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Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

https://doi.org/10.1016/j.jmb.2011.01.018

138/138 checkable references clean · checked 2026-07-22

Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.

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The 138 checked references that resolve

resolves10.1038/nrmicro787

The regulation of bacterial transcription initiation

resolves10.1038/nrmicro1912

Advances in bacterial promoter recognition and its control by factors that do not bind DNA

resolves10.1111/j.1365-2958.2008.06181.x

Modus operandi of the bacterial RNA polymerase containing the σ54 promoter‐specificity factor

resolves10.1128/JB.180.12.3019-3025.1998

RNA Polymerase-Promoter Interactions: the Comings and Goings of RNA Polymerase

resolves10.1146/annurev.micro.57.030502.090913

Multiple Sigma Subunits and the Partitioning of Bacterial Transcription Space

resolves10.1186/gb-2003-4-1-203

resolves10.1016/j.tim.2007.12.006

RNA polymerase: the vehicle of transcription

resolves10.1111/j.1574-6976.2010.00239.x

Mechanisms for activating bacterial RNA polymerase

resolves10.1073/pnas.0908782106

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

resolves10.1371/journal.pbio.1000483

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

resolves10.1016/j.jmb.2009.10.063

Molecular Evolution of Multisubunit RNA Polymerases: Structural Analysis

resolves10.1021/bi051835v

Solute Probes of Conformational Changes in Open Complex (RPo) Formation by Escherichia coli RNA Polymerase at the λPR Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RPo

resolves10.1016/j.jmb.2007.11.064

Late Steps in the Formation of E. coli RNA Polymerase—λPR Promoter Open Complexes: Characterization of Conformational Changes by Rapid [Perturbant] Upshift Experiments

resolves10.1021/bi100092a

Probing DNA Binding, DNA Opening, and Assembly of a Downstream Clamp/Jaw in Escherichia coli RNA Polymerase−λPR Promoter Complexes Using Salt and the Physiological Anion Glutamate

resolves10.1073/pnas.0609888104

Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase

resolves10.1038/nature05932

Structural basis for transcription elongation by bacterial RNA polymerase

resolves10.1038/221043a0

Factor Stimulating Transcription by RNA Polymerase

resolves10.1038/222537a0

Cyclic Re-use of the RNA Polymerase Sigma Factor

resolves10.1128/jb.174.12.3843-3849.1992

The sigma 70 family: sequence conservation and evolutionary relationships

resolves10.1046/j.1365-2958.2000.01972.x

UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition

resolves10.1016/0092-8674(80)90613-3

E. coli RNA polymerase interacts homologously with two different promoters

resolves10.1093/emboj/16.13.4034

Region 2.5 of the Escherichia coli RNA polymerase σ70 subunit is responsible for the recognition of the ‘extended −10’ motif at promoters

resolves10.1093/nar/gkg694

Identification and analysis of 'extended -10' promoters in Escherichia coli

resolves10.1016/S0014-5793(03)00500-3

Substitutions in the Escherichia coli RNA polymerase σ70 factor that affect recognition of extended −10 elements at promoters

resolves10.1016/S0021-9258(18)45582-2

Constitutive function of a positively regulated promoter reveals new sequences essential for activity.

resolves10.1016/j.molcel.2006.06.010

A Basal Promoter Element Recognized by Free RNA Polymerase σ Subunit Determines Promoter Recognition by RNA Polymerase Holoenzyme

resolves10.1016/j.cell.2006.04.034

rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase

resolves10.1093/nar/22.22.4667

Start site selection atlacUV5 promoter affected by the sequence context around the initiation sites

resolves10.1128/jb.176.10.2938-2945.1994

Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli

resolves10.1128/JB.184.17.4783-4791.2002

Factors Affecting Start Site Selection at the Escherichia coli fis Promoter

resolves10.1128/jb.178.23.6945-6951.1996

Upstream interactions at the lambda pRM promoter are sequence nonspecific and activate the promoter to a lesser extent than an introduced UP element of an rRNA promoter

resolves10.1073/pnas.0405779102

The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase

resolves10.1073/pnas.0405814102

Sequence-independent upstream DNA–αCTD interactions strongly stimulate Escherichia coli RNA polymerase- lacUV5 promoter association

resolves10.1016/S0092-8674(00)80872-7

Structural Organization of the RNA Polymerase-Promoter Open Complex

resolves10.1073/pnas.1000967107

One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex

resolves10.1016/S0092-8674(00)80122-1

Base-Specific Recognition of the Nontemplate Strand of Promoter DNA by E. coli RNA Polymerase

resolves10.1073/pnas.0709513105

Fine structure of the promoter–σ region 1.2 interaction

resolves10.1093/nar/28.9.1864

DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: a systematic study

resolves10.1074/jbc.M702232200

Strand Opening-deficient Escherichia coli RNA Polymerase Facilitates Investigation of Closed Complexes with Promoter DNA

resolves10.1126/science.1131399

Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism

resolves10.1126/science.1131398

Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching

resolves10.1021/bi701289g

DNA Bubble Formation in Transcription Initiation

resolves10.1002/j.1460-2075.1986.tb04596.x

Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures.

resolves10.1021/bi060247u

Initial Transcribed Sequence Mutations Specifically Affect Promoter Escape Properties

resolves10.1073/pnas.0906979106

Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase

resolves10.1126/science.1169237

Direct Detection of Abortive RNA Transcripts in Vivo

resolves10.1016/j.molcel.2005.10.015

Sigma and RNA Polymerase: An On-Again, Off-Again Relationship?

resolves10.1126/science.1069595

Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex

resolves10.1038/nature752

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution

resolves10.1016/S0092-8674(01)00398-1

A Coiled-Coil from the RNA Polymerase β′ Subunit Allosterically Induces Selective Nontemplate Strand Binding by σ70

resolves10.1016/0092-8674(94)90300-X

Function of a nontranscribed DNA strand site in transcription elongation

resolves10.1038/nsmb768

The σ70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription

resolves10.1038/nsmb757

The σ70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter

resolves10.1111/j.1365-2958.2008.06138.x

Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation

resolves10.1016/S0092-8674(00)81515-9

Crystal Structure of Thermus aquaticus Core RNA Polymerase at 3.3 Å Resolution

resolves10.1126/science.1069594

Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution

resolves10.1101/gad.13.22.3015

The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized

resolves10.1016/S0022-2836(02)00293-0

Kinetic Studies and Structural Models of the Association of E.coli σ70 RNA Polymerase with the λPR Promoter: Large Scale Conformational Changes in Forming the Kinetically Significant Intermediates

resolves10.1016/S0076-6879(03)70004-4

Crystallographic Analysis of Thermus aquaticus RNA Polymerase Holoenzyme and a Holoenzyme⧸Promoter DNA Complex

resolves10.1073/pnas.1003533107

Promoter melting triggered by bacterial RNA polymerase occurs in three steps

resolves10.1016/S0959-440X(02)00005-2

Bacterial RNA polymerases: the wholo story

resolves10.1038/nature07510

Transcription inactivation through local refolding of the RNA polymerase structure

resolves10.1016/j.sbi.2009.10.010

Structures of RNA polymerase–antibiotic complexes

resolves10.1038/emboj.2010.135

The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site

resolves10.1046/j.1365-2443.1997.1600357.x

Regions of the Escherichia coli primary sigma factor σ70 that are involved in interaction with RNA polymerase core enzyme

resolves10.1016/S0092-8674(02)00667-0

Structural Organization of Bacterial RNA Polymerase Holoenzyme and the RNA Polymerase-Promoter Open Complex

resolves10.1073/pnas.052054099

Conformational flexibility of bacterial RNA polymerase

resolves10.1016/0022-2836(84)90174-8

Kinetics and mechanism of the interaction of Escherichia coli RNA polymerase with the λPR promoter

resolves10.1021/bi00332a018

Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps

resolves10.1016/0022-2836(85)90293-1

Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-λP promoter interaction

resolves10.1006/jmbi.1998.2129

DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA 1 1Edited by R. Ebright

resolves10.1016/S0021-9258(19)76477-1

The 0 degree C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5.

resolves10.1016/0022-2836(89)90128-9

Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor σ32 at the groE promoter

resolves10.1002/j.1460-2075.1990.tb07391.x

Topography of intermediates in transcription initiation of E.coli.

resolves10.1021/bi990206g

Protein−Nucleic Acid Interactions during Open Complex Formation Investigated by Systematic Alteration of the Protein and DNA Binding Partners

resolves10.1093/nar/gkp560

DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37°C and results in the accumulation of an off-pathway intermediate

resolves10.1073/pnas.0408218102

Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter

resolves10.1016/j.jmb.2008.10.023

Evidence for a Tyrosine–Adenine Stacking Interaction and for a Short-lived Open Intermediate Subsequent to Initial Binding of Escherichia coli RNA Polymerase to Promoter DNA

resolves10.1021/bi00332a019

Changes in the DNA structure of the lac UV5 promoter during formation of an open complex with Escherichia coli RNA polymerase

resolves10.1006/jmbi.1998.2130

Quantitative analysis of multiple-hit footprinting studies to characterize DNA conformational changes in protein-DNA complexes: application to DNA opening by Eσ 70 RNA polymerase 1 1Edited by R. Ebright

resolves10.1016/0022-2836(91)90102-C

Development of RNA polymerase-promoter contacts during open complex formation

resolves10.1006/jmbi.1998.1779

RNA polymerase mutants that destabilize RNA Polymerase-Promoter complexes alter NTP-sensing by rrn P1 promoters

resolves10.1074/jbc.273.36.23549

Characterization of the Closed Complex Intermediate Formed during Transcription Initiation by Escherichia coli RNA Polymerase

resolves10.1101/gad.1745409

Allosteric control of Escherichia coli rRNA promoter complexes by DksA

resolves10.1021/bi00048a004

HO.bul. and DNase I Probing of E.sigma.70 RNA Polymerase-.lambda.PR Promoter Open Complexes: Mg2+ Binding and Its Structural Consequences at the Transcription Start Site

resolves10.1126/science.8248780

A Third Recognition Element in Bacterial Promoters: DNA Binding by the α Subunit of RNA Polymerase

resolves10.1006/jmbi.1999.3161

Transcription activation by catabolite activator protein (CAP)

resolves10.1002/j.1460-2075.1996.tb00928.x

Influence of DNA geometry on transcriptional activation in Escherichia coli.

resolves10.1016/0022-2836(92)90514-K

Stimulation of the phage λ pL promoter by integration host factor requires the carboxy terminus of the α-subunit of RNA polymerase

resolves10.1093/nar/29.20.4166

UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker

resolves10.1016/S1097-2765(03)00201-6

Functional Interaction between RNA Polymerase α Subunit C-Terminal Domain and σ70 in UP-Element- and Activator-Dependent Transcription

resolves10.1101/gad.1079403

An intersubunit contact stimulating transcription initiation by E. coli RNA polymerase: interaction of the α C-terminal domain and ς region 4

resolves10.1074/jbc.M308300200

Exploitation of a Chemical Nuclease to Investigate the Location and Orientation of the Escherichia coli RNA Polymerase α Subunit C-terminal Domains at Simple Promoters That Are Activated by Cyclic AMP Receptor Protein

resolves10.1006/jmbi.1998.2268

Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase σ 70 subunit 1 1Edited by R. Ebright

resolves10.1093/nar/21.2.319

E.coliRNA polymerase, deleted in the C-terminal part of its α-subunit, interacts differently with the cAMP-CRP complex at thelacP1 and at thegaP1 promoter

resolves10.1126/science.8303294

Coupling of Local Folding to Site-Specific Binding of Proteins to DNA

resolves10.1126/science.1077464

Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase

resolves10.1074/jbc.M207038200

The Downstream DNA Jaw of Bacterial RNA Polymerase Facilitates Both Transcriptional Initiation and Pausing

resolves10.1073/pnas.92.5.1739

Translocation of the Escherichia coli transcription complex observed in the registers 11 to 20: "jumping" of RNA polymerase and asymmetric expansion and contraction of the "transcription bubble".

resolves10.1016/j.jmb.2005.05.048

Remodeling of the σ70 Subunit Non-template DNA Strand Contacts During the Final Step of Transcription Initiation

resolves10.1016/j.chembiol.2008.09.008

A Full-Length Group 1 Bacterial Sigma Factor Adopts a Compact Structure Incompatible with DNA Binding

resolves10.1073/pnas.132033899

Autoregulation of a bacterial σ factor explored by using segmental isotopic labeling and NMR

resolves10.1016/0092-8674(92)90174-B

Polypeptides containing highly conserved regions of transcription initiation factor σ70 exhibit specificity of binding to promoter DNA

resolves10.1006/jmbi.1995.0333

TheBacillus subtilisFlagellar Regulatory Protein σD: Overproduction, Domain Analysis and DNA-binding Properties

resolves10.1128/JB.01193-10

DNA-Binding Properties of the Bacillus subtilis and Aeribacillus pallidus AC6 σ D Proteins

resolves10.1074/jbc.M110.174102

Interaction of Escherichia coli RNA Polymerase σ70 Subunit with Promoter Elements in the Context of Free σ70, RNA Polymerase Holoenzyme, and the β′-σ70 Complex

resolves10.1111/j.1365-2958.2009.07021.x

Utilization of variably spaced promoter‐like elements by the bacterial RNA polymerase holoenzyme during early elongation

resolves10.1074/jbc.M507984200

Escherichia coli RNA Polymerase Contacts outside the –10 Promoter Element Are Not Essential for Promoter Melting

resolves10.1016/0092-8674(84)90493-8

The htpR gene product of E. coli is a sigma factor for heat-shock promoters

resolves10.1101/gad.1.2.179

Sigma 32 synthesis can regulate the synthesis of heat shock proteins in Escherichia coli.

resolves10.1111/j.1365-2958.2009.06690.x

Dissection of recognition determinants of Escherichia coli σ32 suggests a composite −10 region with an ‘extended −10’ motif and a core −10 element

resolves10.1101/gad.1843709

Reduced capacity of alternative σs to melt promoters ensures stringent promoter recognition

resolves10.1073/pnas.95.20.11655

Promoter opening via a DNA fork junction binding activity

resolves10.1074/jbc.M601364200

A Consensus Adenine at Position –11 of the Nontemplate Strand of Bacterial Promoter Is Important for Nucleation of Promoter Melting

resolves10.1073/pnas.261517398

A “master” in base unpairing during isomerization of a promoter upon RNA polymerase binding

resolves10.1021/bi001433h

Sequence Determinants for the Recognition of the Fork Junction DNA Containing the −10 Region of Promoter DNA by E. coli RNA Polymerase

resolves10.1021/bi026539m

RNA Polymerase Alters the Mobility of an A-Residue Crucial to Polymerase-Induced Melting of Promoter DNA

resolves10.1093/nar/gkl956

Anatomy of Escherichia coli σ 70 promoters

resolves10.1074/jbc.273.36.23558

Stimulation of Open Complex Formation by Nicks and Apurinic Sites Suggests a Role for Nucleation of DNA Melting in Escherichia coli Promoter Function

resolves10.1093/nar/gkm431

The -11A of promoter DNA and two conserved amino acids in the melting region of 70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact

resolves10.1016/S0092-8674(00)81329-X

Crystal Structure of a σ70 Subunit Fragment from E. coli RNA Polymerase

resolves10.1016/S1097-2765(02)00470-7

Structure of the Bacterial RNA Polymerase Promoter Specificity σ Subunit

resolves10.1093/emboj/19.5.1130

Escherichia coli promoter opening and −10 recognition: mutational analysis of σ70

resolves10.1006/jmbi.2000.3808

Aromatic amino acids in region 2.3 of Escherichia coli sigma 70 participate collectively in the formation of an RNA polymerase-promoter open complex

resolves10.1006/jmbi.1994.1102

A Promoter Melting Region in the Primary σ Factor of Bacillus subtilis

resolves10.1074/jbc.M105027200

Different Roles for Basic and Aromatic Amino Acids in Conserved Region 2 of Escherichia coli ς70 in the Nucleation and Maintenance of the Single-stranded DNA Bubble in Open RNA Polymerase-Promoter Complexes

resolves10.1146/annurev.bi.57.070188.004203

STRUCTURE AND FUNCTION OF BACTERIAL SIGMA FACTORS

resolves10.1021/bi990043w

Enthalpy and Heat Capacity Changes for Formation of an Oligomeric DNA Duplex: Interpretation in Terms of Coupled Processes of Formation and Association of Single-Stranded Helices

resolves10.1016/S0092-8674(01)00461-5

Isolation and Characterization of σ70-Retaining Transcription Elongation Complexes from Escherichia coli

resolves10.1016/S0092-8674(01)00464-0

Translocation of σ70 with RNA Polymerase during Transcription

resolves10.1016/j.molcel.2005.10.011

Holoenzyme Switching and Stochastic Release of Sigma Factors from RNA Polymerase In Vivo

resolves10.1016/S0092-8674(00)80121-X

Function of E. coli RNA Polymerase σ Factor- σ70 in Promoter-Proximal Pausing

resolves10.1111/j.1365-2958.2008.06136.x

Post‐initiation control by the initiation factor sigma

resolves10.1074/jbc.M109.053983

Early Transcriptional Arrest at Escherichia coli rplN and ompX Promoters

resolves10.1016/S1097-2765(00)00126-X

Function of Transcription Cleavage Factors GreA and GreB at a Regulatory Pause Site

resolves10.1016/S0021-9258(18)67321-1

Release of the sigma subunit of Escherichia coli DNA-dependent RNA polymerase depends mainly on time elapsed after the start of initiation, not on length of product RNA.

resolves10.1016/j.jmb.2009.05.078

Two Structurally Independent Domains of E. coli NusG Create Regulatory Plasticity via Distinct Interactions with RNA Polymerase and Regulators

resolves10.1038/emboj.2008.268

Functional specialization of transcription elongation factors

The 1 reference without a DOI — listed, not checked

no DOI — not checkedTranscription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters

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