Domain Architectures of σ<sup>54</sup>-Dependent Transcriptional Activators

Studholme, David J.; Dixon, Ray

doi:10.1128/jb.185.6.1757-1767.2003

Cited by 276 publications

(297 citation statements)

References 74 publications

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“…Using knowledge-based sequence motifs recognition software such as Virtual Footprint [30], SCOPE [31] and PromoScan [32], our initial analysis of the genomic sequence of this region to identify potential binding sites of various transcriptional regulators revealed two potential Fnr binding sites: one centered at -72.5 (TTAACCTGGCTCAA; bolded bases represent perfect matches to the Fnr consensus sequence) and another one located further upstream at -188.5 (TTGCTTATTATCAG) ( Fig. 2A,B).…”

Section: Accepted Manuscriptmentioning

confidence: 99%

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

Wong

Bhandari

Janga

et al. 2017

Journal of Molecular Biology

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Highlights1. RavA-ViaA form a chaperone-like complex interacting with respiratory chains. 2.RavA-ViaA are induced under oxygen-limiting conditions. 3.RavA-ViaA interact with the flavin-containing subunit of fumarate reductase. 4.RavA-ViaA modulate the activity of the fumarate reductase complex. AbstractRavA is a MoxR AAA+ protein that functions together with a partner protein that we termed [187 words]

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Section: Accepted Manuscriptmentioning

confidence: 99%

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

Wong

Bhandari

Janga

et al. 2017

Journal of Molecular Biology

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“…Activators of 54 -holoenzyme are modular in structure, generally consisting of an N-terminal regulatory domain, a central domain required for ATP hydrolysis and transcriptional activation, and a C-terminal DNA-binding domain (39). The central domain is well conserved among 54 -dependent activators and for some activators is sufficient to activate transcription if it is expressed at higher than normal levels (7,8).…”

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confidence: 99%

“…54 -Holoenzyme regulates the expression of genes involved in a variety of cellular processes, including nitrogen assimilation and fixation, C 4 -dicarboxylic acid transport, degradation of aromatic compounds, hydrogen metabolism, flagellar biogenesis, and response to phage infection (13,20,39). 54 -Holoenzyme binds to the promoter to form a stable closed complex, but isomerization of this complex to an open complex that can initiate transcription requires a transcriptional activator (21,30,37).…”

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confidence: 99%

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator

Nixon

et al. 2004

J Bacteriol

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“…8 -10). Members of EBPs include the well studied NtrC, PspF, DctD, XylR, NifA, and DmpR proteins (11). PspF is the phage shock protein F that activates transcription of psp genes involved in the phage shock response in Escherichia coli (12,13).…”

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confidence: 99%

Sensor I Threonine of the AAA+ ATPase Transcriptional Activator PspF Is Involved in Coupling Nucleotide Triphosphate Hydrolysis to the Restructuring of σ54-RNA Polymerase

Schumacher

Joly

Rappas

et al. 2007

Journal of Biological Chemistry

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Transcriptional initiation invariably involves the transitionRegulation of transcription enables cells to adapt and differentiate through coordination of protein synthesis. Two major mechanisms exist to control gene transcription as follows: one through recruitment to or preventing the RNA polymerase (RNAP) 4 binding to promoter DNA and one through activation or inhibition of the RNA polymerase activity. Despite the variations in subunit numbers that constitute the basal transcription machinery, RNA polymerases are structurally and functionally highly conserved in all kingdoms of life (1). During the initiation of transcription, RNA polymerases invariably melt the promoter DNA and have to engage the single-stranded template DNA in the structurally conserved catalytic cleft (2).The major variant bacterial 54 -RNAP is regulated by an activating mechanism with some resemblance to the operation of eukaryotic RNAP II. In both cases, passing from the closed to the open RNAP promoter complex requires activator proteins that hydrolyze nucleoside triphosphate to drive open RNAP promoter complex formation (3). The 54 -RNAP binds to specific promoter sites centered on positions Ϫ24 and Ϫ12 relative to the transcription start site and remains in a transcriptionally silent conformation. Open complexes of the 54 -RNAP promoter complexes are thermodynamically labile, and activation relies on the productive coupling of nucleoside triphosphate hydrolysis (energy coupling) from 54 activators to the 54 -RNAP promoter complex. The 54 activator-dependent initial events in open complex formation are mediated by structural changes between 54 and the promoter DNA, which can be melted from position Ϫ12 to Ϫ5 in a reaction that can occur independently from RNAP core determinants. The restructuring of promoter DNA by activated 54 has been termed 54 isomerization (4 -6). Following the initial events and requiring the presence of the RNAP core, the promoter DNA opening extends to position ϩ3 relative to the transcription start site (7).Energy coupling primarily involves intimate interactions between the activator and the 54 promoter complex. 54 activators, also termed enhancer-binding proteins (EBP), belong to the versatile AAAϩ protein (ATPases associated with various cellular activities) family of molecular machines (for review see Refs. 8 -10). Members of EBPs include the well studied NtrC, PspF, DctD, XylR, NifA, and DmpR proteins (11). PspF is the phage shock protein F that activates transcription of psp genes involved in the phage shock response in Escherichia coli (12, * This work was supported in part by the Biotechnology and Biological Sciences Research Council. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. 1 To whom correspondence may be addressed. Tel.: 44-207-5945366; Fax: 44-207-5842056; E-mail: j.schumacher@imperial.ac.uk. 2 Recipient of EMBO F...

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Domain Architectures of σ⁵⁴-Dependent Transcriptional Activators

Cited by 276 publications

References 74 publications

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator

Sensor I Threonine of the AAA+ ATPase Transcriptional Activator PspF Is Involved in Coupling Nucleotide Triphosphate Hydrolysis to the Restructuring of σ54-RNA Polymerase

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Domain Architectures of σ54-Dependent Transcriptional Activators

Cited by 276 publications

References 74 publications

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ54-Dependent Transcriptional Activator

Sensor I Threonine of the AAA+ ATPase Transcriptional Activator PspF Is Involved in Coupling Nucleotide Triphosphate Hydrolysis to the Restructuring of σ54-RNA Polymerase

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Domain Architectures of σ⁵⁴-Dependent Transcriptional Activators

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator