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1. Full Text RNA Polymerase Pausing during Initial Transcription
by Duchi, Diego and Bauer, David L.V and Fernandez, Laurent and Evans, Geraint and Robb, Nicole and Hwang, Ling Chin and Gryte, Kristofer and Tomescu, Alexandra and Zawadzki, Pawel and Morichaud, Zakia and Brodolin, Konstantin and Kapanidis, Achillefs N
Molecular Cell, ISSN 1097-2765, 09/2016, Volume 63, Issue 6, pp. 939 - 950
In bacteria, RNA polymerase (RNAP) initiates transcription by synthesizing short transcripts that are either released or extended to allow RNAP to escape from... 
promoter escape | DNA scrunching | transcriptional pausing | single-molecule FRET | initial transcription | RNA polymerase | LAC UV5 PROMOTER | SINGLE-MOLECULE FRET | ANGSTROM RESOLUTION | ABORTIVE INITIATION | IN-VITRO | STRUCTURAL BASIS | BIOCHEMISTRY & MOLECULAR BIOLOGY | RESONANCE ENERGY-TRANSFER | ALTERNATING-LASER EXCITATION | RIFAMPICIN INHIBITION | OPEN COMPLEX | CELL BIOLOGY | Promoter Regions, Genetic | Nucleic Acid Synthesis Inhibitors - pharmacology | RNA, Messenger - genetics | Escherichia coli Proteins - metabolism | DNA-Directed RNA Polymerases - genetics | Single Molecule Imaging - methods | RNA, Messenger - biosynthesis | Time Factors | Escherichia coli - genetics | Base Sequence | RNA, Messenger - antagonists & inhibitors | Escherichia coli - metabolism | Escherichia coli Proteins - genetics | Fluorescence Resonance Energy Transfer | RNA, Bacterial - genetics | Transcription, Genetic | Rifampin - pharmacology | DNA-Directed RNA Polymerases - metabolism | RNA, Bacterial - metabolism | Lac Operon | Genetic research | Fluorescence | Genetic transcription | RNA | Analysis | RNA polymerases | Index Medicus
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2. Full Text Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation
by Sergey Proshkin and A. Rachid Rahmouni and Alexander Mironov and Evgeny Nudler
Science, ISSN 0036-8075, 4/2010, Volume 328, Issue 5977, pp. 504 - 508
During transcription of protein-coding genes, bacterial RNA polymerase (RNAP) is closely followed by a ribosome that translates the newly synthesized... 
Cell growth | RNA probes | RNA | Antibiotics | Plasmids | Genes | REPORTS | Ribosomes | Amino acids | Codons | Repressor proteins | MECHANISM | GENE | DNA | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | GROWTH | ATTENUATION | CODON USAGE | TERMINATION | EXPRESSION | GENOME | Genes, Bacterial | Transcription, Genetic - drug effects | Streptomycin - pharmacology | RNA, Messenger - genetics | Ribosomes - metabolism | Peptide Chain Elongation, Translational - drug effects | RNA, Messenger - metabolism | Codon | beta-Galactosidase - biosynthesis | Escherichia coli - genetics | Escherichia coli Proteins - biosynthesis | Chloramphenicol - pharmacology | Escherichia coli - metabolism | Escherichia coli Proteins - genetics | RNA, Bacterial - genetics | Protein Biosynthesis - drug effects | Anti-Bacterial Agents - pharmacology | Escherichia coli - growth & development | DNA-Directed RNA Polymerases - metabolism | RNA, Bacterial - metabolism | Lac Operon | Physiological aspects | Ribosomal proteins | Properties | Genetic translation | RNA polymerases | Proteins | Bacteria | RNA polymerase | Molecular biology | Ribonucleic acid--RNA | Index Medicus
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3. Full Text Opening and Closing of the Bacterial RNA Polymerase Clamp
by Anirban Chakraborty and Dongye Wang and Yon W. Ebright and You Korlann and Ekaterine Kortkhonjia and Taiho Kim and Saikat Chowdhury and Sivaramesh Wigneshweraraj and Herbert Irschik and Rolf Jansen and B. Tracy Nixon and Jennifer Knight and Shimon Weiss and Richard H. Ebright
Science, ISSN 0036-8075, 8/2012, Volume 337, Issue 6094, pp. 591 - 595
Using single-molecule fluorescence resonance energy transfer, we have defined bacterial RNA polymerase (RNAP) clamp conformation at each step in transcription... 
Molecules | Ligation | RNA | DNA probes | Collapsed states | DNA | Isomerization | REPORTS | Biochemistry | Molecular probes | Crystal structure | PROTEIN | STRUCTURAL BASIS | INITIATION | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | TRANSCRIPTION ELONGATION | SWITCH REGION | ALTERNATING-LASER EXCITATION | 3.3 ANGSTROM RESOLUTION | SINGLE MOLECULES | DNA Polymerase III - chemistry | Fluorescence Resonance Energy Transfer - methods | Protein Conformation | Transcription, Genetic | Gene Expression Regulation, Bacterial | DNA Polymerase III - drug effects | Physiological aspects | Genetic transcription | Research | Bacterial genetics | RNA polymerases | Bacteria | RNA polymerase | Microbiology | Deoxyribonucleic acid--DNA | Index Medicus | Polymerase | Ribonucleic acids | Deoxyribonucleic acid | Fluorescence | Clamps | Energy transfer | Binding sites
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4. Full Text Structural basis for transcription elongation by bacterial RNA polymerase
by Artsimovitch, Irina and Vassylyev, Dmitry G and Vassylyeva, Marina N and Perederina, Anna and Tahirov, Tahir H
Nature, ISSN 0028-0836, 07/2007, Volume 448, Issue 7150, pp. 157 - 162
The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the... 
TRANSLOCATION | COMPLEX | MECHANISM | INITIATION | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | DNA HYBRID | ELECTRON-DENSITY MAPS | LID ELEMENT | 3.3 ANGSTROM RESOLUTION | THERMUS-THERMOPHILUS | Promoter Regions, Genetic | Thermus thermophilus - enzymology | Thermus thermophilus - chemistry | DNA, Bacterial - metabolism | Bacterial Proteins - chemistry | Models, Molecular | Thermus thermophilus - metabolism | Crystallography, X-Ray | DNA, Bacterial - chemistry | Multiprotein Complexes - metabolism | Thermus thermophilus - genetics | Multiprotein Complexes - chemistry | RNA, Bacterial - chemistry | Bacterial Proteins - metabolism | Transcription, Genetic | DNA-Directed RNA Polymerases - chemistry | DNA-Directed RNA Polymerases - metabolism | Nucleic Acid Conformation | Binding Sites | RNA, Bacterial - metabolism | DNA binding proteins | Research | Genetic transcription | Gene expression | RNA polymerases | Crystallization | Genetics | RNA polymerase | Deoxyribonucleic acid | DNA | Substrates | Binding sites | Polymerase | Ribonucleic acids | Strands | Bacteria | Nucleotides | Elongation | Displacement | Index Medicus
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5. Full Text Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase
by Maffioli, Sonia I and Zhang, Yu and Degen, David and Carzaniga, Thomas and Del Gatto, Giancarlo and Serina, Stefania and Monciardini, Paolo and Mazzetti, Carlo and Guglierame, Paola and Candiani, Gianpaolo and Chiriac, Alina Iulia and Facchetti, Giuseppe and Kaltofen, Petra and Sahl, Hans-Georg and Dehò, Gianni and Donadio, Stefano and Ebright, Richard H
Cell, ISSN 0092-8674, 06/2017, Volume 169, Issue 7, pp. 1240 - 1248.e23
Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog... 
antibiotic | transcription | antimicrobial resistance | RNA polymerase inhibitor | nucleoside-analog inhibitor | transcription inhibitor | antibacterial | Pseudouridimycin (PUM) | RNA polymerase | microbial extract screening | MYCOBACTERIUM-TUBERCULOSIS | STRUCTURAL BASIS | TRANSCRIPTION INHIBITION | NUCLEOTIDE ADDITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI K-12 | ACTIVE-CENTER | STAPHYLOCOCCUS-AUREUS | SWITCH REGION | FLUCTUATION ANALYSIS | RPOB GENE | CELL BIOLOGY | Transcription, Genetic - drug effects | Streptococcus pyogenes - drug effects | DNA-Directed RNA Polymerases - antagonists & inhibitors | Soil Microbiology | Streptomyces - chemistry | Humans | Bacteria - drug effects | Drug Resistance, Bacterial | Anti-Bacterial Agents - isolation & purification | Mice, Inbred ICR | Bacteria - growth & development | Animals | Anti-Bacterial Agents - chemistry | Bacteria - classification | Female | Streptococcal Infections - drug therapy | Anti-Bacterial Agents - pharmacology | DNA-Directed RNA Polymerases - chemistry | Mice | HeLa Cells | RNA | Analysis | Nucleosides | Drug resistance | Glycine | Rifampin | RNA polymerases | Glutamine | Drug resistance in microorganisms | Microbiology | Genetic transcription | Public health | Index Medicus
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6. Full Text Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme
by Basu, Ritwika S and Warner, Brittany A and Molodtsov, Vadim and Pupov, Danil and Esyunina, Daria and Fernández-Tornero, Carlos and Kulbachinskiy, Andrey and Murakami, Katsuhiko S
Journal of Biological Chemistry, ISSN 0021-9258, 2014, Volume 289, Issue 35, pp. 24549 - 24559
Background: Cellular RNA polymerases start transcription by de novo RNA priming. Results: Structures and biochemical studies of initially transcribing... 
ABORTIVE INITIATION | Transcription | SPECIFICITY | MECHANISM | X-ray Crystallography | BIOCHEMISTRY & MOLECULAR BIOLOGY | SIGMA-SUBUNIT | PROMOTER CLEARANCE | II-TFIIB COMPLEX | Promoter | Transcription Initiation Factor | NUCLEOTIDE | ACTIVE-CENTER | X-RAY | GENE-EXPRESSION | RNA Polymerase | Promoter Regions, Genetic | Thermus thermophilus - enzymology | Crystallization | Models, Molecular | Molecular Sequence Data | Crystallography, X-Ray | Sequence Homology, Nucleic Acid | DNA, Bacterial - genetics | Base Sequence | Transcription Initiation Site | DNA-Directed RNA Polymerases - chemistry | DNA-Directed RNA Polymerases - metabolism | Binding Sites | Index Medicus | Gene Regulation
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7. Full Text Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes
by Comas, Iñaki and Borrell, Sonia and Roetzer, Andreas and Rose, Graham and Malla, Bijaya and Kato-Maeda, Midori and Galagan, James and Niemann, Stefan and Gagneux, Sebastien
Nature Genetics, ISSN 1061-4036, 01/2012, Volume 44, Issue 1, pp. 106 - 110
Epidemics of drug-resistant bacteria emerge worldwide, even as resistant strains frequently have reduced fitness compared to their drug-susceptible... 
FITNESS | BACTERIA | EVOLUTION | PHYLOGEOGRAPHY | GENETICS | BEIJING GENOTYPE | GENETICS & HEREDITY | ANTIBIOTIC-RESISTANCE | DRUG-RESISTANCE | BIOLOGICAL COST | PROTEINS | Genome, Bacterial | Tuberculosis, Multidrug-Resistant - microbiology | Models, Molecular | DNA-Directed RNA Polymerases - genetics | Tuberculosis, Multidrug-Resistant - genetics | Mutation | Rifampin - pharmacology | Drug Resistance, Bacterial - genetics | Mycobacterium tuberculosis - drug effects | Sequence Analysis, DNA | Tuberculosis, Multidrug-Resistant - epidemiology | Mycobacterium tuberculosis - genetics | Drug resistance in microorganisms | Usage | Gene mutations | Mycobacterium tuberculosis | Genetic aspects | Research | Nucleotide sequencing | Health aspects | DNA sequencing | Bacteria | Tuberculosis | Drug resistance | Index Medicus
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8. Full Text Structural basis for substrate loading in bacterial RNA polymerase
by Landick, Robert and Zhang, Jinwei and Artsimovitch, Irina and Vassylyev, Dmitry G and Vassylyeva, Marina N and Palangat, Murali
Nature, ISSN 0028-0836, 07/2007, Volume 448, Issue 7150, pp. 163 - 168
The mechanism of substrate loading in multisubunit RNA polymerase is crucial for understanding the general principles of transcription yet remains hotly... 
MECHANISM | DISCRIMINATION | CRYSTAL-STRUCTURE | CATALYTIC RESIDUES | MULTIDISCIPLINARY SCIENCES | II ELONGATION COMPLEX | ACTIVE-CENTER | ELECTRON-DENSITY MAPS | TRANSCRIPTION ELONGATION | NTP | 3.3 ANGSTROM RESOLUTION | Thermus thermophilus - enzymology | DNA-Directed RNA Polymerases - antagonists & inhibitors | Protein Structure, Secondary | Models, Molecular | Substrate Specificity | Crystallography, X-Ray | Nucleotides - metabolism | Adenosine Triphosphate - analogs & derivatives | Protein Folding | Multiprotein Complexes - metabolism | Multiprotein Complexes - chemistry | Adenosine Triphosphate - metabolism | Bacterial Proteins - metabolism | Protein Conformation | Transcription, Genetic | DNA-Directed RNA Polymerases - chemistry | Aminoglycosides - pharmacology | DNA-Directed RNA Polymerases - metabolism | Research | Genetic transcription | Gene expression | RNA polymerases | Crystallization | Bacteria | Genetics | Biochemistry | RNA polymerase | Catalysis | Substrates | Polymerase | Inhibitors | Ribonucleic acids | Insertion | Elongation | Displacement | Index Medicus
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9. Full Text Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells
by Bakshi, Somenath and Siryaporn, Albert and Goulian, Mark and Weisshaar, James C
Molecular Microbiology, ISSN 0950-382X, 07/2012, Volume 85, Issue 1, pp. 21 - 38
Quantitative spatial distributions of ribosomes (S2‐YFP) and RNA polymerase (RNAP; β′‐yGFP) in live Escherichia coli are measured by superresolution... 
NUCLEOID-ASSOCIATED PROTEIN | MESSENGER-RNA | BACILLUS-SUBTILIS | CAULOBACTER-CRESCENTUS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ACTIVE TRANSCRIPTION | B-R | MICROBIOLOGY | BACTERIAL CHROMOSOME SEGREGATION | FLUORESCENT PROTEIN | SPATIAL-DISTRIBUTION | E. COLI | DNA-Directed RNA Polymerases - analysis | Escherichia coli - enzymology | Image Processing, Computer-Assisted | Ribosomes - chemistry | DNA, Bacterial - analysis | DNA-Directed RNA Polymerases - chemistry | Escherichia coli Proteins - chemistry | Escherichia coli Proteins - analysis | Microscopy, Fluorescence | E coli | Microscopy | Microbiology | Fluorescence | RNA polymerase | Ribonucleic acid--RNA | Deoxyribonucleic acid--DNA | Index Medicus
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10. Full Text Structure of a bacterial RNA polymerase holoenzyme open promoter complex
by Bae, Brian and Feklistov, Andrey and Lass-Napiorkowska, Agnieszka and Landick, Robert and Darst, Seth A and Argonne National Lab. (ANL), Argonne, IL (United States)
eLife, ISSN 2050-084X, 09/2015, Volume 4, Issue 2015
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter... 
ANGSTROM RESOLUTION | AROMATIC-AMINO-ACIDS | CONSERVED REGION-2 | CONFORMATIONAL-CHANGES | BACILLUS-SUBTILIS | CRYSTAL-STRUCTURE | BIOLOGY | LAMBDA-PR PROMOTER | TRANSCRIPTION INITIATION | ESCHERICHIA-COLI SIGMA | II-TFIIB COMPLEX | Promoter Regions, Genetic | DNA, Bacterial - metabolism | Thermus - enzymology | Models, Molecular | Crystallography, X-Ray | Holoenzymes - chemistry | DNA, Bacterial - chemistry | Holoenzymes - metabolism | Protein Binding | Protein Conformation | DNA-Directed RNA Polymerases - chemistry | DNA-Directed RNA Polymerases - metabolism | Nucleic Acid Conformation | Thermus - chemistry | Index Medicus | BASIC BIOLOGICAL SCIENCES
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