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Molecular Mechanisms of Transcription Initiation at gal Promoters and their Multi-Level Regulation by GalR, CRP and DNA Loop

by Dale E.A. Lewis and Sankar Adhya

Biomolecules 2015, 5(4), 2782-2807; https://doi.org/10.3390/biom5042782 - 16 Oct 2015

Cited by 10 | Viewed by 12938

Abstract

Studying the regulation of transcription of the gal operon that encodes the amphibolic pathway of d-galactose metabolism in Escherichia coli discerned a plethora of principles that operate in prokaryotic gene regulatory processes. In this chapter, we have reviewed some of the more recent [...] Read more.

Studying the regulation of transcription of the gal operon that encodes the amphibolic pathway of d-galactose metabolism in Escherichia coli discerned a plethora of principles that operate in prokaryotic gene regulatory processes. In this chapter, we have reviewed some of the more recent findings in gal that continues to reveal unexpected but important mechanistic details. Since the operon is transcribed from two overlapping promoters, P1 and P2, regulated by common regulatory factors, each genetic or biochemical experiment allowed simultaneous discernment of two promoters. Recent studies range from genetic, biochemical through biophysical experiments providing explanations at physiological, mechanistic and single molecule levels. The salient observations highlighted here are: the axiom of determining transcription start points, discovery of a new promoter element different from the known ones that influences promoter strength, occurrence of an intrinsic DNA sequence element that overrides the transcription elongation pause created by a DNA-bound protein roadblock, first observation of a DNA loop and determination its trajectory, and piggybacking proteins and delivering to their DNA target. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution

by Mark S. Paget

Biomolecules 2015, 5(3), 1245-1265; https://doi.org/10.3390/biom5031245 - 26 Jun 2015

Cited by 220 | Viewed by 28318

Abstract

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the [...] Read more.

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2–4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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New Insights into the Functions of Transcription Factors that Bind the RNA Polymerase Secondary Channel

by Nikolay Zenkin and Yulia Yuzenkova

Biomolecules 2015, 5(3), 1195-1209; https://doi.org/10.3390/biom5031195 - 25 Jun 2015

Cited by 30 | Viewed by 7819

Abstract

Transcription elongation is regulated at several different levels, including control by various accessory transcription elongation factors. A distinct group of these factors interacts with the RNA polymerase secondary channel, an opening at the enzyme surface that leads to its active center. Despite investigation [...] Read more.

Transcription elongation is regulated at several different levels, including control by various accessory transcription elongation factors. A distinct group of these factors interacts with the RNA polymerase secondary channel, an opening at the enzyme surface that leads to its active center. Despite investigation for several years, the activities and in vivo roles of some of these factors remain obscure. Here, we review the recent progress in understanding the functions of the secondary channel binding factors in bacteria. In particular, we highlight the surprising role of global regulator DksA in fidelity of RNA synthesis and the resolution of RNA polymerase traffic jams by the Gre factor. These findings indicate a potential link between transcription fidelity and collisions of the transcription and replication machineries. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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Regulation of Transcription Elongation and Termination

by Robert S. Washburn and Max E. Gottesman

Biomolecules 2015, 5(2), 1063-1078; https://doi.org/10.3390/biom5021063 - 29 May 2015

Cited by 40 | Viewed by 9234

Abstract

This article will review our current understanding of transcription elongation and termination in E. coli. We discuss why transcription elongation complexes pause at certain template sites and how auxiliary host and phage transcription factors affect elongation and termination. The connection between translation [...] Read more.

This article will review our current understanding of transcription elongation and termination in E. coli. We discuss why transcription elongation complexes pause at certain template sites and how auxiliary host and phage transcription factors affect elongation and termination. The connection between translation and transcription elongation is described. Finally we present an overview indicating where progress has been made and where it has not. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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Initial Events in Bacterial Transcription Initiation

by Emily F. Ruff, M. Thomas Record, Jr. and Irina Artsimovitch

Biomolecules 2015, 5(2), 1035-1062; https://doi.org/10.3390/biom5021035 - 27 May 2015

Cited by 115 | Viewed by 14483

Abstract

Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of [...] Read more.

Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of the upstream duplex facilitates bending of the downstream duplex into the active site cleft, nucleating opening of 13 bp in the cleft. The rate-determining opening step, driven by binding free energy, forms an unstable open complex, probably with the template strand in the active site. At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the −10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP. The rate of open complex formation is regulated by effects on the rapidly-reversible steps preceding DNA opening, while open complex lifetime is regulated by effects on the stabilization of the initial open complex. Intrinsic DNA opening-closing appears less regulated. This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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A Perspective on the Enhancer Dependent Bacterial RNA Polymerase

by Nan Zhang and Martin Buck

Biomolecules 2015, 5(2), 1012-1019; https://doi.org/10.3390/biom5021012 - 21 May 2015

Cited by 21 | Viewed by 10361

Abstract

Here we review recent findings and offer a perspective on how the major variant RNA polymerase of bacteria, which contains the sigma54 factor, functions for regulated gene expression. We consider what gaps exist in our understanding of its genetic, biochemical and biophysical functioning [...] Read more.

Here we review recent findings and offer a perspective on how the major variant RNA polymerase of bacteria, which contains the sigma54 factor, functions for regulated gene expression. We consider what gaps exist in our understanding of its genetic, biochemical and biophysical functioning and how they might be addressed. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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Structural Biology of Bacterial RNA Polymerase

by Katsuhiko S. Murakami

Biomolecules 2015, 5(2), 848-864; https://doi.org/10.3390/biom5020848 - 11 May 2015

Cited by 84 | Viewed by 14459

Abstract

Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477–42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In [...] Read more.

Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477–42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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Base Flipping in Open Complex Formation at Bacterial Promoters

by Mary E. Karpen and Pieter L. DeHaseth

Biomolecules 2015, 5(2), 668-678; https://doi.org/10.3390/biom5020668 - 28 Apr 2015

Cited by 10 | Viewed by 7477

Abstract

In the process of transcription initiation, the bacterial RNA polymerase binds double-stranded (ds) promoter DNA and subsequently effects strand separation of 12 to 14 base pairs (bp), including the start site of transcription, to form the so-called “open complex” (also referred to as [...] Read more.

In the process of transcription initiation, the bacterial RNA polymerase binds double-stranded (ds) promoter DNA and subsequently effects strand separation of 12 to 14 base pairs (bp), including the start site of transcription, to form the so-called “open complex” (also referred to as RP_o). This complex is competent to initiate RNA synthesis. Here we will review the role of σ⁷⁰ and its homologs in the strand separation process, and evidence that strand separation is initiated at the −11A (the A of the non-template strand that is 11 bp upstream from the transcription start site) of the promoter. By using the fluorescent adenine analog, 2-aminopurine, it was demonstrated that the −11A on the non-template strand flips out of the DNA helix and into a hydrophobic pocket where it stacks with tyrosine 430 of σ⁷⁰. Open complexes are remarkably stable, even though in vivo, and under most experimental conditions in vitro, dsDNA is much more stable than its strand-separated form. Subsequent structural studies of other researchers have confirmed that in the open complex the −11A has flipped into a hydrophobic pocket of σ⁷⁰. It was also revealed that RP_o was stabilized by three additional bases of the non-template strand being flipped out of the helix and into hydrophobic pockets, further preventing re-annealing of the two complementary DNA strands. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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Structural and Biochemical Investigation of Bacteriophage N4-Encoded RNA Polymerases

by Bryan R. Lenneman and Lucia B. Rothman-Denes

Biomolecules 2015, 5(2), 647-667; https://doi.org/10.3390/biom5020647 - 27 Apr 2015

Cited by 27 | Viewed by 8665

Abstract

Bacteriophage N4 regulates the temporal expression of its genome through the activity of three distinct RNA polymerases (RNAP). Expression of the early genes is carried out by a phage-encoded, virion-encapsidated RNAP (vRNAP) that is injected into the host at the onset of infection [...] Read more.

Bacteriophage N4 regulates the temporal expression of its genome through the activity of three distinct RNA polymerases (RNAP). Expression of the early genes is carried out by a phage-encoded, virion-encapsidated RNAP (vRNAP) that is injected into the host at the onset of infection and transcribes the early genes. These encode the components of new transcriptional machinery (N4 RNAPII and cofactors) responsible for the synthesis of middle RNAs. Both N4 RNAPs belong to the T7-like “single-subunit” family of polymerases. Herein, we describe their mechanisms of promoter recognition, regulation, and roles in the phage life cycle. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

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