Structural basis for initiation of transcription from an RNA polymerase–promoter complex

Nature ◽  
10.1038/19999 ◽  
1999 ◽  
Vol 399 (6731) ◽  
pp. 80-83 ◽  
Author(s):  
Graham M. T. Cheetham ◽  
David Jeruzalmi ◽  
Thomas A Steitz
Keyword(s):  
Rna Polymerase ◽  
Structural Basis ◽  
Promoter Complex ◽  
Initiation Of Transcription ◽  
Rna Polymerase Promoter

scholarly journals Correction: Structural basis for initiation of transcription from an RNA polymerase–promoter complex

Nature ◽  
10.1038/21929 ◽  
1999 ◽  
Vol 400 (6739) ◽  
pp. 89-89
Author(s):  
Graham M. T. Cheetham ◽  
David Jeruzalmi ◽  
Thomas A. Steitz
Keyword(s):  
Rna Polymerase ◽  
Structural Basis ◽  
Promoter Complex ◽  
Initiation Of Transcription ◽  
Rna Polymerase Promoter

scholarly journals Structural basis for transcription activation by Crl through tethering of σS and RNA polymerase

2019 ◽  
Vol 116 (38) ◽  
pp. 18923-18927 ◽  
Author(s):  
Alexis Jaramillo Cartagena ◽  
Amy B. Banta ◽  
Nikhil Sathyan ◽  
Wilma Ross ◽  
Richard L. Gourse ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Structural Basis ◽  
Functional Importance ◽  
Structural Element ◽  
Cryo Electron Microscopy ◽  
Promoter Complex ◽  
Σ Factor ◽  
Promoter Dna ◽  
Transcription Activators

In bacteria, a primary σ-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative σ-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative σ-factors are negatively regulated by anti–σ-factors. In Escherichia coli, Salmonella enterica, and many other γ-proteobacteria, the transcription factor Crl positively regulates the alternative σS-regulon by promoting the association of σS with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-σS-RNAP in an open promoter complex with a σS-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of σS (σS2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP β′-subunit that we call the β′-clamp-toe (β′CT). Deletion of the β′CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-β′CT interaction. We conclude that Crl activates σS-dependent transcription in part through stabilizing σS-RNAP by tethering σS2 and the β′CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated σ-activators.

scholarly journals Promoter Activation by Repositioning of RNA Polymerase

2008 ◽  
Vol 190 (9) ◽  
pp. 3110-3117 ◽  
Author(s):  
Amrita Kumar ◽  
Charles P. Moran
Keyword(s):  
Rna Polymerase ◽  
Binding Sites ◽  
Response Regulator ◽  
Promoter Activation ◽  
Component Type ◽  
Promoter Complex ◽  
Chemical Nuclease ◽  
Rna Polymerase Promoter ◽  
Type Response ◽  
Element Sequence

ABSTRACT Spo0A, a classical two-component-type response regulator in Bacillus subtilis, binds to a specific DNA sequence found in many promoters to repress or activate the transcription of over 100 genes. On the spoIIG promoter, one of the Spo0A binding sites, centered at position −40, overlaps a consensus −35 element that may also interact with region 4 of the sigma A (σA) subunit of RNA polymerase. Molecular modeling corroborated by genetic evidence led us to propose that the binding of Spo0A to this site repositions σA region 4 on the promoter. Therefore, we used a chemical nuclease, p-bromoacetamidobenzyl-EDTA-Fe, that was covalently tethered to a single cysteine in region 4 of σA to map the position of σA on the promoter. The results indicated that in the absence of Spo0A, σA region 4 of the RNA polymerase was located near the −35 element sequence centered at position −40. However, in the presence of Spo0A, σA region 4 was displaced downstream from the −35 element by 4 bp. These and other results support the model in which the binding of Spo0A to the spoIIG promoter stimulates promoter utilization by repositioning prebound RNA polymerase and stabilizing the repositioned RNA polymerase-promoter complex at a new position that aligns σA region 2 with the −10 region sequences of the promoter, thus facilitating open complex formation.

scholarly journals New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase–promoter complex

2015 ◽  
Vol 43 (10) ◽  
pp. 5249-5262 ◽  
Author(s):  
Nicola Doniselli ◽  
Piere Rodriguez-Aliaga ◽  
Davide Amidani ◽  
Jorge A. Bardales ◽  
Carlos Bustamante ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Regulatory Mechanisms ◽  
Promoter Complex ◽  
Rna Polymerase Promoter

scholarly journals E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
James Chen ◽  
Saumya Gopalkrishnan ◽  
Courtney Chiu ◽  
Albert Y Chen ◽  
Elizabeth A Campbell ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Conformational Changes ◽  
Transcription Initiation ◽  
Structural Changes ◽  
Structural Basis ◽  
E Coli ◽  
Bacterial Proteins ◽  
Promoter Complex ◽  
Promoter Dna ◽  
Induced Changes

TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.

The Structure of the RNA Polymerase-Promoter Complex

1994 ◽  
Vol 236 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Franz-Josef Meyer-Almes ◽  
Hermann Heumann ◽  
Dietmar Porschke
Keyword(s):  
Rna Polymerase ◽  
Promoter Complex ◽  
Rna Polymerase Promoter

scholarly journals Activation and Repression at the Escherichia coli ynfEFGHI Operon Promoter

2009 ◽  
Vol 191 (9) ◽  
pp. 3172-3176 ◽  
Author(s):  
Meng Xu ◽  
Stephen J. W. Busby ◽  
Douglas F. Browning
Keyword(s):  
Escherichia Coli ◽  
Transcription Factor ◽  
Rna Polymerase ◽  
Class Ii ◽  
Nitrate Ions ◽  
Single Target ◽  
Promoter Complex ◽  
Polymerase Binding ◽  
K 12 ◽  
Rna Polymerase Promoter

ABSTRACT Induction of the Escherichia coli K-12 ynfEFGHI operon in response to anaerobiosis is repressed by nitrate ions. In this study, we show that the global transcription factor FNR is a class II activator at the ynfEFGHI promoter and that NarL represses activation by binding to a single target that overlaps the promoter −10 element. Electromobility shift assays show that NarL does not prevent RNA polymerase binding and suggest that repression may involve a quaternary NarL-FNR-RNA polymerase-promoter complex.

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