메뉴 건너뛰기




Volumn 65, Issue 1, 2009, Pages 66-76

In vivo assembly and single-molecule characterization of the transcription machinery from Shewanella oneidensis MR-1

Author keywords

Factor; Alternating laser excitation; Co overexpression; RNA polymerase; Shewanella oneidensis; Single molecule spectroscopy

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; MESSENGER RNA; RNA POLYMERASE II; SIGMA FACTOR;

EID: 60349083955     PISSN: 10465928     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pep.2008.11.013     Document Type: Article
Times cited : (5)

References (73)
  • 1
    • 0024219883 scopus 로고
    • Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor
    • Myers C.R., and Nealson K.H. Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240 (1988) 1319-1321
    • (1988) Science , vol.240 , pp. 1319-1321
    • Myers, C.R.1    Nealson, K.H.2
  • 2
    • 0036842435 scopus 로고    scopus 로고
    • Shewanella-the environmentally versatile genome
    • Tiedje J.M. Shewanella-the environmentally versatile genome. Nature Biotechnology 20 (2002) 1093-1094
    • (2002) Nature Biotechnology , vol.20 , pp. 1093-1094
    • Tiedje, J.M.1
  • 11
    • 34547886838 scopus 로고    scopus 로고
    • Immunoaffinity purification and characterization of RNA polymerase from Shewanella oneidensis
    • Probasco M.D., Thompson N.E., and Burgess R.R. Immunoaffinity purification and characterization of RNA polymerase from Shewanella oneidensis. Protein Expression and Purification 55 (2007) 23-30
    • (2007) Protein Expression and Purification , vol.55 , pp. 23-30
    • Probasco, M.D.1    Thompson, N.E.2    Burgess, R.R.3
  • 12
    • 33644811688 scopus 로고    scopus 로고
    • One-step, non-denaturing isolation of an RNA polymerase enzyme complex using an improved multi-use affinity probe resin
    • Mayer M.U., Shi L., and Squier T.C. One-step, non-denaturing isolation of an RNA polymerase enzyme complex using an improved multi-use affinity probe resin. Molecular BioSystems 1 (2005) 53-56
    • (2005) Molecular BioSystems , vol.1 , pp. 53-56
    • Mayer, M.U.1    Shi, L.2    Squier, T.C.3
  • 13
    • 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., Svetlor V., Murakami K.S., and Landick R. Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. Journal of Biological Chemistry 278 (2003) 12344-12355
    • (2003) Journal of Biological Chemistry , vol.278 , pp. 12344-12355
    • Artsimovitch, I.1    Svetlor, V.2    Murakami, K.S.3    Landick, R.4
  • 14
    • 0347381303 scopus 로고    scopus 로고
    • Preparation and characterization of recombinant Thermus aquaticus RNA polymerase
    • Kuznedelov K., Minakhin L., and Severinov K. Preparation and characterization of recombinant Thermus aquaticus RNA polymerase. Methods Enzymology 370 (2003) 94-108
    • (2003) Methods Enzymology , vol.370 , pp. 94-108
    • Kuznedelov, K.1    Minakhin, L.2    Severinov, K.3
  • 15
    • 40849113038 scopus 로고    scopus 로고
    • Overproduction and purification of recombinant Bacillus subtilis RNA polymerase
    • Yang X., and Lewis P.J. Overproduction and purification of recombinant Bacillus subtilis RNA polymerase. Protein Expression Purification 59 (2008) 86-93
    • (2008) Protein Expression Purification , vol.59 , pp. 86-93
    • Yang, X.1    Lewis, P.J.2
  • 16
    • 0029797365 scopus 로고    scopus 로고
    • Reconstitution of RNA polymerase
    • Fujita N., and Ishihama A. Reconstitution of RNA polymerase. Methods in Enzymology 273 (1996) 121-130
    • (1996) Methods in Enzymology , vol.273 , pp. 121-130
    • Fujita, N.1    Ishihama, A.2
  • 18
    • 33751212468 scopus 로고    scopus 로고
    • Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
    • Kapanidis A.N., Margeat E., Ho S.O., Kortkhonjia E., Weiss S., and Ebright R.H. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314 (2006) 1144-1147
    • (2006) Science , vol.314 , pp. 1144-1147
    • Kapanidis, A.N.1    Margeat, E.2    Ho, S.O.3    Kortkhonjia, E.4    Weiss, S.5    Ebright, R.H.6
  • 19
    • 33751218319 scopus 로고    scopus 로고
    • Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
    • Revyakin A., Liu C., Ebright R.H., and Strick T.R. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314 (2006) 1139-1143
    • (2006) Science , vol.314 , pp. 1139-1143
    • Revyakin, A.1    Liu, C.2    Ebright, R.H.3    Strick, T.R.4
  • 20
    • 44449127089 scopus 로고    scopus 로고
    • Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains
    • Tang G.Q., Roy R., Ha T., and Patel S.S. Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains. Molecular Cell 30 (2008) 567-577
    • (2008) Molecular Cell , vol.30 , pp. 567-577
    • Tang, G.Q.1    Roy, R.2    Ha, T.3    Patel, S.S.4
  • 22
    • 0035943446 scopus 로고    scopus 로고
    • Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA
    • Mukhopadhyay J., Kapanidis A.N., Mekler V., Kortkhonjia E., Ebright Y.W., and Ebright R.H. Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 106 (2001) 453-463
    • (2001) Cell , vol.106 , pp. 453-463
    • Mukhopadhyay, J.1    Kapanidis, A.N.2    Mekler, V.3    Kortkhonjia, E.4    Ebright, Y.W.5    Ebright, R.H.6
  • 23
    • 33751218319 scopus 로고    scopus 로고
    • Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
    • Revyakin A., Liu C., Ebright R.H., and Strick T.R. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314 (2006) 1139-1143
    • (2006) Science , vol.314 , pp. 1139-1143
    • Revyakin, A.1    Liu, C.2    Ebright, R.H.3    Strick, T.R.4
  • 24
    • 27644560257 scopus 로고    scopus 로고
    • Sigma and RNA polymerase: an on-again, off-again relationship?
    • Mooney R.A., Darst S.A., and Landick R. Sigma and RNA polymerase: an on-again, off-again relationship?. Molecular Cell 20 (2005) 335-345
    • (2005) Molecular Cell , vol.20 , pp. 335-345
    • Mooney, R.A.1    Darst, S.A.2    Landick, R.3
  • 25
    • 0023029081 scopus 로고
    • Release of the sigma subunit of Escherichia coli DNA-dependent RNA polymerase depends mainly on time elapsed after the start of initiation, not on length of product RNA
    • Shimamoto N., Kamigochi T., and Utiyama H. Release of the sigma subunit of Escherichia coli DNA-dependent RNA polymerase depends mainly on time elapsed after the start of initiation, not on length of product RNA. Journal of Biological Chemistry 261 (1986) 11859-11865
    • (1986) Journal of Biological Chemistry , vol.261 , pp. 11859-11865
    • Shimamoto, N.1    Kamigochi, T.2    Utiyama, H.3
  • 26
    • 29244442950 scopus 로고    scopus 로고
    • Simplified screening for the detection of soluble fusion constructs expressed in E. coli using a modular set of vectors
    • Dummler A., Lawrence A.-M., and de Marco A. Simplified screening for the detection of soluble fusion constructs expressed in E. coli using a modular set of vectors. Microbial Cell Factories 4 (2005) 34
    • (2005) Microbial Cell Factories , vol.4 , pp. 34
    • Dummler, A.1    Lawrence, A.-M.2    de Marco, A.3
  • 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. Conformational changes of Escherichia coli RNA polymerase sigma70 factor induced by binding to the core enzyme. Journal of Biological Chemistry 273 (1998) 32995-33001
    • (1998) Journal of Biological Chemistry , vol.273 , pp. 32995-33001
    • Callaci, S.1    Heyduk, E.2    Heyduk, T.3
  • 29
    • 0025108594 scopus 로고
    • Use of mono Q high resolution ion exchange chromatography to obtain highly pure and active Escherichia coli RNA polymerase
    • Hager D.A., Jin D.J., and Burgess R.R. Use of mono Q high resolution ion exchange chromatography to obtain highly pure and active Escherichia coli RNA polymerase. Biochemistry 29 (1990) 7890-7894
    • (1990) Biochemistry , vol.29 , pp. 7890-7894
    • Hager, D.A.1    Jin, D.J.2    Burgess, R.R.3
  • 33
    • 34548850026 scopus 로고    scopus 로고
    • 5' end cDNA amplification using classic RACE
    • Scotto-Lavino E., Du G., and Forhman M.A. 5' end cDNA amplification using classic RACE. Nature Protocols 1 (2006) 2555-2562
    • (2006) Nature Protocols , vol.1 , pp. 2555-2562
    • Scotto-Lavino, E.1    Du, G.2    Forhman, M.A.3
  • 34
    • 0345758482 scopus 로고
    • Transcription of glnA by purified Escherichia coli components: core RNA polymerase and the products of glnF, glnG, and glnL
    • Hunt T.P., and Magasanik B. Transcription of glnA by purified Escherichia coli components: core RNA polymerase and the products of glnF, glnG, and glnL. Proceedings of the National Academy of Sciences of the United States America 82 (1985) 8453-8457
    • (1985) Proceedings of the National Academy of Sciences of the United States America , vol.82 , pp. 8453-8457
    • Hunt, T.P.1    Magasanik, B.2
  • 37
    • 22144492905 scopus 로고    scopus 로고
    • Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation
    • Lee N.K., Kapanidis A.N., Wang Y., Michalet X., and Mukhopadhyay J. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophysical Journal 88 (2005) 2939
    • (2005) Biophysical Journal , vol.88 , pp. 2939
    • Lee, N.K.1    Kapanidis, A.N.2    Wang, Y.3    Michalet, X.4    Mukhopadhyay, J.5
  • 38
    • 0024359013 scopus 로고
    • A novel sequence element derived from bacteriophage T7 mRNA acts as an enhancer of translation of the lacZ gene in Escherichia coli
    • Olins P.O., and Rangwala S.H. A novel sequence element derived from bacteriophage T7 mRNA acts as an enhancer of translation of the lacZ gene in Escherichia coli. Journal of Biological Chemistry 264 (1989) 16973-16976
    • (1989) Journal of Biological Chemistry , vol.264 , pp. 16973-16976
    • Olins, P.O.1    Rangwala, S.H.2
  • 39
    • 0034963119 scopus 로고    scopus 로고
    • A modular polycistronic expression system for overexpressing protein complexes in Escherichia coli
    • Tan S. A modular polycistronic expression system for overexpressing protein complexes in Escherichia coli. Protein Expression and Purification 21 (2001) 224-234
    • (2001) Protein Expression and Purification , vol.21 , pp. 224-234
    • Tan, S.1
  • 41
    • 0033048415 scopus 로고    scopus 로고
    • The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo
    • Lopez P.J., Marchand I., Joyce S.A., and Dreyfus M. The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Molecular Microbiology 33 (1999) 188-199
    • (1999) Molecular Microbiology , vol.33 , pp. 188-199
    • Lopez, P.J.1    Marchand, I.2    Joyce, S.A.3    Dreyfus, M.4
  • 43
    • 0021019879 scopus 로고
    • Vectors bearing a hybrid trp-lac promoter useful for regulated expression of cloned genes in Escherichia coli
    • Amann E., Brosius J., and Ptashne M. Vectors bearing a hybrid trp-lac promoter useful for regulated expression of cloned genes in Escherichia coli. Gene 25 (1983) 167-178
    • (1983) Gene , vol.25 , pp. 167-178
    • Amann, E.1    Brosius, J.2    Ptashne, M.3
  • 44
    • 0029822194 scopus 로고    scopus 로고
    • Purification of overproduced Escherichia coli RNA polymerase [sigma] factors by solubilizing inclusion bodies and refolding from Sarkosyl
    • Burgess R.R., and Sankar A. Purification of overproduced Escherichia coli RNA polymerase [sigma] factors by solubilizing inclusion bodies and refolding from Sarkosyl. Methods in Enzymology 273 (1996) 145-149
    • (1996) Methods in Enzymology , vol.273 , pp. 145-149
    • Burgess, R.R.1    Sankar, A.2
  • 45
    • 0346120333 scopus 로고    scopus 로고
    • Purification of highly-active and soluble Escherichia coli [sigma]70 polypeptide overproduced at low temperature
    • Zhi H., and Jin D.J. Purification of highly-active and soluble Escherichia coli [sigma]70 polypeptide overproduced at low temperature. Methods in Enzymology 370 (2003) 174-180
    • (2003) Methods in Enzymology , vol.370 , pp. 174-180
    • Zhi, H.1    Jin, D.J.2
  • 52
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    • Roth F.P., Hughes J.D., Estep P.W., and Church G.M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology 16 (1998) 939-945
    • (1998) Nature Biotechnology , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 53
    • 0037608789 scopus 로고    scopus 로고
    • Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis
    • Saffarini D.A., Schultz R., and Beliaev A. Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis. Journal of Bacteriology 185 (2003) 3668-3671
    • (2003) Journal of Bacteriology , vol.185 , pp. 3668-3671
    • Saffarini, D.A.1    Schultz, R.2    Beliaev, A.3
  • 54
    • 0027469990 scopus 로고
    • Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, {sigma}38, is a second principal {sigma} factor of RNA polymerase in stationary-phase Escherichia coli
    • Tanaka K., Takayanagi Y., Fujita N., Ishihama A., and Takahashi H. Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, {sigma}38, is a second principal {sigma} factor of RNA polymerase in stationary-phase Escherichia coli. Proceedings of the National Academy of Sciences of the United States America 90 (1993) 3511-3515
    • (1993) Proceedings of the National Academy of Sciences of the United States America , vol.90 , pp. 3511-3515
    • Tanaka, K.1    Takayanagi, Y.2    Fujita, N.3    Ishihama, A.4    Takahashi, H.5
  • 55
    • 0017388978 scopus 로고
    • Binding of Escherichia coli RNA polymerase to T7 DNA. Displacement of holoenzyme from promoter complexes by heparin
    • Pfeffer S.R., Stahl S.J., and Chamberlin M.J. Binding of Escherichia coli RNA polymerase to T7 DNA. Displacement of holoenzyme from promoter complexes by heparin. Journal of Biological Chemistry 252 (1977) 5403-5407
    • (1977) Journal of Biological Chemistry , vol.252 , pp. 5403-5407
    • Pfeffer, S.R.1    Stahl, S.J.2    Chamberlin, M.J.3
  • 59
    • 0037123763 scopus 로고    scopus 로고
    • Views of transcription initiation
    • Young B.A., Gruber T.M., and Gross C.A. Views of transcription initiation. Cell 109 (2002) 417-420
    • (2002) Cell , vol.109 , pp. 417-420
    • Young, B.A.1    Gruber, T.M.2    Gross, C.A.3
  • 60
    • 0037073077 scopus 로고    scopus 로고
    • Promoter clearance and escape in prokaryotes
    • Hsu L.M. Promoter clearance and escape in prokaryotes. Biochimica et Biophysica Acta 1577 (2002) 191-207
    • (2002) Biochimica et Biophysica Acta , vol.1577 , pp. 191-207
    • Hsu, L.M.1
  • 61
    • 0037474104 scopus 로고    scopus 로고
    • Analytical chemistry. How to detect weak pairs
    • Laurence T.A., and Weiss S. Analytical chemistry. How to detect weak pairs. Science 299 (2003) 667-668
    • (2003) Science , vol.299 , pp. 667-668
    • Laurence, T.A.1    Weiss, S.2
  • 62
    • 0030271890 scopus 로고    scopus 로고
    • Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase
    • Malhotra A., Severinova E., and Darst S.A. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell 87 (1996) 127-136
    • (1996) Cell , vol.87 , pp. 127-136
    • Malhotra, A.1    Severinova, E.2    Darst, S.A.3
  • 66
    • 0022247421 scopus 로고
    • Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. Footprinting, methylation, and rifampicin-sensitivity changes accompanying transcription initiation
    • Carpousis A.J., and Gralla J.D. Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. Footprinting, methylation, and rifampicin-sensitivity changes accompanying transcription initiation. Journal of Molecular Biology 183 (1985) 165-177
    • (1985) Journal of Molecular Biology , vol.183 , pp. 165-177
    • Carpousis, A.J.1    Gralla, J.D.2
  • 67
    • 0036840677 scopus 로고    scopus 로고
    • Role of the RNA polymerase sigma subunit in transcription initiation
    • Borukhov S., and Severinov K. Role of the RNA polymerase sigma subunit in transcription initiation. Research in Microbiology 153 (2002) 557-562
    • (2002) Research in Microbiology , vol.153 , pp. 557-562
    • Borukhov, S.1    Severinov, K.2
  • 68
    • 0034671288 scopus 로고    scopus 로고
    • RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II
    • Ebright R.H. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. Journal of Molecular Biology 304 (2000) 687-698
    • (2000) Journal of Molecular Biology , vol.304 , pp. 687-698
    • Ebright, R.H.1
  • 70
    • 0037123602 scopus 로고    scopus 로고
    • Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex
    • Murakami K.S., Masuda S., Campbell E.A., Muzzin O., and Darst S.A. 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
  • 71
    • 0037123659 scopus 로고    scopus 로고
    • Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution
    • Murakami K.S., Masuda S., and Darst S.A. 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
  • 72
    • 0347381289 scopus 로고    scopus 로고
    • Crystallographic analysis of Thermus aquaticus RNA polymerase holoenzyme and a holoenzyme/promoter DNA complex
    • Murakami K.S., Masuda S., and Darst S.A. Crystallographic analysis of Thermus aquaticus RNA polymerase holoenzyme and a holoenzyme/promoter DNA complex. Methods Enzymology 370 (2003) 42-53
    • (2003) Methods Enzymology , vol.370 , pp. 42-53
    • Murakami, K.S.1    Masuda, S.2    Darst, S.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.