Mechanisms of σ54-Dependent Transcription Initiation and Regulation

Danson, Amy E.; Jovanovic, Milija; Buck, Martin; Zhang, Xiaodong

doi:10.1016/j.jmb.2019.04.022

Cited by 59 publications

(46 citation statements)

References 80 publications

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“…By this approach, we identified 30 putative SigL-dependent promoters corresponding to about 95 controlled genes (Table 4). As described in other bacteria (Danson et al, 2019;Nie et al, 2019), it is worth noting that 23 genes or operons with a "−24,−12" promoter out of 30 are adjacent on the chromosome to genes encoding a sigma 54-dependent activator (EBP), which is probably involved in their control.…”

Section: Sigl-dependent Promoters In C Difficilementioning

confidence: 95%

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

et al. 2020

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Section: Sigl-dependent Promoters In C Difficilementioning

confidence: 95%

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

et al. 2020

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“…PR is a selenoenzyme complex encoded by the prd operon CD3237 to CD3247 that is upregulated in a proline-responsive manner by PrdR (49). Acting as a 54 -dependent activator protein, PrdR is a member of the bacterial enhancer binding proteins (bEBPs), many of which respond to environmental signals through ligand-binding regulatory domains (63,64). Our finding of high PR activity in the absence of proline indicates that transcription of the prd operon is unlikely to be activated solely by a PrdR-dependent mechanism and suggests the additional involvement of 70 or a different alternative sigma factor.…”

Section: Induction Of Wlp Expression Under the Newly Developed Growthmentioning

confidence: 99%

Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway

Gencic

Grahame

2020

J Bacteriol

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Clostridium difficile is the leading cause of hospital-acquired, antibiotic-associated diarrhea, and is the only wide-spread human pathogen that contains a complete set of genes encoding the Wood-Ljungdahl pathway (WLP). In acetogenic bacteria, synthesis of acetate from 2 CO2 by the WLP functions as a terminal electron accepting pathway, however, C. difficile contains various other reductive pathways including a heavy reliance on Stickland reactions, which questions the role of the WLP in this bacterium. In rich medium containing high levels of electron acceptor substrates only trace levels of key WLP enzymes were found, therefore, conditions were developed to adapt C. difficile to grow in the absence of amino acid Stickland acceptors. Growth conditions were identified that produce the highest levels of WLP activity, determined by Western blot analyses of the central component acetyl-CoA synthase (AcsB) and assays of other WLP enzymes. Fermentation substrate and product analyses, enzyme assays of cell extracts, and characterization of an ΔacsB mutant, demonstrated that the WLP functions to dispose of metabolically-generated reducing equivalents. While WLP activity in C. difficile does not reach the levels seen in classical acetogens, coupling of the WLP to butyrate formation provides a highly efficient system for regeneration of NAD+ “acetobutyrogenesis” requiring only low flux through the pathways to support efficient ATP production from glucose oxidation. Additional insights redefine the amino acid requirements in C. difficile, explore the relationship of the WLP to toxin production, and provide a rationale for co-localization of genes involved in glycine synthesis and cleavage within the WLP operon. IMPORTANCE Clostridium difficile is an anaerobic multidrug-resistant, toxin-producing pathogen with major health impacts worldwide. It is the only wide-spread pathogen harboring a complete set of Wood-Ljungdahl pathway (WLP) genes, however, the role of the WLP in C. difficile is poorly understood. In other anaerobic bacteria and Archaea, the WLP can operate in one direction to convert CO2 to acetic acid for biosynthesis, or in either direction for energy conservation. Herein, conditions are defined in which WLP levels in C. difficile increase markedly, functioning to support metabolism of carbohydrates. Amino acid nutritional requirements were better defined, with new insight into how the WLP and butyrate pathways act in concert, contributing significantly to energy metabolism by a mechanism that may have broad physiological significance within the group of non-classical acetogens.

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“…In contrast, the σ 54 family contains only one member, σ 54 (also known as σ N ), which binds to similar regions of RNAP, but has no discernible sequence homology and has significant differences in structure (with the exception of the helix-turn-helix motifs) and modes of RNAP regulation [3,6,7]. σ 54 is present in an estimated 60% of bacterial genomes [8], and there are over 135 genes in Escherichia coli regulated by σ 54 that cover a diverse range of stress responses [9], including nitrogen assimilation during starvation, response to antibiotics, carbon metabolism and loss of membrane integrity [10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Bacterial Enhancer Binding Proteins—AAA+ Proteins in Transcription Activation

Gao

Danson

et al. 2020

Biomolecules

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Bacterial enhancer-binding proteins (bEBPs) are specialised transcriptional activators. bEBPs are hexameric AAA+ ATPases and use ATPase activities to remodel RNA polymerase (RNAP) complexes that contain the major variant sigma factor, σ54 to convert the initial closed complex to the transcription competent open complex. Earlier crystal structures of AAA+ domains alone have led to proposals of how nucleotide-bound states are sensed and propagated to substrate interactions. Recently, the structure of the AAA+ domain of a bEBP bound to RNAP-σ54-promoter DNA was revealed. Together with structures of the closed complex, an intermediate state where DNA is partially loaded into the RNAP cleft and the open promoter complex, a mechanistic understanding of how bEBPs use ATP to activate transcription can now be proposed. This review summarises current structural models and the emerging understanding of how this special class of AAA+ proteins utilises ATPase activities to allow σ54-dependent transcription initiation.

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Mechanisms of σ54-Dependent Transcription Initiation and Regulation

Cited by 59 publications

References 80 publications

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway

Bacterial Enhancer Binding Proteins—AAA+ Proteins in Transcription Activation

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