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Volumn 377, Issue 2, 2008, Pages 551-564

Corrigendum to "Still Looking for the Magic Spot: The Crystallographically Defined Binding Site for ppGpp on RNA Polymerase Is Unlikely toBe Responsible for rRNA Transcription Regulation" [J. Mol. Biol. 377 (2008) 551-564] (DOI:10.1016/j.jmb.2008.01.042);Still Looking for the Magic Spot: The Crystallographically Defined Binding Site for ppGpp on RNA Polymerase Is Unlikely to Be Responsible for rRNA Transcription Regulation

Author keywords

DksA; omega; ppGpp; ppGpp binding site; RNA polymerase

Indexed keywords

RIBOSOME RNA; RNA POLYMERASE;

EID: 40049090539     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.04.059     Document Type: Erratum
Times cited : (67)

References (45)
  • 1
    • 0003174053 scopus 로고    scopus 로고
    • The stringent response
    • M. Cashel D.R. Gentry V.H. Hernandez D. Vinella The stringent response F.C. Neidhardt Escherichia coli and Salmonella : Cellular and Molecular Biology 1996 ASM Press Washington, DC 1458 1496
    • (1996) , pp. 1458-1496
    • Cashel, M.1    Gentry, D.R.2    Hernandez, V.H.3    Vinella, D.4
  • 2
    • 0041669435 scopus 로고    scopus 로고
    • Control of rRNA expression by small molecules is dynamic and nonredundant
    • H.D. Murray D.A. Schneider R.L. Gourse Control of rRNA expression by small molecules is dynamic and nonredundant Mol. Cell 12 2003 125 134
    • (2003) Mol. Cell , vol.12 , pp. 125-134
    • Murray, H.D.1    Schneider, D.A.2    Gourse, R.L.3
  • 3
    • 33748662456 scopus 로고    scopus 로고
    • DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli
    • P. Mallik B.J. Paul S.T. Rutherford R.L. Gourse R. Osuna DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli J. Bacteriol. 188 2006 5775 5782
    • (2006) J. Bacteriol. , vol.188 , pp. 5775-5782
    • Mallik, P.1    Paul, B.J.2    Rutherford, S.T.3    Gourse, R.L.4    Osuna, R.5
  • 4
    • 4043069926 scopus 로고    scopus 로고
    • DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP
    • B.J. Paul M.M. Barker W. Ross D.A. Schneider C. Webb J.W. Foster R.L. Gourse DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP Cell 118 2004 311 322
    • (2004) Cell , vol.118 , pp. 311-322
    • Paul, B.J.1    Barker, M.M.2    Ross, W.3    Schneider, D.A.4    Webb, C.5    Foster, J.W.6    Gourse, R.L.7
  • 5
    • 33645860823 scopus 로고    scopus 로고
    • The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription
    • L.M. Bernardo L.U. Johansson D. Solera E. Skarfstad V. Shingler The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription Mol. Microbiol. 60 2006 749 764
    • (2006) Mol. Microbiol. , vol.60 , pp. 749-764
    • Bernardo, L.M.1    Johansson, L.U.2    Solera, D.3    Skarfstad, E.4    Shingler, V.5
  • 6
    • 33745463774 scopus 로고    scopus 로고
    • Growth phase-dependent regulation of the extracytoplasmic stress factor, sigma E, by guanosine 3′5′ bisphosphate, ppGpp
    • A. Costanzo S.E. Ades Growth phase-dependent regulation of the extracytoplasmic stress factor, sigma E, by guanosine 3′5′ bisphosphate, ppGpp J. Bacteriol. 188 2006 4589 4591
    • (2006) J. Bacteriol. , vol.188 , pp. 4589-4591
    • Costanzo, A.1    Ades, S.E.2
  • 7
    • 33745221184 scopus 로고    scopus 로고
    • ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorragic Escherichia coli through activation of two virulence regulatory genes
    • N. Nakanishi H. Abe Y. Ogura T. Hayashi K. Tashiro S. Kuhara ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorragic Escherichia coli through activation of two virulence regulatory genes Mol. Microbiol. 61 2006 194 205
    • (2006) Mol. Microbiol. , vol.61 , pp. 194-205
    • Nakanishi, N.1    Abe, H.2    Ogura, Y.3    Hayashi, T.4    Tashiro, K.5    Kuhara, S.6
  • 8
    • 20344363655 scopus 로고    scopus 로고
    • DksA potentiates direct activation of amino acid promoters by ppGpp
    • B.J. Paul M.B. Berkmen R.L. Gourse DksA potentiates direct activation of amino acid promoters by ppGpp Proc. Natl Acad. Sci. USA 102 2005 7823 7828
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 7823-7828
    • Paul, B.J.1    Berkmen, M.B.2    Gourse, R.L.3
  • 9
    • 33749177569 scopus 로고    scopus 로고
    • Induction of expression of hfq by DksA is essential for Shigella flexneri virulence
    • A.K. Sharma S.M. Payne Induction of expression of hfq by DksA is essential for Shigella flexneri virulence Mol. Microbiol. 62 2006 469 479
    • (2006) Mol. Microbiol. , vol.62 , pp. 469-479
    • Sharma, A.K.1    Payne, S.M.2
  • 10
    • 0035951301 scopus 로고    scopus 로고
    • Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP
    • M.M. Barker T. Gaal R.L. Gourse Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP J. Mol. Biol. 305 2001 689 702
    • (2001) J. Mol. Biol. , vol.305 , pp. 689-702
    • Barker, M.M.1    Gaal, T.2    Gourse, R.L.3
  • 11
    • 0032539903 scopus 로고    scopus 로고
    • The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like “stringent” RNA polymerases in Escherichia coli
    • Y.N. Zhou D.J. Jin The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like “stringent” RNA polymerases in Escherichia coli Proc. Natl Acad. Sci. USA 95 1998 2908 2913
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 2908-2913
    • Zhou, Y.N.1    Jin, D.J.2
  • 12
    • 0035951305 scopus 로고    scopus 로고
    • Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro
    • M.M. Barker T. Gaal C.A. Josaitis R.L. Gourse Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro J. Mol. Biol. 305 2001 673 688
    • (2001) J. Mol. Biol. , vol.305 , pp. 673-688
    • Barker, M.M.1    Gaal, T.2    Josaitis, C.A.3    Gourse, R.L.4
  • 13
    • 0035685975 scopus 로고    scopus 로고
    • Regulation of rRNA transcription correlates with NTP-sensing
    • M.M. Barker R.L. Gourse Regulation of rRNA transcription correlates with NTP-sensing J. Bacteriol. 183 2001 6315 6323
    • (2001) J. Bacteriol. , vol.183 , pp. 6315-6323
    • Barker, M.M.1    Gourse, R.L.2
  • 14
    • 33744981130 scopus 로고    scopus 로고
    • rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase
    • S.P. Haugen M.B. Berkmen W. Ross T. Gaal C. Ward R.L. Gourse rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase Cell 125 2006 1069 1082
    • (2006) Cell , vol.125 , pp. 1069-1082
    • Haugen, S.P.1    Berkmen, M.B.2    Ross, W.3    Gaal, T.4    Ward, C.5    Gourse, R.L.6
  • 16
    • 0026788401 scopus 로고
    • Toxic effects of high levels of ppGpp are relieved by rpoB mutations
    • K. Tedin H. Bremer Toxic effects of high levels of ppGpp are relieved by rpoB mutations J. Biol. Chem. 267 1992 2337 2344
    • (1992) J. Biol. Chem. , vol.267 , pp. 2337-2344
    • Tedin, K.1    Bremer, H.2
  • 17
    • 0028967087 scopus 로고
    • Evidence for a ppGpp binding site on Escherichia coli RNA polymerase: proximity relationship with the rifampicin-binding domain
    • P.S. Reddy A. Raghavan D. Chatterji Evidence for a ppGpp binding site on Escherichia coli RNA polymerase: proximity relationship with the rifampicin-binding domain Mol. Microbiol. 15 1995 255 265
    • (1995) Mol. Microbiol. , vol.15 , pp. 255-265
    • Reddy, P.S.1    Raghavan, A.2    Chatterji, D.3
  • 18
    • 0031949801 scopus 로고    scopus 로고
    • The mediator for stringent control, ppGpp, binds to the beta-subunit of Escherichia coli RNA polymerase
    • D. Chatterji N. Fujita A. Ishihama The mediator for stringent control, ppGpp, binds to the beta-subunit of Escherichia coli RNA polymerase Genes Cells 3 1998 279 287
    • (1998) Genes Cells , vol.3 , pp. 279-287
    • Chatterji, D.1    Fujita, N.2    Ishihama, A.3
  • 19
    • 0035847007 scopus 로고    scopus 로고
    • Binding of the transcription effector ppGpp to Escherichia coli RNA polymerase is allosteric, modular, and occurs near the N-terminus of the β′-subunit
    • I. Toulokhonov I. Shulgina V.J. Hernandez Binding of the transcription effector ppGpp to Escherichia coli RNA polymerase is allosteric, modular, and occurs near the N-terminus of the β′-subunit J. Biol. Chem. 276 2001 1220 1225
    • (2001) J. Biol. Chem. , vol.276 , pp. 1220-1225
    • Toulokhonov, I.1    Shulgina, I.2    Hernandez, V.J.3
  • 21
    • 0037123602 scopus 로고    scopus 로고
    • Structural basis of transcription initiation: an RNA polymerase holoenzyme–DNA complex
    • K.S. Murakami S. Masuda E.A. Campbell O. Muzzin S.A. Darst Structural basis of transcription initiation: an RNA polymerase holoenzyme–DNA complex Science 296 2002 1285 1290
    • (2002) Science , vol.296 , pp. 1285-1290
    • Murakami, K.S.1    Masuda, S.2    Campbell, E.A.3    Muzzin, O.4    Darst, S.A.5
  • 22
    • 0037123659 scopus 로고    scopus 로고
    • Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution
    • K.S. Murakami S. Masuda S.A. Darst Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution Science 296 2002 1280 1284
    • (2002) Science , vol.296 , pp. 1280-1284
    • Murakami, K.S.1    Masuda, S.2    Darst, S.A.3
  • 24
    • 0038823636 scopus 로고    scopus 로고
    • Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions
    • I. Artsimovitch V. Svetlov K.S. Murakami R. Landick Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions J. Biol. Chem. 278 2003 12344 12355
    • (2003) J. Biol. Chem. , vol.278 , pp. 12344-12355
    • Artsimovitch, I.1    Svetlov, V.2    Murakami, K.S.3    Landick, R.4
  • 25
    • 25844499174 scopus 로고    scopus 로고
    • Response of RNA polymerase to ppGpp: requirement for omega and relief of this requirement by DksA
    • C.E. Vrentas T. Gaal W.E. Ross R.E. Ebright R.L. Gourse Response of RNA polymerase to ppGpp: requirement for omega and relief of this requirement by DksA Genes Dev. 19 2005 2378 2387
    • (2005) Genes Dev. , vol.19 , pp. 2378-2387
    • Vrentas, C.E.1    Gaal, T.2    Ross, W.E.3    Ebright, R.E.4    Gourse, R.L.5
  • 27
    • 33751235874 scopus 로고    scopus 로고
    • Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
    • D. Wang D.A. Bushnell K.D. Westover C.D. Kaplan R.D. Kornberg Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis Cell 127 2006 941 954
    • (2006) Cell , vol.127 , pp. 941-954
    • Wang, D.1    Bushnell, D.A.2    Westover, K.D.3    Kaplan, C.D.4    Kornberg, R.D.5
  • 28
    • 8344234112 scopus 로고    scopus 로고
    • Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center
    • K.D. Westover D.A. Bushnell R.D. Kornberg Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center Cell 119 2004 481 489
    • (2004) Cell , vol.119 , pp. 481-489
    • Westover, K.D.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 30
    • 27944496101 scopus 로고    scopus 로고
    • NTP-entry routes in multi-subunit RNA polymerases
    • R.L. Landick NTP-entry routes in multi-subunit RNA polymerases Trends Biochem. Sci. 30 2005 651 654
    • (2005) Trends Biochem. Sci. , vol.30 , pp. 651-654
    • Landick, R.L.1
  • 31
    • 10044225617 scopus 로고    scopus 로고
    • An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation
    • L. Krasny R.L. Gourse An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation EMBO J. 23 2004 4473 4483
    • (2004) EMBO J. , vol.23 , pp. 4473-4483
    • Krasny, L.1    Gourse, R.L.2
  • 32
    • 33749646813 scopus 로고    scopus 로고
    • Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus
    • K. Kasai T. Nishizawa K. Takahashi T. Hosaka H. Aoki K. Ochi Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus J. Bacteriol. 188 2006 7111 7122
    • (2006) J. Bacteriol. , vol.188 , pp. 7111-7122
    • Kasai, K.1    Nishizawa, T.2    Takahashi, K.3    Hosaka, T.4    Aoki, H.5    Ochi, K.6
  • 33
    • 0031443321 scopus 로고    scopus 로고
    • Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria
    • T. Gaal M.S. Bartlett W. Ross C.L. Turnbough Jr R.L. Gourse Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria Science 278 1997 2092 2097
    • (1997) Science , vol.278 , pp. 2092-2097
    • Gaal, T.1    Bartlett, M.S.2    Ross, W.3    Turnbough, C.L.4    Gourse, R.L.5
  • 35
    • 0023749808 scopus 로고
    • Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance
    • D. Jin C.A. Gross Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance J. Mol. Biol. 202 1988 45 58
    • (1988) J. Mol. Biol. , vol.202 , pp. 45-58
    • Jin, D.1    Gross, C.A.2
  • 36
    • 2942696237 scopus 로고    scopus 로고
    • Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel
    • J. Mukhopadhyay E. Sineva J. Knight R.M. Levy R.H. Ebright Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel Mol. Cell 14 2004 739 751
    • (2004) Mol. Cell , vol.14 , pp. 739-751
    • Mukhopadhyay, J.1    Sineva, E.2    Knight, J.3    Levy, R.M.4    Ebright, R.H.5
  • 37
    • 0024403619 scopus 로고
    • High-resolution epitope mapping of hGH–receptor interactions by alanine-scanning mutagenesis
    • B.C. Cunningham J.A. Wells High-resolution epitope mapping of hGH–receptor interactions by alanine-scanning mutagenesis Science 244 1989 1081 1085
    • (1989) Science , vol.244 , pp. 1081-1085
    • Cunningham, B.C.1    Wells, J.A.2
  • 38
    • 1542320134 scopus 로고    scopus 로고
    • Inducible expression, enzymatic activity, and origin of higher plant homologues of bacterial RelA/SpoT stress proteins in Nicotiana tabacum
    • R.M. Givens M.H. Lin D.J. Taylor U. Mechold J.O. Berry V.J. Hernandez Inducible expression, enzymatic activity, and origin of higher plant homologues of bacterial RelA/SpoT stress proteins in Nicotiana tabacum J. Biol. Chem. 279 2004 7495 7504
    • (2004) J. Biol. Chem. , vol.279 , pp. 7495-7504
    • Givens, R.M.1    Lin, M.H.2    Taylor, D.J.3    Mechold, U.4    Berry, J.O.5    Hernandez, V.J.6
  • 39
    • 0037930838 scopus 로고    scopus 로고
    • Essential steps in the ppGpp-dependent regulation of bacterial ribosomal RNA promoters can be explained by substrate competition
    • L. Jores R. Wagner Essential steps in the ppGpp-dependent regulation of bacterial ribosomal RNA promoters can be explained by substrate competition J. Biol. Chem. 278 2003 16834 16843
    • (2003) J. Biol. Chem. , vol.278 , pp. 16834-16843
    • Jores, L.1    Wagner, R.2
  • 40
    • 0028220191 scopus 로고
    • High concentrations of ppGpp decrease the RNA chain growth rate. Implications for protein synthesis and translational fidelity during amino acid starvation in Escherichia coli
    • M.A. Sorensen K.F. Jensen S. Pedersen High concentrations of ppGpp decrease the RNA chain growth rate. Implications for protein synthesis and translational fidelity during amino acid starvation in Escherichia coli J. Mol. Biol. 236 1994 441 454
    • (1994) J. Mol. Biol. , vol.236 , pp. 441-454
    • Sorensen, M.A.1    Jensen, K.F.2    Pedersen, S.3
  • 41
    • 34547204502 scopus 로고    scopus 로고
    • A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing
    • I. Toulokhonov J. Zhang M. Palangat R. Landick A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing Mol. Cell 27 2007 406 419
    • (2007) Mol. Cell , vol.27 , pp. 406-419
    • Toulokhonov, I.1    Zhang, J.2    Palangat, M.3    Landick, R.4
  • 42
    • 4644265121 scopus 로고    scopus 로고
    • Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase
    • V. Svetlov D.G. Vassylyev I. Artsimovitch Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase J. Biol. Chem. 279 2004 38087 38090
    • (2004) J. Biol. Chem. , vol.279 , pp. 38087-38090
    • Svetlov, V.1    Vassylyev, D.G.2    Artsimovitch, I.3
  • 43
    • 0028840061 scopus 로고
    • Stringent control and growth-rate-dependent control have nonidentical promoter sequence requirements
    • C.A. Josaitis T. Gaal R.L. Gourse Stringent control and growth-rate-dependent control have nonidentical promoter sequence requirements Proc. Natl Acad. Sci. USA 92 1995 1117 1121
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 1117-1121
    • Josaitis, C.A.1    Gaal, T.2    Gourse, R.L.3
  • 45
    • 12244264445 scopus 로고    scopus 로고
    • Sequence-independent upstream DNA–alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase–lacUV5 promoter association
    • W. Ross R.L. Gourse Sequence-independent upstream DNA–alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase– lacUV5 promoter association Proc. Natl Acad. Sci. USA 102 2005 1 296
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 1-296
    • Ross, W.1    Gourse, R.L.2


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