Bacterial transcription terminators: the RNA 3'-end chronicles.
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[1] C. Ingham,et al. Rho-independent terminators without 3' poly-U tails from the early region of actinophage øC31. , 1995, Nucleic acids research.
[2] A. Bolshoy,et al. New Elements of the Termination of Transcription in Prokaryotes , 2004, Journal of biomolecular structure & dynamics.
[3] P. V. von Hippel,et al. The elongation-termination decision in transcription. , 1992, Science.
[4] M. Tomita,et al. Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination. , 1998, Nucleic acids research.
[5] Smita S. Patel. Structural biology: Steps in the right direction , 2009, Nature.
[6] R. Sen,et al. Transcription Termination Factor Rho Prefers Catalytically Active Elongation Complexes for Releasing RNA* , 2008, Journal of Biological Chemistry.
[7] J. Rossi,et al. The tyrT locus: Termination and processing of a complex transcript , 1981, Cell.
[8] D. Herschlag,et al. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[9] T. Wood,et al. The NMR structure of the RNA binding domain of E.coli rho factor suggests possible RNA–protein interactions , 1998, Nature Structural Biology.
[10] Jeffrey W. Roberts,et al. Forward translocation is the natural pathway of RNA release at an intrinsic terminator. , 2004, Molecular cell.
[11] T. Platt,et al. Evidence supporting a tethered tracking model for helicase activity of Escherichia coli Rho factor. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[12] Anirban Mitra,et al. WebGeSTer DB—a transcription terminator database , 2010, Nucleic Acids Res..
[13] Jeffrey W. Roberts,et al. Mechanism of intrinsic transcription termination and antitermination. , 1999, Science.
[14] E. Nudler,et al. The mechanism of intrinsic transcription termination. , 1999, Molecular cell.
[15] R. Sen,et al. Interaction surface of the transcription terminator Rho required to form a complex with the C-terminal domain of the antiterminator NusG. , 2011, Journal of molecular biology.
[16] K. Severinov,et al. The role of the bacterial RNA polymerase β subunit flexible flap domain in transcription termination , 2006, Doklady Biochemistry and Biophysics.
[17] M. Chamberlin,et al. Pausing and termination of transcription within the early region of bacteriophage T7 DNA in vitro. , 1981, The Journal of biological chemistry.
[18] Sharmistha Banerjee,et al. Rho-dependent transcription termination: more questions than answers. , 2006, Journal of microbiology.
[19] J. Richardson. Rho-dependent termination and ATPases in transcript termination. , 2002, Biochimica et biophysica acta.
[20] M. Kashlev,et al. Mechanism of sequence-specific pausing of bacterial RNA polymerase , 2009, Proceedings of the National Academy of Sciences.
[21] J. Gowrishankar,et al. Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli. , 2003, Journal of molecular biology.
[22] C. Yanofsky,et al. Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.
[23] R. Landick,et al. Allosteric Control of RNA Polymerase by a Site That Contacts Nascent RNA Hairpins , 2001, Science.
[24] P. Cramer,et al. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution , 2001, Science.
[25] M. Kashlev,et al. Functional topography of nascent RNA in elongation intermediates of RNA polymerase. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[26] J. Roberts,et al. Rho-dependent transcription termination at lambda R1 requires upstream sequences. , 1985, The Journal of biological chemistry.
[27] R. Landick,et al. Direct Versus Limited-step Reconstitution Reveals Key Features of an RNA Hairpin-stabilized Paused Transcription Complex* , 2007, Journal of Biological Chemistry.
[28] C. Yanofsky,et al. Rho-dependent transcription termination in the tryptophanase operon leader region of Escherichia coli K-12 , 1986, Journal of bacteriology.
[29] C. Chan,et al. Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin. , 1993, Journal of molecular biology.
[30] K. Shigesada,et al. Structural and functional dissections of transcription termination factor rho by random mutagenesis. , 1995, Journal of molecular biology.
[31] T. Platt,et al. Effects of decreased cytosine content on rho interaction with the rho-dependent terminator trp t' in Escherichia coli. , 1992, The Journal of biological chemistry.
[32] P. V. von Hippel,et al. Regulation of rho-dependent transcription termination by NusG is specific to the Escherichia coli elongation complex. , 2000, Biochemistry.
[33] M. Chamberlin,et al. Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators. , 1992, Journal of molecular biology.
[34] J. Richardson. Loading Rho to Terminate Transcription , 2003, Cell.
[35] Jonathan Tennyson,et al. Water vapour in the atmosphere of a transiting extrasolar planet , 2007, Nature.
[36] E. Brody,et al. Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. , 1990 .
[37] M. Kashlev,et al. Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. , 2002, Molecular cell.
[38] P. V. von Hippel,et al. Transcription termination at intrinsic terminators: the role of the RNA hairpin. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[39] D. Court,et al. Sequences required for transcription termination at the intrinsic lambdatI terminator. , 2010, Canadian journal of microbiology.
[40] Jens Michaelis,et al. Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex , 2009, Nucleic acids research.
[41] Vitaly Epshtein,et al. An allosteric mechanism of Rho-dependent transcription termination , 2010, Nature.
[42] J. Geiselmann,et al. A simple polypyrimidine repeat acts as an artificial Rho-dependent terminator in vivo and in vitro. , 1998, Nucleic acids research.
[43] Jeffrey W. Roberts,et al. Role of DNA bubble rewinding in enzymatic transcription termination. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[44] M. Ciampi,et al. Rho-dependent terminators and transcription termination. , 2006, Microbiology.
[45] Ravindra V Dalal,et al. Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing. , 2006, Molecular cell.
[46] V. Nagaraja,et al. Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium. , 2008, Tuberculosis.
[47] J. Richardson,et al. An RNA-dependent nucleoside triphosphate phosphohydrolase (ATPase) associated with rho termination factor. , 1974, Proceedings of the National Academy of Sciences of the United States of America.
[48] E. Margeat,et al. Keeping up to speed with the transcription termination factor Rho motor , 2010, Transcription.
[49] T. Platt,et al. Transcription termination factor rho is an RNA-DNA helicase , 1987, Cell.
[50] C. Yanofsky,et al. Release of transcript and template during transcription termination at the trp operon attenuator. , 1983, Journal of Biological Chemistry.
[51] E. Anderson. Hudson et al. , 1977 .
[52] M. Gottesman,et al. Requirement for E. coli NusG protein in factor-dependent transcription termination , 1992, Cell.
[53] Julio Collado-Vides,et al. RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units) , 2010, Nucleic Acids Res..
[54] E. Margeat,et al. Mutagenesis-based evidence for an asymmetric configuration of the ring-shaped transcription termination factor Rho. , 2011, Journal of molecular biology.
[55] H. Heumann,et al. 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". , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[56] C. Squires,et al. Proteins shared by the transcription and translation machines. , 2000, Annual review of microbiology.
[57] R. Landick,et al. Nuclease Cleavage of the Upstream Half of the Nontemplate Strand DNA in an Escherichia coli Transcription Elongation Complex Causes Upstream Translocation and Transcriptional Arrest* , 1997, The Journal of Biological Chemistry.
[58] Jayanta Mukhopadhyay,et al. The RNA Polymerase “Switch Region” Is a Target for Inhibitors , 2008, Cell.
[59] E. Nudler,et al. Mechanistic model of the elongation complex of Escherichia coli RNA polymerase. , 1998, Cold Spring Harbor symposia on quantitative biology.
[60] R. Landick,et al. Nonequilibrium mechanism of transcription termination from observations of single RNA polymerase molecules. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[61] R. Landick,et al. Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators. , 2009, Journal of molecular biology.
[62] Martin Depken,et al. The origin of short transcriptional pauses. , 2009, Biophysical journal.
[63] R. Landick. RNA Polymerase Clamps Down , 2001, Cell.
[64] M. Chamberlin,et al. Parameters affecting transcription termination by Escherichia coli RNA polymerase. I. Analysis of 13 rho-independent terminators. , 1992, Journal of molecular biology.
[65] E. Nudler,et al. An allosteric path to transcription termination. , 2007, Molecular cell.
[66] S. Adhya,et al. Control of transcription termination. , 1978, Annual review of biochemistry.
[67] Chyi-Ying A. Chen,et al. Transcription termination at λ tR1 is mediated by interaction of rho with specific single-stranded domains near the 3′ end of cro mRNA , 1986, Cell.
[68] R. Burgess,et al. Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[69] Vivek K. Mutalik,et al. Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[70] J. Berger,et al. Structural Insights into RNA-Dependent Ring Closure and ATPase Activation by the Rho Termination Factor , 2006, Cell.
[71] Willy Wriggers,et al. Conformational flexibility of bacterial RNA polymerase , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[72] C. Yanofsky,et al. Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[73] S. Yokoyama,et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution , 2002, Nature.
[74] W. Mcallister,et al. Termination and slippage by bacteriophage T7 RNA polymerase. , 1993, Journal of Molecular Biology.
[75] Björn M. Burmann,et al. A NusE:NusG Complex Links Transcription and Translation , 2010, Science.
[76] B. Stitt,et al. Evidence for amino acid roles in the chemistry of ATP hydrolysis in Escherichia coli Rho. , 2010, Journal of molecular biology.
[77] V. Markovtsov,et al. Transcription Processivity: Protein-DNA Interactions Holding Together the Elongation Complex , 1996, Science.
[78] S. Salzberg,et al. Prediction of transcription terminators in bacterial genomes. , 2000, Journal of molecular biology.
[79] J M Berger,et al. The structural basis for terminator recognition by the Rho transcription termination factor. , 1999, Molecular cell.
[80] A. Ansari,et al. Regulator trafficking on bacterial transcription units in vivo. , 2009, Molecular cell.
[81] D. Court,et al. Functional importance of sequence in the stem-loop of a transcription terminator. , 1991, Science.
[82] Robert Landick,et al. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. , 2007, Molecular cell.
[83] J. Berger,et al. Structure of the Rho Transcription Terminator Mechanism of mRNA Recognition and Helicase Loading , 2003, Cell.
[84] G. Crooks,et al. WebLogo: a sequence logo generator. , 2004, Genome research.
[85] M. Gottesman,et al. Transcription termination maintains chromosome integrity , 2010, Proceedings of the National Academy of Sciences.
[86] M. Kashlev,et al. Transcription Termination: Primary Intermediates and Secondary Adducts* , 2002, The Journal of Biological Chemistry.
[87] Masaki Yamamoto,et al. Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein , 2010, Nature.
[88] T. D. Schneider,et al. Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.
[89] E. Margeat,et al. Transcription Termination Factor Rho Can Displace Streptavidin from Biotinylated RNA* , 2007, Journal of Biological Chemistry.
[90] I. Pastan,et al. Effect of Rho on transcription of bacterial operons. , 1973, Nature: New biology.
[91] G. Dougan,et al. Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation , 2010, Science.
[92] P. V. von Hippel,et al. Structure and assembly of the Escherichia coli transcription termination factor rho and its interaction with RNA. I. Cryoelectron microscopic studies. , 1991, Journal of molecular biology.
[93] K. Shigesada,et al. Studies on the altered rho factor in a nitA mutants of Escherichia coli defective in transcription termination. I. Characterization and quantitative determination of rho in cell extracts. , 1978, Journal of molecular biology.
[94] Jeffrey W. Roberts,et al. Role of the non-template strand of the elongation bubble in intrinsic transcription termination. , 2003, Journal of molecular biology.
[95] C. Y. Chen,et al. Sequence elements essential for rho-dependent transcription termination at lambda tR1. , 1987, The Journal of biological chemistry.
[96] M. Chamberlin,et al. Terminator-distal sequences determine the in vitro efficiency of the early terminators of bacteriophages T3 and T7. , 1989, Biochemistry.
[97] C. Bruni,et al. A consensus motif common to all rho-dependent prokaryotic transcription terminators , 1991, Cell.
[98] Robert Landick,et al. Transcriptional pausing without backtracking , 2009, Proceedings of the National Academy of Sciences.
[99] T. Platt,et al. Tandem termination sites in the tryptophan operon of Escherichia coli. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[100] V. Nagaraja,et al. Occurrence, divergence and evolution of intrinsic terminators across eubacteria. , 2009, Genomics.
[101] A. Rahmouni,et al. Noncanonical interactions in the management of RNA structural blocks by the transcription termination rho helicase. , 2007, Biochemistry.
[102] Evgeny Nudler,et al. Termination Factor Rho and Its Cofactors NusA and NusG Silence Foreign DNA in E. coli , 2008, Science.
[103] E. Nudler,et al. The RNA–DNA Hybrid Maintains the Register of Transcription by Preventing Backtracking of RNA Polymerase , 1997, Cell.
[104] M. Kashlev,et al. RNA Polymerase Switches between Inactivated and Activated States By Translocating Back and Forth along the DNA and the RNA* , 1997, The Journal of Biological Chemistry.
[105] J. Richardson,et al. ATP-induced changes in the binding of RNA synthesis termination protein Rho to RNA. , 1980, Journal of molecular biology.
[106] Nancy R Forde,et al. Thermal probing of E. coli RNA polymerase off-pathway mechanisms. , 2008, Journal of molecular biology.
[107] H. Aiba,et al. Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization. , 1996, Biochimie.
[108] I. Tinoco,et al. A thermodynamic study of unusually stable RNA and DNA hairpins. , 1991, Nucleic acids research.
[109] V. Nagaraja,et al. Conserved economics of transcription termination in eubacteria. , 2002, Nucleic acids research.
[110] F. Imamoto,et al. Promoters and autogenous control of the Escherichia coli hupA and hupB genes. , 1990, Journal of molecular biology.
[111] S. Darst,et al. A Structural Model of Transcription Elongation , 2000 .
[112] T. Platt,et al. Signals sufficient for rho-dependent transcription termination at trp t' span a region centered 60 base pairs upstream of the earliest 3' end point. , 1988, The Journal of biological chemistry.
[113] Pei Fen Kuan,et al. Rho directs widespread termination of intragenic and stable RNA transcription , 2009, Proceedings of the National Academy of Sciences.
[114] I. Tinoco,et al. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. , 1992, Nucleic acids research.
[115] W. Greenleaf,et al. Single-molecule studies of RNA polymerase: motoring along. , 2008, Annual review of biochemistry.
[116] S. Salzberg,et al. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake , 2007, Genome Biology.
[117] Jeffrey W. Roberts. Termination Factor for RNA Synthesis , 1969, Nature.
[118] J. Berger,et al. Running in Reverse: The Structural Basis for Translocation Polarity in Hexameric Helicases , 2009, Cell.
[119] Robert Landick,et al. The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. , 2003, Molecular cell.
[120] M. Chamberlin,et al. Sequences linked to prokaryotic promoters can affect the efficiency of downstream termination sites. , 1989, Journal of molecular biology.
[121] P. V. von Hippel,et al. Stability of Escherichia coli transcription complexes near an intrinsic terminator. , 1994, Journal of molecular biology.
[122] R. Landick,et al. Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. , 1990, The Journal of biological chemistry.
[123] J. Roberts,et al. Rho-dependent transcription termination. Characterization of the requirement for cytidine in the nascent transcript. , 1991, The Journal of biological chemistry.
[124] Martin Gruebele,et al. Exploring the energy landscape of a small RNA hairpin. , 2006, Journal of the American Chemical Society.
[125] M. Palumbo,et al. Widespread Antisense Transcription in Escherichia coli , 2010, mBio.
[126] P. V. von Hippel,et al. Rho-dependent termination of transcription. II. Kinetics of mRNA elongation during transcription from the bacteriophage lambda PR promoter. , 1983, The Journal of biological chemistry.
[127] C. Chan,et al. Multiple interactions stabilize a single paused transcription intermediate in which hairpin to 3' end spacing distinguishes pause and termination pathways. , 1997, Journal of molecular biology.
[128] V. Nagaraja,et al. Alternate Paradigm for Intrinsic Transcription Termination in Eubacteria* 210 , 2001, The Journal of Biological Chemistry.
[129] P. V. von Hippel,et al. Interactions of Escherichia coli transcription termination factor rho with RNA. I. Binding stoichiometries and free energies. , 1988, Journal of molecular biology.
[130] C. Condon,et al. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non‐ribosomal and ribosomal RNA antitermination , 2001, The EMBO journal.
[131] J. Mcneil,et al. Prediction of rho-independent transcriptional terminators in Escherichia coli. , 2001, Nucleic acids research.
[132] Steven M. Block,et al. Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination , 2008, Cell.
[133] D Court,et al. Regulatory sequences involved in the promotion and termination of RNA transcription. , 1979, Annual review of genetics.
[134] Satoru Miyano,et al. Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species , 2005, PLoS Comput. Biol..
[135] J. Roberts,et al. Early transcribed sequences affect termination efficiency of Escherichia coli RNA polymerase. , 1989, Journal of molecular biology.
[136] Tahir H. Tahirov,et al. Structural basis for transcription elongation by bacterial RNA polymerase , 2007, Nature.