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This review focuses on the sequence elements involved in transcription pausing and termination, and possible mechanisms of interaction with RNA polymerase in the elongation complex
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0031024660
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0032540286
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NMR structure of the bacteriophage λ N peptide/boxB RNA complex: Recognition of a GNRA fold by an arginine-rich motif
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The mode of RNA recognition by the λ N protein is examined in detail, and is shown to represent a novel pattern of RNA-protein binding
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Legault P., Li J., Mogridge J., Kay L.E., Greenblatt J. NMR structure of the bacteriophage λ N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell. 93:1998;289-299. The mode of RNA recognition by the λ N protein is examined in detail, and is shown to represent a novel pattern of RNA-protein binding.
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Legault, P.1
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11
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0031916834
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Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex
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Examination of RNA recognition of P22 N protein offers an interesting comparison to λ N protein
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Cai Z., Gorin A., Frederick R., Ye X., Hu W., Majumdar A., Kettani A., Patel D.J. Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex. Nat Struct Biol. 5:1998;203-212. Examination of RNA recognition of P22 N protein offers an interesting comparison to λ N protein.
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Cai, Z.1
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Patel, D.J.8
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12
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0031614914
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Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage λ N protein
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The functional roles of multiple domains within the λ N protein are explored
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Mogridge J., Legault P., Li J., Van Oene M.D., Kay L.E., Greenblatt J. Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage λ N protein. Mol Cell. 1:1998;265-275. The functional roles of multiple domains within the λ N protein are explored.
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Mogridge, J.1
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13
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0032532456
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70 required for promotor function and antitermination by phage λ Q protein
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A novel role for the σ subunit in recognition of a pause site required for Q-mediated antitermination is described
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70 required for promotor function and antitermination by phage λ Q protein. Genes Dev. 12:1998;3276-3285. A novel role for the σ subunit in recognition of a pause site required for Q-mediated antitermination is described.
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Ko, D.C.1
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Guo, J.3
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14
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0033597435
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Mechanism of intrinsic transcription termination and antitermination
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Analysis of the Q antitermination system is used to obtain basic information about intrinsic termination, and the role of the hairpin in destabilization of the elongation complex
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Yarnell W.S., Roberts J.W. Mechanism of intrinsic transcription termination and antitermination. Science. 284:1999;611-615. Analysis of the Q antitermination system is used to obtain basic information about intrinsic termination, and the role of the hairpin in destabilization of the elongation complex.
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Yarnell, W.S.1
Roberts, J.W.2
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0030979021
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NusA is required for ribosomal antitermination and for modulation of the transcription elongation rate of both antiterminated RNA and mRNA
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Vogel U., Jensen K.F. NusA is required for ribosomal antitermination and for modulation of the transcription elongation rate of both antiterminated RNA and mRNA. J Biol Chem. 272:1997;12265-12271.
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Vogel, U.1
Jensen, K.F.2
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0033032384
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This study investigates the role of Nus factors in controlling transcription elongation during rrn transcription in E. coli
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Zellars M., Squires C.L. Antiterminator-dependent modulation of transcription elongation rates by NusB and NusG. Mol Microbiol. 32:1999;1296-1304. This study investigates the role of Nus factors in controlling transcription elongation during rrn transcription in E. coli.
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Zellars, M.1
Squires, C.L.2
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17
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0032904686
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Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis
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Rho-dependent termination appears to play a smaller role in B. subtilis than in E. coli, and the physiological functions of the Nus factors may also be somewhat different in the two systems
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Ingham C.J., Dennis J., Furneaux P.A. Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis. Mol Microbiol. 31:1999;651-663. Rho-dependent termination appears to play a smaller role in B. subtilis than in E. coli, and the physiological functions of the Nus factors may also be somewhat different in the two systems.
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Mol Microbiol
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Ingham, C.J.1
Dennis, J.2
Furneaux, P.A.3
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0030718529
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RfaH and the ops element, components of a novel system controlling bacterial transcription elongation
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Bailey M.J.A., Hughes C., Koronaikis V. RfaH and the ops element, components of a novel system controlling bacterial transcription elongation. Mol Microbiol. 26:1997;845-851.
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Bailey, M.J.A.1
Hughes, C.2
Koronaikis, V.3
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19
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Enhancing transcription through the Escherichia coli hemolysin operon, hlyCABD: RfaH and upstream JUMPStart DNA sequences function together via a postinitiation mechanism
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Leeds J.A., Welch R.A. Enhancing transcription through the Escherichia coli hemolysin operon, hlyCABD: RfaH and upstream JUMPStart DNA sequences function together via a postinitiation mechanism. J Bacteriol. 179:1997;3519-3527.
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Leeds, J.A.1
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20
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0031802195
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Promoter region of the Escherichia coli O7-specific lipopolysaccharide gene cluster: Structural and functional characterization of an upstream untranslated mRNA sequence
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Marolda C.L., Valvano M.A. Promoter region of the Escherichia coli O7-specific lipopolysaccharide gene cluster: structural and functional characterization of an upstream untranslated mRNA sequence. J Bacteriol. 180:1998;3070-3079.
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Marolda, C.L.1
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22
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0029022188
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A zinc binding region in the β' subunit of RNA polymerase is involved in antitermination of early transcription of phage HK022
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Clerget M., Jin D.J., Weisberg R.A. A zinc binding region in the β' subunit of RNA polymerase is involved in antitermination of early transcription of phage HK022. J Mol Biol. 248:1995;768-780.
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Clerget, M.1
Jin, D.J.2
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23
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0033579287
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Binding of transcription termination protein Nun to nascent RNA and template DNA
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This paper describes detailed biochemical analysis of the interaction of the novel Nun protein with the transcription elongation complex; of particular note is the interaction with both the nascent transcript and the template DNA
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Watnick R.S., Gottesman M.E. Binding of transcription termination protein Nun to nascent RNA and template DNA. Science. 286:1999;2337-2339. This paper describes detailed biochemical analysis of the interaction of the novel Nun protein with the transcription elongation complex; of particular note is the interaction with both the nascent transcript and the template DNA.
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Science
, vol.286
, pp. 2337-2339
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Watnick, R.S.1
Gottesman, M.E.2
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24
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0032539685
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Escherichia coli NusA is required for efficient RNA binding of phage HK022 Nun protein
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Watnick R.S., Gottesman M.E. Escherichia coli NusA is required for efficient RNA binding of phage HK022 Nun protein. Proc Natl Acad Sci USA. 95:1998;1546-1551.
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Watnick, R.S.1
Gottesman, M.E.2
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25
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0033031457
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Escherichia coli nusG mutations that block transcription termination by coliphage HK022 Nun protein
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Burova E., Hung S.C., Chen J., Court D.L., Zhou J-G., Mogilnitskiy G., Gottesman M.E. Escherichia coli nusG mutations that block transcription termination by coliphage HK022 Nun protein. Mol Microbiol. 31:1999;1783-1793.
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Burova, E.1
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Zhou, J.-G.5
Mogilnitskiy, G.6
Gottesman, M.E.7
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26
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0027339573
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Transcriptional regulation of the bgl operon of Escherichia coli involves phosphotransferase system-mediated phosphorylation of a transcriptional antiterminator
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Amster-Choder O., Wright A. Transcriptional regulation of the bgl operon of Escherichia coli involves phosphotransferase system-mediated phosphorylation of a transcriptional antiterminator. J Cell Biochem. 51:1993;83-90.
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27
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0030832399
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Crystal structure of a new RNA-binding domain from the antiterminator protein SacY of Bacillus subtilis
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van Tilbeurgh H., Manival X., Aymerich S., Lhoste J-M., Dumas C.D., Kochoyan M. Crystal structure of a new RNA-binding domain from the antiterminator protein SacY of Bacillus subtilis. EMBO J. 16:1997;5030-5036.
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Van Tilbeurgh, H.1
Manival, X.2
Aymerich, S.3
Lhoste, J.-M.4
Dumas, C.D.5
Kochoyan, M.6
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28
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0033060293
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Characterization of the dimerization domain in BglG, an RNA-binding transcriptional antiterminator from Escherichia coli
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Dimerization of BglG is required for RNA binding, and is controlled by phosphorylation. This paper describes the unusual dimerization properties of the BglG protein
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Boss A., Nussbaum-Schochat A., Amster-Choder O. Characterization of the dimerization domain in BglG, an RNA-binding transcriptional antiterminator from Escherichia coli. J Bacteriol. 181:1999;1755-1766. Dimerization of BglG is required for RNA binding, and is controlled by phosphorylation. This paper describes the unusual dimerization properties of the BglG protein.
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J Bacteriol
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Boss, A.1
Nussbaum-Schochat, A.2
Amster-Choder, O.3
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29
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0033551179
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BglG, the transcriptional antiterminator of the bgl system, interacts with the β′ subunit of the Escherichia coli RNA polymerase
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In addition to its previously defined role in controlling nascent transcript structure, BglG also appears to interact directly with RNA polymerase; the functional role of this interaction is not yet understood
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Nussbaum-Schochat A., Amster-Choder O. BglG, the transcriptional antiterminator of the bgl system, interacts with the β′ subunit of the Escherichia coli RNA polymerase. Proc Natl Acad Sci USA. 96:1999;4336-4341. In addition to its previously defined role in controlling nascent transcript structure, BglG also appears to interact directly with RNA polymerase; the functional role of this interaction is not yet understood.
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Proc Natl Acad Sci USA
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Nussbaum-Schochat, A.1
Amster-Choder, O.2
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30
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0031886850
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Antiterminator protein GlpP of Bacillus subtilis binds to glpD leader RNA
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Glatz E., Persson M., Rutberg B. Antiterminator protein GlpP of Bacillus subtilis binds to glpD leader RNA. Microbiol. 144:1998;449-456.
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Glatz, E.1
Persson, M.2
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31
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0033578787
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RNA sequence requirements for NasR mediated, nitrate-responsive transcription antitermination of the Klebsiella oxytoca M5al nasF operon leader
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NasR binds to an RNA stem-loop to direct antitermination, but the mechanism for termination control remains to be determined, since there is no evidence for competing RNA structures
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Chai W., Stewart V. RNA sequence requirements for NasR mediated, nitrate-responsive transcription antitermination of the Klebsiella oxytoca M5al nasF operon leader. J Mol Biol. 292:1999;203-216. NasR binds to an RNA stem-loop to direct antitermination, but the mechanism for termination control remains to be determined, since there is no evidence for competing RNA structures.
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J Mol Biol
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Chai, W.1
Stewart, V.2
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32
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0033214785
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Crystal structure and induction mechanism of AmiC-AmiR: A ligand-regulated transcription antitermination complex
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Structural studies of the AmiC-AmiR complex provide insight into possible mechanisms for control of AmiR activity in antitermination of the amidase operon
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O'Hara B.P., Norman R.A., Wan P.T.C., Roe S.M., Barrett T.E., Drew R.E., Pearl L.H. Crystal structure and induction mechanism of AmiC-AmiR: a ligand-regulated transcription antitermination complex. EMBO J. 18:1999;5175-5186. Structural studies of the AmiC-AmiR complex provide insight into possible mechanisms for control of AmiR activity in antitermination of the amidase operon.
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EMBO J
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, pp. 5175-5186
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O'Hara, B.P.1
Norman, R.A.2
Wan, P.T.C.3
Roe, S.M.4
Barrett, T.E.5
Drew, R.E.6
Pearl, L.H.7
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33
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0030821725
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Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel
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Babitzke P. Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel. Mol Microbiol. 26:1997;1-9.
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Babitzke, P.1
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34
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0032601488
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Regulation of the Bacillus subtilis pyrimidine biosynthetic operon by transcriptional attenuation: Control of gene expression by an mRNA-binding protein
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This paper summarizes a large body of information on the pyr operon, where PyrR directs termination by stabilization of an anti-antiterminator structure, which competes with an antiterminator, which competes with a terminator
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Switzer R.L., Turner R.J., Lu Y. Regulation of the Bacillus subtilis pyrimidine biosynthetic operon by transcriptional attenuation: control of gene expression by an mRNA-binding protein. Prog Nucl Acid Res Mol Biol. 62:1999;329-367. This paper summarizes a large body of information on the pyr operon, where PyrR directs termination by stabilization of an anti-antiterminator structure, which competes with an antiterminator, which competes with a terminator.
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Prog Nucl Acid Res Mol Biol
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, pp. 329-367
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Switzer, R.L.1
Turner, R.J.2
Lu, Y.3
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35
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0033575897
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Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA
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The molecular interactions of the 11-mer TRAP ring with 11 triplet repeats in its RNA target are beautifully demonstrated
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Antson A.A., Dodson E.J., Dodson G., Greaves R.B., Chen X., Gollnick P. Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature. 401:1999;235-242. The molecular interactions of the 11-mer TRAP ring with 11 triplet repeats in its RNA target are beautifully demonstrated.
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Nature
, vol.401
, pp. 235-242
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Antson, A.A.1
Dodson, E.J.2
Dodson, G.3
Greaves, R.B.4
Chen, X.5
Gollnick, P.6
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36
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0032882591
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A 5′ RNA stem loop participates in the transcription attenuation mechanism that controls expression of the Bacillus subtilis trpEDCFBA operon
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Binding of TRAP to its RNA target is apparently facilitated by another RNA element that may serve as a loading zone for TRAP
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Sudershana S., Du H., Mahalanabis M., Babitzke P. A 5′ RNA stem loop participates in the transcription attenuation mechanism that controls expression of the Bacillus subtilis trpEDCFBA operon. J Bacteriol. 181:1999;5742-5749. Binding of TRAP to its RNA target is apparently facilitated by another RNA element that may serve as a loading zone for TRAP.
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J Bacteriol
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Sudershana, S.1
Du, H.2
Mahalanabis, M.3
Babitzke, P.4
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37
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0032521544
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Adaptation of an enzyme to regulatory function: Structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase
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This paper describes the structure of the PyrR protein, which functions as an RNA-binding protein to control transcription termination and senses its effectors by virtue of its similarity to uracil phosphoribosyltransferases
-
Tomchick D.R., Turner R.J., Switzer R.L., Smith J.L. Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase. Structure. 6:1998;337-350. This paper describes the structure of the PyrR protein, which functions as an RNA-binding protein to control transcription termination and senses its effectors by virtue of its similarity to uracil phosphoribosyltransferases.
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Structure
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, pp. 337-350
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Tomchick, D.R.1
Turner, R.J.2
Switzer, R.L.3
Smith, J.L.4
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38
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0031735563
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The S box regulon: A new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria
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Identification of a conserved motif revealed a large set of transcriptional units that appear to be regulated in concert at the level of transcription termination by methionine availability; the molecular details of the regulatory mechanism remain to be elucidated
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Grundy F.J., Henkin T.M. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria. Mol Microbiol. 30:1998;737-749. Identification of a conserved motif revealed a large set of transcriptional units that appear to be regulated in concert at the level of transcription termination by methionine availability; the molecular details of the regulatory mechanism remain to be elucidated.
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Mol Microbiol
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, pp. 737-749
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Grundy, F.J.1
Henkin, T.M.2
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39
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0030795362
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Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene
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Rollins S.M., Grundy F.J., Henkin T.M. Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene. Mol Microbiol. 25:1997;411-421.
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Rollins, S.M.1
Grundy, F.J.2
Henkin, T.M.3
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40
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0030901060
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Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination
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Grundy F.J., Hodil S.E., Rollins S.M., Henkin T.M. Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination. J Bacteriol. 179:1997;2587-2594.
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Grundy, F.J.1
Hodil, S.E.2
Rollins, S.M.3
Henkin, T.M.4
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41
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0030970446
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The Staphylococcus aureus ileS gene, encoding isoleucyl-tRNA synthetase, is a member of the T-box family
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Grundy F.J., Haldeman M.T., Hornblow G.M., Ward J.M., Chalker A.F., Henkin T.M. The Staphylococcus aureus ileS gene, encoding isoleucyl-tRNA synthetase, is a member of the T-box family. J Bacteriol. 179:1997;3767-3772.
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J Bacteriol
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Grundy, F.J.1
Haldeman, M.T.2
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