메뉴 건너뛰기




Volumn 53, Issue 2, 2014, Pages 282-292

Next generation sequencing-based parallel analysis of melting kinetics of 4096 variants of a bacterial promoter

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROMOTERS; MELTING KINETICS; NEXT-GENERATION SEQUENCING; PARALLEL ANALYSIS; PROMOTER ELEMENTS; SEQUENCE VARIANTS; SEQUENCE-DEPENDENT; TRANSCRIPTION INITIATION;

EID: 84892687466     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi401277w     Document Type: Article
Times cited : (17)

References (35)
  • 1
    • 0035075383 scopus 로고    scopus 로고
    • How sigma docks to RNA polymerase and what sigma does
    • Burgess, R. R. and Anthony, L. (2001) How sigma docks to RNA polymerase and what sigma does Curr. Opin. Microbiol. 4, 126-131
    • (2001) Curr. Opin. Microbiol. , vol.4 , pp. 126-131
    • Burgess, R.R.1    Anthony, L.2
  • 2
  • 3
    • 0038013991 scopus 로고    scopus 로고
    • RNA polymerase holoenzyme: Structure, function and biological implications
    • Borukhov, S. and Nudler, E. (2003) RNA polymerase holoenzyme: structure, function and biological implications Curr. Opin. Microbiol. 6, 93-100
    • (2003) Curr. Opin. Microbiol. , vol.6 , pp. 93-100
    • Borukhov, S.1    Nudler, E.2
  • 4
    • 0001416657 scopus 로고    scopus 로고
    • (Neidhardt, F. C. Curtis, R. III, Ingraham, J. L. Lin, E. C. C. Low, K. R. Magasanik, B. Reznikoff, W. S. Riley, M. Schaechter, M. and Umbarger, H. E. Eds.) 2 nd ed. ASM Press, Washington, DC
    • Record, M. T., Jr., Reznikoff, W. S., Craig, M. L., McQuade, K. L., and Schlax, P. J. (1996) In Escherichia coli and Salmonella: Cellular and Molecular Biology (Neidhardt, F. C., Curtis, R., III, Ingraham, J. L., Lin, E. C. C., Low, K. R., Magasanik, B., Reznikoff, W. S., Riley, M., Schaechter, M., and Umbarger, H. E., Eds.) 2 nd ed., pp 792-820, ASM Press, Washington, DC.
    • (1996) Escherichia Coli and Salmonella: Cellular and Molecular Biology , pp. 792-820
    • Record Jr., M.T.1    Reznikoff, W.S.2    Craig, M.L.3    McQuade, K.L.4    Schlax, P.J.5
  • 6
    • 79959368804 scopus 로고    scopus 로고
    • Mechanism of bacterial transcription initiation: RNA polymerase - Promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis
    • Saecker, R. M., Record, M. T., Jr., and Dehaseth, P. L. (2011) Mechanism of bacterial transcription initiation: RNA polymerase-promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis J. Mol. Biol. 412, 754-771
    • (2011) J. Mol. Biol. , vol.412 , pp. 754-771
    • Saecker, R.M.1    Record Jr., M.T.2    Dehaseth, P.L.3
  • 7
    • 0029094575 scopus 로고
    • Open complex formation by Escherichia coli RNA polymerase: The mechanism of polymerase-induced strand separation of double helical DNA
    • deHaseth, P. L. and Helmann, J. D. (1995) Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA Mol. Microbiol. 16, 817-824
    • (1995) Mol. Microbiol. , vol.16 , pp. 817-824
    • Dehaseth, P.L.1    Helmann, J.D.2
  • 8
    • 18344418394 scopus 로고    scopus 로고
    • Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners
    • Helmann, J. D. and deHaseth, P. L. (1999) Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners Biochemistry 38, 5959-5967
    • (1999) Biochemistry , vol.38 , pp. 5959-5967
    • Helmann, J.D.1    Dehaseth, P.L.2
  • 9
    • 0023918675 scopus 로고
    • Structure and function of bacterial sigma factors
    • Helmann, J. D. and Chamberlin, M. J. (1988) Structure and function of bacterial sigma factors Annu. Rev. Biochem. 57, 839-872
    • (1988) Annu. Rev. Biochem. , vol.57 , pp. 839-872
    • Helmann, J.D.1    Chamberlin, M.J.2
  • 10
    • 0343597687 scopus 로고
    • Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter
    • Pribnow, D. (1975) Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter Proc. Natl. Acad. Sci. U. S. A. 72, 784-788
    • (1975) Proc. Natl. Acad. Sci. U. S. A. , vol.72 , pp. 784-788
    • Pribnow, D.1
  • 12
    • 0039967392 scopus 로고
    • Binding of RNA-polymerase from Escherichia coli with oligodeoxyribonucleotides homologous to transcribed and non-transcribed DNA stands in the "-10"-promoter region of bacterial genes
    • Savinkova, L. K., Baranova, L. V., Knorre, V. L., and Salganik, R. I. (1988) [Binding of RNA-polymerase from Escherichia coli with oligodeoxyribonucleotides homologous to transcribed and non-transcribed DNA stands in the "-10"-promoter region of bacterial genes] Mol. Biol. (Mosk) 22, 807-812
    • (1988) Mol. Biol. (Mosk) , vol.22 , pp. 807-812
    • Savinkova, L.K.1    Baranova, L.V.2    Knorre, V.L.3    Salganik, R.I.4
  • 13
    • 0030915128 scopus 로고    scopus 로고
    • Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide
    • Marr, M. T. and Roberts, J. W. (1997) Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide Science 276, 1258-1260
    • (1997) Science , vol.276 , pp. 1258-1260
    • Marr, M.T.1    Roberts, J.W.2
  • 14
    • 0030576519 scopus 로고    scopus 로고
    • Base-specific recognition of the nontemplate strand of promoter DNA by E. Coli RNA polymerase
    • Roberts, C. W. and Roberts, J. W. (1996) Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase Cell 86, 495-501
    • (1996) Cell , vol.86 , pp. 495-501
    • Roberts, C.W.1    Roberts, J.W.2
  • 15
    • 0032502311 scopus 로고    scopus 로고
    • Conformation and DNA binding properties of a single-stranded DNA binding region of sigma 70 subunit from Escherichia coli RNA polymerase are modulated by an interaction with the core enzyme
    • Callaci, S. and Heyduk, T. (1998) Conformation and DNA binding properties of a single-stranded DNA binding region of sigma 70 subunit from Escherichia coli RNA polymerase are modulated by an interaction with the core enzyme Biochemistry 37, 3312-3320
    • (1998) Biochemistry , vol.37 , pp. 3312-3320
    • Callaci, S.1    Heyduk, T.2
  • 16
    • 0030576532 scopus 로고    scopus 로고
    • Function of E. Coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing
    • Ring, B. Z., Yarnell, W. S., and Roberts, J. W. (1996) Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing Cell 86, 485-493
    • (1996) Cell , vol.86 , pp. 485-493
    • Ring, B.Z.1    Yarnell, W.S.2    Roberts, J.W.3
  • 17
    • 0034633951 scopus 로고    scopus 로고
    • Sequence determinants for the recognition of the fork junction DNA containing the -10 region of promoter DNA by E. Coli RNA polymerase
    • Matlock, D. L. and Heyduk, T. (2000) Sequence determinants for the recognition of the fork junction DNA containing the -10 region of promoter DNA by E. coli RNA polymerase Biochemistry 39, 12274-12283
    • (2000) Biochemistry , vol.39 , pp. 12274-12283
    • Matlock, D.L.1    Heyduk, T.2
  • 18
    • 84883473606 scopus 로고    scopus 로고
    • Cooperativity and interaction energy threshold effects in recognition of the -10 promoter element by bacterial RNA polymerase
    • Mekler, V. and Severinov, K. (2013) Cooperativity and interaction energy threshold effects in recognition of the -10 promoter element by bacterial RNA polymerase Nucleic Acids Res. 41, 7276-7285
    • (2013) Nucleic Acids Res. , vol.41 , pp. 7276-7285
    • Mekler, V.1    Severinov, K.2
  • 19
    • 0037168467 scopus 로고    scopus 로고
    • RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNA
    • Tsujikawa, L., Strainic, M. G., Watrob, H., Barkley, M. D., and DeHaseth, P. L. (2002) RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNA Biochemistry 41, 15334-15341
    • (2002) Biochemistry , vol.41 , pp. 15334-15341
    • Tsujikawa, L.1    Strainic, M.G.2    Watrob, H.3    Barkley, M.D.4    Dehaseth, P.L.5
  • 20
    • 33744958373 scopus 로고    scopus 로고
    • A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting
    • Heyduk, E., Kuznedelov, K., Severinov, K., and Heyduk, T. (2006) A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting J. Biol. Chem. 281, 12362-12369
    • (2006) J. Biol. Chem. , vol.281 , pp. 12362-12369
    • Heyduk, E.1    Kuznedelov, K.2    Severinov, K.3    Heyduk, T.4
  • 21
    • 58149096676 scopus 로고    scopus 로고
    • Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA
    • Schroeder, L. A., Gries, T. J., Saecker, R. M., Record, M. T., Jr., Harris, M. E., and DeHaseth, P. L. (2009) Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA J. Mol. Biol. 385, 339-349
    • (2009) J. Mol. Biol. , vol.385 , pp. 339-349
    • Schroeder, L.A.1    Gries, T.J.2    Saecker, R.M.3    Record Jr., M.T.4    Harris, M.E.5    Dehaseth, P.L.6
  • 22
    • 38049042264 scopus 로고    scopus 로고
    • Threonine 429 of Escherichia coli sigma 70 is a key participant in promoter DNA melting by RNA polymerase
    • Schroeder, L. A., Karpen, M. E., and deHaseth, P. L. (2008) Threonine 429 of Escherichia coli sigma 70 is a key participant in promoter DNA melting by RNA polymerase J. Mol. Biol. 376, 153-165
    • (2008) J. Mol. Biol. , vol.376 , pp. 153-165
    • Schroeder, L.A.1    Karpen, M.E.2    Dehaseth, P.L.3
  • 23
    • 83255167029 scopus 로고    scopus 로고
    • Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit
    • Feklistov, A. and Darst, S. A. (2011) Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit Cell 147, 1257-1269
    • (2011) Cell , vol.147 , pp. 1257-1269
    • Feklistov, A.1    Darst, S.A.2
  • 24
    • 0031582060 scopus 로고    scopus 로고
    • DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally
    • Chen, Y. F. and Helmann, J. D. (1997) DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally J. Mol. Biol. 267, 47-59
    • (1997) J. Mol. Biol. , vol.267 , pp. 47-59
    • Chen, Y.F.1    Helmann, J.D.2
  • 25
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - The next generation
    • Metzker, M. L. (2010) Sequencing technologies-the next generation Nat Rev Genet 11, 31-46
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 26
    • 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., and Landick, R. (2003) Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions J. Biol. Chem. 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
  • 27
    • 0032484021 scopus 로고    scopus 로고
    • Conformational changes of Escherichia coli RNA polymerase sigma70 factor induced by binding to the core enzyme
    • Callaci, S., Heyduk, E., and Heyduk, T. (1998) Conformational changes of Escherichia coli RNA polymerase sigma70 factor induced by binding to the core enzyme J. Biol. Chem. 273, 32995-33001
    • (1998) J. Biol. Chem. , vol.273 , pp. 32995-33001
    • Callaci, S.1    Heyduk, E.2    Heyduk, T.3
  • 28
    • 77956285690 scopus 로고    scopus 로고
    • Illumina sequencing library preparation for highly multiplexed target capture and sequencing
    • DOI: 10.1101/pdb.prot5448.
    • Meyer, M. and Kircher, M. (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing, Cold Spring Harbor Protoc., DOI: 10.1101/pdb.prot5448.
    • (2010) Cold Spring Harbor Protoc.
    • Meyer, M.1    Kircher, M.2
  • 29
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: Software for nucleic acid folding and hybridization
    • Markham, N. R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization Methods Mol. Biol. 453, 3-31
    • (2008) Methods Mol. Biol. , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 30
    • 23144440350 scopus 로고    scopus 로고
    • DINAMelt web server for nucleic acid melting prediction
    • Markham, N. R. and Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction Nucleic Acids Res. 33, W577-581
    • (2005) Nucleic Acids Res. , vol.33 , pp. 577-581
    • Markham, N.R.1    Zuker, M.2
  • 31
    • 34547640998 scopus 로고    scopus 로고
    • The -11A of promoter DNA and two conserved amino acids in the melting region of sigma70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact
    • Schroeder, L. A., Choi, A. J., and DeHaseth, P. L. (2007) The -11A of promoter DNA and two conserved amino acids in the melting region of sigma70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact Nucleic Acids Res. 35, 4141-4153
    • (2007) Nucleic Acids Res. , vol.35 , pp. 4141-4153
    • Schroeder, L.A.1    Choi, A.J.2    Dehaseth, P.L.3
  • 32
    • 0028568951 scopus 로고
    • Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis
    • Fried, M. G. and Liu, G. (1994) Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis Nucleic Acids Res. 22, 5054-5059
    • (1994) Nucleic Acids Res. , vol.22 , pp. 5054-5059
    • Fried, M.G.1    Liu, G.2
  • 33
    • 0031016591 scopus 로고    scopus 로고
    • Factors that affect the stability of protein-DNA complexes during gel electrophoresis
    • Fried, M. G. and Bromberg, J. L. (1997) Factors that affect the stability of protein-DNA complexes during gel electrophoresis Electrophoresis 18, 6-11
    • (1997) Electrophoresis , vol.18 , pp. 6-11
    • Fried, M.G.1    Bromberg, J.L.2
  • 34
    • 0031080891 scopus 로고    scopus 로고
    • Sequestration stabilizes lac repressor-DNA complexes during gel electrophoresis
    • Vossen, K. M. and Fried, M. G. (1997) Sequestration stabilizes lac repressor-DNA complexes during gel electrophoresis Anal. Biochem. 245, 85-92
    • (1997) Anal. Biochem. , vol.245 , pp. 85-92
    • Vossen, K.M.1    Fried, M.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.