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Volumn 38, Issue 5, 2009, Pages 1636-1651

Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; MESSENGER RNA; OLIGONUCLEOTIDE; PROTEIN GRAL; PROTEIN GREA; RNA POLYMERASE; UNCLASSIFIED DRUG; BACTERIAL RNA; ESCHERICHIA COLI PROTEIN; GREA PROTEIN, E COLI; TRANSCRIPTION FACTOR;

EID: 77950489765     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1150     Document Type: Article
Times cited : (16)

References (48)
  • 1
    • 0036668461 scopus 로고    scopus 로고
    • Transcription termination and anti-termination in E. coli
    • Nudler, E. and Gottesman, M. (2002) Transcription termination and anti-termination in E. coli. Genes Cells, 7, 755-768.
    • (2002) Genes Cells , vol.7 , pp. 755-768
    • Nudler, E.1    Gottesman, M.2
  • 2
    • 40749126459 scopus 로고    scopus 로고
    • Transcription termination: pulling out all the stops
    • Greenblatt, J.F. (2008) Transcription termination: pulling out all the stops. Cell, 132, 917-918.
    • (2008) Cell , vol.132 , pp. 917-918
    • Greenblatt, J.F.1
  • 3
    • 0033597435 scopus 로고    scopus 로고
    • Mechanism of intrinsic transcription termination and antitermination
    • Yarnell, W.S. and Roberts, J.W. (1999) Mechanism of intrinsic transcription termination and antitermination. Science, 284, 611-615.
    • (1999) Science , vol.284 , pp. 611-615
    • Yarnell, W.S.1    Roberts, J.W.2
  • 4
    • 0036863659 scopus 로고    scopus 로고
    • Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination
    • Komissarova, N., Becker, J., Solter, S., Kireeva, M. and Kashlev, M. (2002) Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol. Cell, 10, 1151-1162.
    • (2002) Mol. Cell , vol.10 , pp. 1151-1162
    • Komissarova, N.1    Becker, J.2    Solter, S.3    Kireeva, M.4    Kashlev, M.5
  • 5
    • 0344413496 scopus 로고    scopus 로고
    • The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination
    • Toulokhonov, I. and Landick, R. (2003) The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. Mol. Cell, 12, 1125-1136.
    • (2003) Mol. Cell , vol.12 , pp. 1125-1136
    • Toulokhonov, I.1    Landick, R.2
  • 6
    • 1842715585 scopus 로고    scopus 로고
    • Forward translocation is the natural pathway of RNA release at an intrinsic terminator
    • Santangelo, T.J. and Roberts, J.W. (2004) Forward translocation is the natural pathway of RNA release at an intrinsic terminator. Mol. Cell, 14, 117-126.
    • (2004) Mol. Cell , vol.14 , pp. 117-126
    • Santangelo, T.J.1    Roberts, J.W.2
  • 8
    • 41249091442 scopus 로고    scopus 로고
    • Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework
    • Datta, K. and von Hippel, P.H. (2008) Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. J. Biol. Chem., 283, 3537-3549.
    • (2008) J. Biol. Chem. , vol.283 , pp. 3537-3549
    • Datta, K.1    von Hippel, P.H.2
  • 9
    • 40749096382 scopus 로고    scopus 로고
    • Applied force reveals mechanistic and energetic details of transcription termination
    • Larson, M.H., Greenleaf, W.J., Landick, R. and Block, S.M. (2008) Applied force reveals mechanistic and energetic details of transcription termination. Cell, 132, 971-982.
    • (2008) Cell , vol.132 , pp. 971-982
    • Larson, M.H.1    Greenleaf, W.J.2    Landick, R.3    Block, S.M.4
  • 10
    • 0033120034 scopus 로고    scopus 로고
    • The mechanism of intrinsic transcription termination
    • Gusarov, I. and Nudler, E. (1999) The mechanism of intrinsic transcription termination. Mol. Cell, 3, 495-504.
    • (1999) Mol. Cell , vol.3 , pp. 495-504
    • Gusarov, I.1    Nudler, E.2
  • 11
    • 0031059249 scopus 로고    scopus 로고
    • Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded
    • Komissarova, N. and Kashlev, M. (1997) Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl Acad. Sci. USA, 94, 1755-1780.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 1755-1780
    • Komissarova, N.1    Kashlev, M.2
  • 12
    • 4043135220 scopus 로고    scopus 로고
    • Regulation of RNA polymerase through the secondary channel
    • Nickels, B.E. and Hochschild, A. (2004) Regulation of RNA polymerase through the secondary channel. Cell, 118, 281-284.
    • (2004) Cell , vol.118 , pp. 281-284
    • Nickels, B.E.1    Hochschild, A.2
  • 13
    • 0027536870 scopus 로고
    • Transcript cleavage factors from E. coli
    • Borukhov, S., Sagitov, V. and Goldfarb, A. (1993) Transcript cleavage factors from E. coli. Cell, 72, 459-466.
    • (1993) Cell , vol.72 , pp. 459-466
    • Borukhov, S.1    Sagitov, V.2    Goldfarb, A.3
  • 14
    • 0029614716 scopus 로고
    • Escherichia coli transcript cleavage factors GreA and GreB stimulate promoter escape and gene expression in vivo and in vitro
    • Hsu, L.M., Vo, N.V. and Chamberlin, M.J. (1995) Escherichia coli transcript cleavage factors GreA and GreB stimulate promoter escape and gene expression in vivo and in vitro. Proc. Natl Acad. Sci. USA, 92, 11588-11592.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 11588-11592
    • Hsu, L.M.1    Vo, N.V.2    Chamberlin, M.J.3
  • 15
    • 0346243938 scopus 로고    scopus 로고
    • Transcript cleavage factors GreA and GreB act as a transient catalytic components of RNA polymerase
    • Laptenko, O., Lee, J., Lomakin, I. and Borukhov, S. (2003) Transcript cleavage factors GreA and GreB act as a transient catalytic components of RNA polymerase. EMBO J., 22, 6322-6334.
    • (2003) EMBO J , vol.22 , pp. 6322-6334
    • Laptenko, O.1    Lee, J.2    Lomakin, I.3    Borukhov, S.4
  • 16
    • 14844329013 scopus 로고    scopus 로고
    • Bacterial transcription elongation factors: new insights into molecular mechanism of action
    • Borukhov, S., Lee, J. and Laptenko, O. (2005) Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol. Microbiol., 55, 1315-1324.
    • (2005) Mol. Microbiol. , vol.55 , pp. 1315-1324
    • Borukhov, S.1    Lee, J.2    Laptenko, O.3
  • 19
    • 30344459408 scopus 로고    scopus 로고
    • Crystal structure of Thermus aquaticus Gfh1, a Gre-factor paralog that inhibits rather than stimulates transcript cleavage
    • Lamour, V., Hogan, B.P., Erie, D.A. and Darst, S.A. (2006) Crystal structure of Thermus aquaticus Gfh1, a Gre-factor paralog that inhibits rather than stimulates transcript cleavage. J. Mol. Biol., 356, 179-188.
    • (2006) J. Mol. Biol. , vol.356 , pp. 179-188
    • Lamour, V.1    Hogan, B.P.2    Erie, D.A.3    Darst, S.A.4
  • 22
    • 4043108470 scopus 로고    scopus 로고
    • Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription
    • Perederina, A., Svetlov, V., Vassylyeva, M.N., Tahirov, T.H., Yokoyama, S., Artsimovitch, I. and Vassylyev, D.G. (2004) Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription. Cell, 118, 297-309.
    • (2004) Cell , vol.118 , pp. 297-309
    • Perederina, A.1    Svetlov, V.2    Vassylyeva, M.N.3    Tahirov, T.H.4    Yokoyama, S.5    Artsimovitch, I.6    Vassylyev, D.G.7
  • 23
    • 20344363655 scopus 로고    scopus 로고
    • DksA potentiates direct activation of amino acid promoters by ppGpp
    • Paul, B.J., Berkmen, M.B. and Gourse, R.L. (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. Proc. Natl Acad. Sci. USA, 102, 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
  • 25
    • 34447540221 scopus 로고    scopus 로고
    • Identical, Independent, and Opposing roles of ppGpp and DksA in Escherichia coli
    • Magnusson, L.U., Gummesson, B., Joksimovic, P., Farewell, A. and Nystrom, T. (2007) Identical, Independent, and Opposing roles of ppGpp and DksA in Escherichia coli. J. Bacteriol., 189, 5193-5202.
    • (2007) J. Bacteriol. , vol.189 , pp. 5193-5202
    • Magnusson, L.U.1    Gummesson, B.2    Joksimovic, P.3    Farewell, A.4    Nystrom, T.5
  • 26
    • 39849100395 scopus 로고    scopus 로고
    • Regulation of the fimB promoter: a case of differential regulation by ppGpp and DksA in vivo
    • Aberg, A., Shingler, V. and Balsalobre, C. (2008) Regulation of the fimB promoter: a case of differential regulation by ppGpp and DksA in vivo. Mol. Microbiol., 67, 1223-1241.
    • (2008) Mol. Microbiol. , vol.67 , pp. 1223-1241
    • Aberg, A.1    Shingler, V.2    Balsalobre, C.3
  • 27
    • 33744962968 scopus 로고    scopus 로고
    • Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA
    • Potrykus, K., Vinella, D., Murphy, H., Szalewska-Palasz, A., D'Ari, R. and Cashel, M. (2006) Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA. J. Biol. Chem., 281, 15238-15248.
    • (2006) J. Biol. Chem. , vol.281 , pp. 15238-15248
    • Potrykus, K.1    Vinella, D.2    Murphy, H.3    Szalewska-Palasz, A.4    D'Ari, R.5    Cashel, M.6
  • 28
    • 33846604629 scopus 로고    scopus 로고
    • Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase
    • Rutherford, S.T., Lemke, J.J., Vrentas, C.E., Gaal, T., Ross, W. and Gourse, R.L. (2007) Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase. J. Mol. Biol., 366, 1243-1257.
    • (2007) J. Mol. Biol. , vol.366 , pp. 1243-1257
    • Rutherford, S.T.1    Lemke, J.J.2    Vrentas, C.E.3    Gaal, T.4    Ross, W.5    Gourse, R.L.6
  • 29
  • 30
    • 0023255472 scopus 로고
    • Improved single and multicopy lac-based cloning vectors for protein and operon fusions
    • Simons, R.W., Houman, F. and Kleckner, N. (1987) Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene, 53, 85-96.
    • (1987) Gene , vol.53 , pp. 85-96
    • Simons, R.W.1    Houman, F.2    Kleckner, N.3
  • 32
    • 18444368425 scopus 로고    scopus 로고
    • Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli
    • Vinella, D., Albrecht, C., Cashel, M. and D'Ari, R. (2005) Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli. Mol. Microbiol., 56, 958-970.
    • (2005) Mol. Microbiol. , vol.56 , pp. 958-970
    • Vinella, D.1    Albrecht, C.2    Cashel, M.3    D'Ari, R.4
  • 33
    • 0015947670 scopus 로고
    • Preparation of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) from Escherichia coli ribosomes
    • Cashel, M. (1974) Preparation of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) from Escherichia coli ribosomes. Anal. Biochem., 57, 100-107.
    • (1974) Anal. Biochem. , vol.57 , pp. 100-107
    • Cashel, M.1
  • 34
    • 33748625150 scopus 로고    scopus 로고
    • The structural basis for promoter -35 element recognition by the group IV σ factors
    • Lane, W.J. and Darst, S.A. (2006) The structural basis for promoter -35 element recognition by the group IV σ factors. PLoS Biol., 4, e269.
    • (2006) PLoS Biol. , vol.4
    • Lane, W.J.1    Darst, S.A.2
  • 35
    • 0037177866 scopus 로고    scopus 로고
    • Transcription termination: primary intermediates and secondary adducts
    • Kashlev, M. and Komissarova, N. (2002) Transcription termination: primary intermediates and secondary adducts. J. Biol. Chem., 277, 14501-14508.
    • (2002) J. Biol. Chem. , vol.277 , pp. 14501-14508
    • Kashlev, M.1    Komissarova, N.2
  • 36
    • 51249094291 scopus 로고    scopus 로고
    • DNA sequences in gal operon override transcription elongation blocks
    • Lewis, D.E.A., Komissarova, N., Le, P., Kashlev, M. and Adhya, S. (2008) DNA sequences in gal operon override transcription elongation blocks. J. Mol. Biol., 382, 843-858.
    • (2008) J. Mol. Biol. , vol.382 , pp. 843-858
    • Lewis, D.E.A.1    Komissarova, N.2    Le, P.3    Kashlev, M.4    Adhya, S.5
  • 37
    • 31144454629 scopus 로고    scopus 로고
    • Conserved and variable functions of the sigmaE stress response in related genomes
    • Rhodius, V.A., Suh, W.C., Nonaka, G., West, J. and Gross, C.A. (2006) Conserved and variable functions of the sigmaE stress response in related genomes. PLoS Biol., 4, e2.
    • (2006) PLoS Biol. , vol.4
    • Rhodius, V.A.1    Suh, W.C.2    Nonaka, G.3    West, J.4    Gross, C.A.5
  • 38
    • 0011170748 scopus 로고
    • Posttranscriptional control of bacteriophage lambda gene expression from a site distal to the gene
    • Guarneros, G., Montañez, C., Hernandez, T. and Court, D. (1982) Posttranscriptional control of bacteriophage lambda gene expression from a site distal to the gene. Proc. Natl Acad. Sci. USA, 79, 238-242.
    • (1982) Proc. Natl Acad. Sci. USA , vol.79 , pp. 238-242
    • Guarneros, G.1    Montañez, C.2    Hernandez, T.3    Court, D.4
  • 39
    • 4344682527 scopus 로고    scopus 로고
    • The small RNA regulators of Escherichia coli, roles and mechanisms
    • Gottesman, S. (2004) The small RNA regulators of Escherichia coli, roles and mechanisms. Annu. Rev. Microbiol., 58, 303-328.
    • (2004) Annu. Rev. Microbiol. , vol.58 , pp. 303-328
    • Gottesman, S.1
  • 40
    • 0037417962 scopus 로고    scopus 로고
    • Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli
    • Cooper, T.F., Rozen, D.E. and Lenski, R.E. (2003) Parallel changes in gene expression after 20, 000 generations of evolution in Escherichia coli. Proc. Natl Acad. Sci. USA, 100, 1072-1077.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 1072-1077
    • Cooper, T.F.1    Rozen, D.E.2    Lenski, R.E.3
  • 41
  • 42
    • 0025663103 scopus 로고
    • Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures
    • d'Aubenton Carafa, Y., Brody, E. and Thermes, C. (1990) Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol., 216, 835-858.
    • (1990) J. Mol. Biol. , vol.216 , pp. 835-858
    • d'Aubenton Carafa, Y.1    Brody, E.2    Thermes, C.3
  • 44
    • 0026544876 scopus 로고
    • Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators
    • Reynolds, R. and Chamberlin, M.J. (1992) Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators. J. Mol. Biol., 224, 53-63.
    • (1992) J. Mol. Biol. , vol.224 , pp. 53-63
    • Reynolds, R.1    Chamberlin, M.J.2
  • 46
    • 36749071435 scopus 로고    scopus 로고
    • Escherichia coli physiology in Luria-Bertani broth
    • Sezonov, G., Joseleau-Petit, D. and D'Ari, R. (2007) Escherichia coli physiology in Luria-Bertani broth. J. Bacteriol., 189, 8746-8749.
    • (2007) J. Bacteriol. , vol.189 , pp. 8746-8749
    • Sezonov, G.1    Joseleau-Petit, D.2    D'Ari, R.3
  • 47
    • 18144396807 scopus 로고    scopus 로고
    • Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli
    • Liu, M., Durfee, T., Cabrera, J.E., Zhao, K., Jin, D.J. and Blattner, F.R. (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J. Biol. Chem., 280, 15921-15927.
    • (2005) J. Biol. Chem. , vol.280 , pp. 15921-15927
    • Liu, M.1    Durfee, T.2    Cabrera, J.E.3    Zhao, K.4    Jin, D.J.5    Blattner, F.R.6
  • 48
    • 11844249959 scopus 로고    scopus 로고
    • Mutations in the RNA polymerase III subunit Rpc11p that decrease RNA 3′ cleavage activity increase 3′-terminal oligo(U) length and La-dependent tRNA processing
    • Huang, Y., Intine, R.V., Mozlin, A., Hasson, S. and Maraia, R.J. (2005) Mutations in the RNA polymerase III subunit Rpc11p that decrease RNA 3′ cleavage activity increase 3′-terminal oligo(U) length and La-dependent tRNA processing. Mol. Cell Biol., 25, 621-636.
    • (2005) Mol. Cell Biol. , vol.25 , pp. 621-636
    • Huang, Y.1    Intine, R.V.2    Mozlin, A.3    Hasson, S.4    Maraia, R.J.5


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