메뉴 건너뛰기




Volumn 50, Issue 3, 2013, Pages 420-429

The magic spot: A ppGpp binding site on E. coli RNA polymerase responsible for regulation of transcription initiation

Author keywords

[No Author keywords available]

Indexed keywords

GUANOSINE 3' DIPHOSPHATE 5' DIPHOSPHATE; GUANOSINE 3' DIPHOSPHATE 5' TRIPHOSPHATE; HYDROXYLAMINE; RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN;

EID: 84887140246     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2013.03.021     Document Type: Article
Times cited : (218)

References (47)
  • 1
    • 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
    • Artsimovitch I., Svetlov V., Murakami K.S., Landick R. Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. J. Biol. Chem. 2003, 278:12344-12355.
    • (2003) J. Biol. Chem. , vol.278 , pp. 12344-12355
    • Artsimovitch, I.1    Svetlov, V.2    Murakami, K.S.3    Landick, R.4
  • 3
    • 79961217635 scopus 로고    scopus 로고
    • The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life
    • Atkinson G.C., Tenson T., Hauryliuk V. The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS ONE 2011, 6:e23479.
    • (2011) PLoS ONE , vol.6
    • Atkinson, G.C.1    Tenson, T.2    Hauryliuk, V.3
  • 4
    • 84866992765 scopus 로고    scopus 로고
    • Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification
    • Baker C.R., Booth L.N., Sorrells T.R., Johnson A.D. Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification. Cell 2012, 151:80-95.
    • (2012) Cell , vol.151 , pp. 80-95
    • Baker, C.R.1    Booth, L.N.2    Sorrells, T.R.3    Johnson, A.D.4
  • 5
    • 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
    • Barker M.M., Gaal T., Gourse R.L. 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. 2001, 305:689-702.
    • (2001) J. Mol. Biol. , vol.305 , pp. 689-702
    • Barker, M.M.1    Gaal, T.2    Gourse, R.L.3
  • 6
    • 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
    • Barker M.M., Gaal T., Josaitis C.A., Gourse R.L. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol. 2001, 305:673-688.
    • (2001) J. Mol. Biol. , vol.305 , pp. 673-688
    • Barker, M.M.1    Gaal, T.2    Josaitis, C.A.3    Gourse, R.L.4
  • 7
    • 0036849768 scopus 로고    scopus 로고
    • Structural and biochemical analysis of the Obg GTP binding protein
    • Buglino J., Shen V., Hakimian P., Lima C.D. Structural and biochemical analysis of the Obg GTP binding protein. Structure 2002, 10:1581-1592.
    • (2002) Structure , vol.10 , pp. 1581-1592
    • Buglino, J.1    Shen, V.2    Hakimian, P.3    Lima, C.D.4
  • 8
    • 0014690559 scopus 로고
    • The control of ribonucleic acid synthesis in Escherichia coli. IV. Relevance of unusual phosphorylated compounds from amino acid-starved stringent strains
    • Cashel M. The control of ribonucleic acid synthesis in Escherichia coli. IV. Relevance of unusual phosphorylated compounds from amino acid-starved stringent strains. J. Biol. Chem. 1969, 244:3133-3141.
    • (1969) J. Biol. Chem. , vol.244 , pp. 3133-3141
    • Cashel, M.1
  • 11
    • 0031949801 scopus 로고    scopus 로고
    • The mediator for stringent control, ppGpp, binds to the beta-subunit of Escherichia coli RNA polymerase
    • Chatterji D., Fujita N., Ishihama A. The mediator for stringent control, ppGpp, binds to the beta-subunit of Escherichia coli RNA polymerase. Genes Cells 1998, 3:279-287.
    • (1998) Genes Cells , vol.3 , pp. 279-287
    • Chatterji, D.1    Fujita, N.2    Ishihama, A.3
  • 12
    • 0035827346 scopus 로고    scopus 로고
    • Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
    • Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 2001, 292:1863-1876.
    • (2001) Science , vol.292 , pp. 1863-1876
    • Cramer, P.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 15
    • 84875623573 scopus 로고    scopus 로고
    • Dose-dependent reduction of replication elongation rate by (p)ppGpp in Escherichia coli and Bacillus subtilis
    • Denapoli J.M., Tehranchi A.K., Wang J.D. Dose-dependent reduction of replication elongation rate by (p)ppGpp in Escherichia coli and Bacillus subtilis. Mol. Microbiol. 2013, 88:93-104.
    • (2013) Mol. Microbiol. , vol.88 , pp. 93-104
    • Denapoli, J.M.1    Tehranchi, A.K.2    Wang, J.D.3
  • 16
    • 38649092391 scopus 로고    scopus 로고
    • Transcription profiling of the stringent response in Escherichia coli
    • Durfee T., Hansen A.-M., Zhi H., Blattner F.R., Jin D.J. Transcription profiling of the stringent response in Escherichia coli. J. Bacteriol. 2008, 190:1084-1096.
    • (2008) J. Bacteriol. , vol.190 , pp. 1084-1096
    • Durfee, T.1    Hansen, A.-M.2    Zhi, H.3    Blattner, F.R.4    Jin, D.J.5
  • 17
    • 33744981130 scopus 로고    scopus 로고
    • RRNA promoter regulation by nonoptimal binding of σ region 1.2: an additional recognition element for RNA polymerase
    • Haugen S.P., Berkmen M.B., Ross W., Gaal T., Ward C., Gourse R.L. rRNA promoter regulation by nonoptimal binding of σ region 1.2: an additional recognition element for RNA polymerase. Cell 2006, 125:1069-1082.
    • (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
  • 18
    • 45449099933 scopus 로고    scopus 로고
    • Advances in bacterial promoter recognition and its control by factors that do not bind DNA
    • Haugen S.P., Ross W., Gourse R.L. Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Nat. Rev. Microbiol. 2008, 6:507-519.
    • (2008) Nat. Rev. Microbiol. , vol.6 , pp. 507-519
    • Haugen, S.P.1    Ross, W.2    Gourse, R.L.3
  • 19
    • 0025103859 scopus 로고
    • Sequence analysis of two temperature-sensitive mutations in the alpha subunit gene (rpoA) of Escherichia coli RNA polymerase
    • Igarashi K., Fujita N., Ishihama A. Sequence analysis of two temperature-sensitive mutations in the alpha subunit gene (rpoA) of Escherichia coli RNA polymerase. Nucleic Acids Res. 1990, 18:5945-5948.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 5945-5948
    • Igarashi, K.1    Fujita, N.2    Ishihama, A.3
  • 20
    • 84866038398 scopus 로고    scopus 로고
    • Direct binding targets of the stringent response alarmone (p)ppGpp
    • Kanjee U., Ogata K., Houry W.A. Direct binding targets of the stringent response alarmone (p)ppGpp. Mol. Microbiol. 2012, 85:1029-1043.
    • (2012) Mol. Microbiol. , vol.85 , pp. 1029-1043
    • Kanjee, U.1    Ogata, K.2    Houry, W.A.3
  • 21
    • 33749646813 scopus 로고    scopus 로고
    • Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus
    • Kasai K., Nishizawa T., Takahashi K., Hosaka T., Aoki H., Ochi K. Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus. J. Bacteriol. 2006, 188:7111-7122.
    • (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
  • 22
    • 10044225617 scopus 로고    scopus 로고
    • An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation
    • Krásný L., Gourse R.L. An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation. EMBO J. 2004, 23:4473-4483.
    • (2004) EMBO J. , vol.23 , pp. 4473-4483
    • Krásný, L.1    Gourse, R.L.2
  • 24
    • 0028860275 scopus 로고
    • A procedure for the rapid preparation of guanosine tetraphosphate (ppGpp) from Escherichia coli ribosomes
    • Krohn M., Wagner R. A procedure for the rapid preparation of guanosine tetraphosphate (ppGpp) from Escherichia coli ribosomes. Anal. Biochem. 1995, 225:188-190.
    • (1995) Anal. Biochem. , vol.225 , pp. 188-190
    • Krohn, M.1    Wagner, R.2
  • 27
    • 0035970037 scopus 로고    scopus 로고
    • Bacterial RNA polymerase subunit ω and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly
    • Minakhin L., Bhagat S., Brunning A., Campbell E.A., Darst S.A., Ebright R.H., Severinov K. Bacterial RNA polymerase subunit ω and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proc. Natl. Acad. Sci. USA 2001, 98:892-897.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 892-897
    • Minakhin, L.1    Bhagat, S.2    Brunning, A.3    Campbell, E.A.4    Darst, S.A.5    Ebright, R.H.6    Severinov, K.7
  • 29
    • 0041669435 scopus 로고    scopus 로고
    • Control of rRNA expression by small molecules is dynamic and nonredundant
    • Murray H.D., Schneider D.A., Gourse R.L. Control of rRNA expression by small molecules is dynamic and nonredundant. Mol. Cell 2003, 12:125-134.
    • (2003) Mol. Cell , vol.12 , pp. 125-134
    • Murray, H.D.1    Schneider, D.A.2    Gourse, R.L.3
  • 31
    • 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
    • Paul B.J., Barker M.M., Ross W., Schneider D.A., Webb C., Foster J.W., Gourse R.L. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 2004, 118:311-322.
    • (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
  • 34
    • 58849139777 scopus 로고    scopus 로고
    • Allosteric control of Escherichia coli rRNA promoter complexes by DksA
    • Rutherford S.T., Villers C.L., Lee J.-H., Ross W., Gourse R.L. Allosteric control of Escherichia coli rRNA promoter complexes by DksA. Genes Dev. 2009, 23:236-248.
    • (2009) Genes Dev. , vol.23 , pp. 236-248
    • Rutherford, S.T.1    Villers, C.L.2    Lee, J.-H.3    Ross, W.4    Gourse, R.L.5
  • 35
    • 84865723619 scopus 로고    scopus 로고
    • Binding mechanism of metal·NTP substrates and stringent-response alarmones to bacterial DnaG-type primases
    • Rymer R.U., Solorio F.A., Tehranchi A.K., Chu C., Corn J.E., Keck J.L., Wang J.D., Berger J.M. Binding mechanism of metal·NTP substrates and stringent-response alarmones to bacterial DnaG-type primases. Structure 2012, 20:1478-1489.
    • (2012) Structure , vol.20 , pp. 1478-1489
    • Rymer, R.U.1    Solorio, F.A.2    Tehranchi, A.K.3    Chu, C.4    Corn, J.E.5    Keck, J.L.6    Wang, J.D.7    Berger, J.M.8
  • 36
    • 79952002951 scopus 로고    scopus 로고
    • Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering
    • Sawitzke J.A., Costantino N., Li X.T., Thomason L.C., Bubunenko M., Court C., Court D.L. Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering. J. Mol. Biol. 2011, 407:45-59.
    • (2011) J. Mol. Biol. , vol.407 , pp. 45-59
    • Sawitzke, J.A.1    Costantino, N.2    Li, X.T.3    Thomason, L.C.4    Bubunenko, M.5    Court, C.6    Court, D.L.7
  • 37
    • 42149158392 scopus 로고    scopus 로고
    • Control of bacterial transcription, translation and replication by (p)ppGpp
    • Srivatsan A., Wang J.D. Control of bacterial transcription, translation and replication by (p)ppGpp. Curr. Opin. Microbiol. 2008, 11:100-105.
    • (2008) Curr. Opin. Microbiol. , vol.11 , pp. 100-105
    • Srivatsan, A.1    Wang, J.D.2
  • 39
    • 79960324770 scopus 로고    scopus 로고
    • A novel conformation of RNA polymerase sheds light on the mechanism of transcription
    • Tagami S., Sekine S.-I., Yokoyama S. A novel conformation of RNA polymerase sheds light on the mechanism of transcription. Transcription 2011, 2:162-167.
    • (2011) Transcription , vol.2 , pp. 162-167
    • Tagami, S.1    Sekine, S.-I.2    Yokoyama, S.3
  • 40
    • 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 beta'-subunit
    • Toulokhonov I.I., Shulgina I., Hernandez V.J. Binding of the transcription effector ppGpp to Escherichia coli RNA polymerase is allosteric, modular, and occurs near the N terminus of the beta'-subunit. J. Biol. Chem. 2001, 276:1220-1225.
    • (2001) J. Biol. Chem. , vol.276 , pp. 1220-1225
    • Toulokhonov, I.I.1    Shulgina, I.2    Hernandez, V.J.3
  • 43
    • 25844499174 scopus 로고    scopus 로고
    • Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA
    • Vrentas C.E., Gaal T., Ross W., Ebright R.H., Gourse R.L. Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA. Genes Dev. 2005, 19:2378-2387.
    • (2005) Genes Dev. , vol.19 , pp. 2378-2387
    • Vrentas, C.E.1    Gaal, T.2    Ross, W.3    Ebright, R.H.4    Gourse, R.L.5
  • 44
    • 40049090539 scopus 로고    scopus 로고
    • 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
    • Vrentas C.E., Gaal T., Berkmen M.B., Rutherford S.T., Haugen S.P., Vassylyev D.G., Ross W., Gourse R.L. 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. J. Mol. Biol. 2008, 377:551-564.
    • (2008) J. Mol. Biol. , vol.377 , pp. 551-564
    • Vrentas, C.E.1    Gaal, T.2    Berkmen, M.B.3    Rutherford, S.T.4    Haugen, S.P.5    Vassylyev, D.G.6    Ross, W.7    Gourse, R.L.8
  • 45
    • 8344234112 scopus 로고    scopus 로고
    • Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center
    • Westover K.D., Bushnell D.A., Kornberg R.D. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 2004, 119:481-489.
    • (2004) Cell , vol.119 , pp. 481-489
    • Westover, K.D.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 47
    • 84887143299 scopus 로고    scopus 로고
    • The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex
    • this issue
    • Zuo Y., Wang Y., Steitz T.A. The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex. Mol Cell 2013, 50:430-436. this issue.
    • (2013) Mol Cell , vol.50 , pp. 430-436
    • Zuo, Y.1    Wang, Y.2    Steitz, T.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.