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CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase

https://doi.org/10.1093/nar/gkz449
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Stalling of Escherichia coli RNA Polymerase in the +6 to +12 Region in Vivo is Associated with Tight Binding to Consensus Promoter Elements
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Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro
inferredcites →https://doi.org/10.1016/0022-2836(92)90660-copenalex-snapshot
Mechanism of initiation of transcription by Bacillus subtilis RNA polymerase at several promoters
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Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data
inferredcites →https://doi.org/10.1016/j.cell.2009.04.041openalex-snapshot
CarD Is an Essential Regulator of rRNA Transcription Required for Mycobacterium tuberculosis Persistence
inferredcites →https://doi.org/10.1016/j.jmb.2011.01.018openalex-snapshot
Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis
inferredcites →https://doi.org/10.1016/j.molcel.2016.08.011openalex-snapshot
RNA Polymerase Pausing during Initial Transcription
inferredcites →https://doi.org/10.1016/j.str.2013.08.014openalex-snapshot
Structure of the Mtb CarD/RNAP β-Lobes Complex Reveals the Molecular Basis of Interaction and Presents a Distinct DNA-Binding Domain for Mtb CarD
inferredcites →https://doi.org/10.1016/j.tim.2007.12.006openalex-snapshot
RNA polymerase: the vehicle of transcription
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Isolation of conditional expression mutants in Mycobacterium tuberculosis by transposon mutagenesis
inferredcites →https://doi.org/10.1016/j.tube.2014.03.008openalex-snapshot
Optimization of recombinant Mycobacterium tuberculosis RNA polymerase expression and purification
inferredcites →https://doi.org/10.1016/j.ymeth.2008.10.018openalex-snapshot
Analysis of RNA polymerase-promoter complex formation
inferredcites →https://doi.org/10.1016/s0021-9258(19)63363-6openalex-snapshot
Binding of Escherichia coli RNA polymerase to T7 DNA. Displacement of holoenzyme from promoter complexes by heparin.
inferredcites →https://doi.org/10.1016/s0092-8674(00)81126-5openalex-snapshot
Protein–Protein Contacts that Activate and Repress Prokaryotic Transcription
inferredcites →https://doi.org/10.1016/s0167-4781(02)00452-9openalex-snapshot
Promoter clearance and escape in prokaryotes
inferredcites →https://doi.org/10.1016/s1097-2765(00)80011-8openalex-snapshot
Transcription Activation or Repression by Phage Φ29 Protein p4 Depends on the Strength of the RNA Polymerase–Promoter Interactions
inferredcites →https://doi.org/10.1021/acs.biochem.5b01184openalex-snapshot
Real-Time Observation of Backtracking by Bacterial RNA Polymerase
inferredcites →https://doi.org/10.1021/acs.biochem.9b00049openalex-snapshot
RNA Polymerase: Step-by-Step Kinetics and Mechanism of Transcription Initiation
inferredcites →https://doi.org/10.1021/bi00009a022openalex-snapshot
Thermodynamics of Charged Oligopeptide-Heparin Interactions
inferredcites →https://doi.org/10.1021/bi0012538openalex-snapshot
Purification and Initial Characterization of RNA Polymerase from Thermus thermophilus Strain HB8
inferredcites →https://doi.org/10.1021/bi0269613openalex-snapshot
In Vitro Studies of Transcript Initiation by Escherichia coli RNA Polymerase. 2. Formation and Characterization of Two Distinct Classes of Initial Transcribing Complexes
inferredcites →https://doi.org/10.1021/bi026962vopenalex-snapshot
In Vitro Studies of Transcript Initiation by Escherichia coli RNA Polymerase. 3. Influences of Individual DNA Elements within the Promoter Recognition Region on Abortive Initiation and Promoter Escape
inferredcites →https://doi.org/10.1021/bi9813431openalex-snapshot
Promoter Recognition by Escherichia coli RNA Polymerase: Effects of the UP Element on Open Complex Formation and Promoter Clearance
inferredcites →https://doi.org/10.1038/ncomms16072openalex-snapshot
Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures
inferredcites →https://doi.org/10.1038/nrmicro.2016.103openalex-snapshot
Local and global regulation of transcription initiation in bacteria
inferredcites →https://doi.org/10.1038/s41467-018-03902-9openalex-snapshot
Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria
inferredcites →https://doi.org/10.1038/s41586-018-0840-5openalex-snapshot
Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding
inferredcites →https://doi.org/10.1042/bcj20170436openalex-snapshot
Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase
inferredcites →https://doi.org/10.1042/bj20140179openalex-snapshot
Kinetics of promoter escape by bacterial RNA polymerase: effects of promoter contacts and transcription bubble collapse
inferredcites →https://doi.org/10.1046/j.1365-2958.2002.02779.xopenalex-snapshot
Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling
inferredcites →https://doi.org/10.1073/pnas.0501170102openalex-snapshot
DksA potentiates direct activation of amino acid promoters by ppGpp
inferredcites →https://doi.org/10.1073/pnas.1308270110openalex-snapshot
Structure and function of CarD, an essential mycobacterial transcription factor
inferredcites →https://doi.org/10.1073/pnas.1504942112openalex-snapshot
Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA
inferredcites →https://doi.org/10.1073/pnas.1605038113openalex-snapshot
Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase
inferredcites →https://doi.org/10.1073/pnas.1618675114openalex-snapshot
Mechanism of transcription initiation and promoter escape by E . coli RNA polymerase
inferredcites →https://doi.org/10.1073/pnas.1809454115openalex-snapshot
The calculation of transcript flux ratios reveals single regulatory mechanisms capable of activation and repression
inferredcites →https://doi.org/10.1073/pnas.1819682116openalex-snapshot
Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase
inferredcites →https://doi.org/10.1073/pnas.93.17.8868openalex-snapshot
Dual regulation of open-complex formation and promoter clearance by Arc explains a novel repressor to activator switch.
inferredcites →https://doi.org/10.1074/jbc.273.51.34042openalex-snapshot
Abortive Initiation of Transcription at a Hybrid Promoter
inferredcites →https://doi.org/10.1074/jbc.c600060200openalex-snapshot
Region 3.2 of the σ Subunit Contributes to the Binding of the 3′-Initiating Nucleotide in the RNA Polymerase Active Center and Facilitates Promoter Clearance during Initiation
inferredcites →https://doi.org/10.1074/jbc.m112481200openalex-snapshot
Generality of the Branched Pathway in Transcription Initiation byEscherichia coli RNA Polymerase
inferredcites →https://doi.org/10.1074/jbc.m113.459883openalex-snapshot
Mycobacterium tuberculosis RNA Polymerase-binding Protein A (RbpA) and Its Interactions with Sigma Factors
inferredcites →https://doi.org/10.1074/jbc.m211214200openalex-snapshot
Co-overexpression of Escherichia coliRNA Polymerase Subunits Allows Isolation and Analysis of Mutant Enzymes Lacking Lineage-specific Sequence Insertions
inferredcites →https://doi.org/10.1074/jbc.m211430200openalex-snapshot
Changes in Conserved Region 3 of Escherichia coliς70 Reduce Abortive Transcription and Enhance Promoter Escape
inferredcites →https://doi.org/10.1093/nar/gkq692openalex-snapshot
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction
inferredcites →https://doi.org/10.1093/nar/gks346openalex-snapshot
Mycobacterium tuberculosis RbpA protein is a new type of transcriptional activator that stabilizes the σ A -containing RNA polymerase holoenzyme
inferredcites →https://doi.org/10.1093/nar/gkt1384openalex-snapshot
Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape
inferredcites →https://doi.org/10.1093/nar/gku1231openalex-snapshot
Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD
inferredcites →https://doi.org/10.1093/nar/gkv078openalex-snapshot
CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism
inferredcites →https://doi.org/10.1093/nar/gkw577openalex-snapshot
Cooperative stabilization ofMycobacterium tuberculosis rrnAP3 promoter open complexes by RbpA and CarD
inferredcites →https://doi.org/10.1093/nar/gky172openalex-snapshot
DNA template sequence control of bacterial RNA polymerase escape from the promoter
inferredcites →https://doi.org/10.1093/nar/gky714openalex-snapshot
RbpA relaxes promoter selectivity of M. tuberculosis RNA polymerase
inferredcites →https://doi.org/10.1099/mic.0.038620-0openalex-snapshot
Comparison of promoter-specific events during transcription initiation in mycobacteria
inferredcites →https://doi.org/10.1111/j.1753-4887.1981.tb06752.xopenalex-snapshot
Proceedings of the National Academy of Sciences of the United States of America
inferredcites →https://doi.org/10.1111/mmi.12681openalex-snapshot
CarD integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria
inferredcites →https://doi.org/10.1126/science.1131398openalex-snapshot
Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching
inferredcites →https://doi.org/10.1126/science.1131399openalex-snapshot
Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism
inferredcites →https://doi.org/10.1126/science.278.5346.2092openalex-snapshot
Transcription Regulation by Initiating NTP Concentration: rRNA Synthesis in Bacteria
inferredcites →https://doi.org/10.1128/jb.00690-17openalex-snapshot
Domains within RbpA Serve Specific Functional Roles That Regulate the Expression of Distinct Mycobacterial Gene Subsets
inferredcites →https://doi.org/10.1128/jb.00879-12openalex-snapshot
Interaction of CarD with RNA Polymerase Mediates Mycobacterium tuberculosis Viability, Rifampin Resistance, and Pathogenesis
inferredcites →https://doi.org/10.1128/mmbr.00055-15openalex-snapshot
Bacterial Transcription as a Target for Antibacterial Drug Development
inferredcites →https://doi.org/10.1146/annurev-micro-092412-155737openalex-snapshot
Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective
inferredcites →https://doi.org/10.1371/journal.pcbi.1000109openalex-snapshot
The Generation of Promoter-Mediated Transcriptional Noise in Bacteria
inferredcites →https://doi.org/10.1371/journal.pone.0021941openalex-snapshot
A Transcript Cleavage Factor of Mycobacterium tuberculosis Important for Its Survival
inferredcites →https://doi.org/10.1371/journal.pone.0043900openalex-snapshot
Distinct and Contrasting Transcription Initiation Patterns at Mycobacterium tuberculosis Promoters
inferredcites →https://doi.org/10.2210/pdb6c04/pdbopenalex-snapshot
Mtb RNAP Holo/RbpA/double fork DNA -closed clamp
inferredcites →https://doi.org/10.3389/fmolb.2016.00073openalex-snapshot
Bacterial RNA Polymerase-DNA Interaction—The Driving Force of Gene Expression and the Target for Drug Action
inferredcites →https://doi.org/10.7554/elife.08505openalex-snapshot
CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex
inferredcites →https://doi.org/10.7554/elife.22520openalex-snapshot
Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA
inferredcites →https://doi.org/10.7554/elife.34823openalex-snapshot
Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Surface Plasmon Resonance as a Tool to Elucidate the Molecular Determinants of Key Transcriptional Regulators Controlling Rhizobial Lifestyles
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Mycobacterium smegmatis MSMEG_0129 is a nutrition-associated regulator that interacts with CarD and ClpP2
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Quantifying the regulatory role of individual transcription factors in Escherichia coli
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Molecular dissection of RbpA-mediated regulation of fidaxomicin sensitivity in mycobacteria
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The unique N-terminal region of Mycobacterium tuberculosis sigma factor A plays a dominant role in the essential function of this protein
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Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics
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Mechanism of δ Mediated Transcription Activation in Bacillus subtilis: Interaction with α CTD of RNA Polymerase Stabilizes δ and Successively Facilitates the Open Complex Formation
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Cell-free genomics reveals fundamental regulatory principles of the Mycobacterium tuberculosis transcription cycle
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Structure and molecular mechanism of bacterial transcription activation
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Single-Molecule methods to investigate mechanisms of transcription by RNA polymerase of Mycobacterium tuberculosis
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Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by Escherichia coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex
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Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase
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Structural Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase
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Diverse and unified mechanisms of transcription initiation in bacteria
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CueR activates transcription through a DNA distortion mechanism
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Conditional down-regulation of GreA impacts expression of rRNA and transcription factors, affecting Mycobacterium smegmatis survival
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Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise
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Mycobacterium tuberculosis DNA repair helicase UvrD1 is activated by redox-dependent dimerization via a 2B domain cysteine
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High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase
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A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators
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Differential association of primary and alternative σ factors with RNA polymerase of Mycobacterium tuberculosis during transcription elongation
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Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations
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The Mycobacterium tuberculosis DNA-repair helicase UvrD1 is activated by redox-dependent dimerization via a 2B domain cysteine conserved in other Actinobacteria
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High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for Mycobacterium tuberculosis RNA polymerase
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Structural Basis of Streptomyces Antibiotic Regulatory Proteins Activating Transcription
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Probing the dependence of transcription factor regulatory modes on promoter features
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Single-stranded DNA drives σ subunit loading onto RNA polymerase to unlock initiation-competent conformations
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Dissection of FixK 2 protein–DNA interaction unveils new insights into Bradyrhizobium diazoefficiens lifestyles control
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PrbP modulates biofilm formation in Liberibacter crescens
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The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa
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E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism
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Recent advances in mycobacterial transcription: insights beyond the general pathway
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Rhodobacter sphaeroides CarD Negatively Regulates Its Own Promoter
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The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation
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Mycobacterium tuberculosis as a model system
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Domains within RbpA Serve Specific Functional Roles That Regulate the Expression of Distinct Mycobacterial Gene Subsets
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Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces
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Regulatory properties of transcription factors with diverse mechanistic function
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Discovery of a role for the single START-domain protein Mtsp17 in transcriptional regulation
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Molecular Insights into the Interaction of Ursolic Acid and Cucurbitacin from Colocynth with Therapeutic Targets of Mycobacterium tuberculosis
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Clp protease and antisense RNA jointly regulate the global regulator CarD to mediate mycobacterial starvation response
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