bacteria. The tight coupling of σ54-dependent transcription to signalling pathways underpins the regulation of such systems, and allows a wide dynamic range of gene expression.

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from Kathryn A. Scott, Elizabeth E. Jefferys, Benjamin A. Hall, Mark A. J. Roberts and Judith P. Armitage writing in Bacterial Regulatory Networks:

Chemotaxis is the process by which bacteria migrate towards environments that are favourable for growth. Changes in the concentration of attractants or repellents are detected by receptors, which are usually transmembrane proteins. These receptors transduce the signal to the interior of the cell where a two-component system ultimately leads to changes in motile behaviour. Chemotaxis emerged as a beneficial trait for survival early in the evolution of bacteria and archaea. A core set of proteins is common to the chemosensory networks in many different species. During the evolution of bacteria this core network has diversified and expanded. Here we describe the conserved apparatus in the steps necessary for chemotaxis; sensing of chemoeffectors, signalling to the motility apparatus, rapid signal termination, and adaptation. We then highlight examples from species with complex chemosensory networks to illustrate the variations in chemotactic apparatus that have arisen from the common core.

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from Petra Tielen, Max Schobert, Elisabeth Hartig and Dieter Jahn writing in Bacterial Regulatory Networks:

Survival and growth during periods of low oxygen tension are essential for the successful colonization of natural habitats by bacteria. For the coordination of the necessary biochemical adaption processes upon oxygen deprivation bacteria employ a fine tuned interplay of various regulatory proteins and sRNAs. The iron sulfur cluster containing oxygen sensor Fnr and its multiple variants are often found involved in the corresponding regulatory networks throughout the bacterial kingdom. Similarly, the alternative electron acceptor nitrate is usually detected by the two-component system NarXL and its derivatives. In contrast, other systems including the quinone pool responsive two component system ArcBA, the ResDE system or the regulatory sRNAs FnrS and ArcZ are limited to certain bacterial groups. Here we describe the regulatory networks and their components underlying the adaption processes of the model bacteria Escherichia coli, Pseudomonas aeruginosa and Bacillus subtilis to an anaerobic life style.

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from Eberhard Klauck and Regine Hengge writing in Bacterial Regulatory Networks:

The σ^S (RpoS) sigma subunit is the master regulator of the general stress response in Escherichia coli, which controls the expression of more than 500 genes during entry into stationary phase or upon exposure to many different stress conditions. σ^S is present at very low levels only in rapidly growing cells, but multiple stress signals are integrated in a way that results in strong σ^S accumulation and efficient σ^S-containing RNAP holoenzyme (Eσ^S) formation. The first part of this review summarizes the molecular control mechanisms of switching from the "low-σ^S" to "high-σ^S" state, which operate at the levels of rpoS transcription, rpoS mRNA turnover and translation, σ^S proteolysis and Eσ^S formation, and outlines multiple stress signal integration into these highly interconnected regulatory processes. We then show that, despite its complexity, the σ^S control network essentially is an intricate combination of a few typical network motifs. These are several key feedforward loops that control σ^S expression, a central and homeostatic negative feedback loop that integrates post-transcriptional σ^S control mechanisms, mutual inhibition of sigma factors competing for RNAP core enzyme governing σ^S activity control, and a series of smaller positive feedback loops that seem to stabilize the "high-σ^S" state.

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