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Volumn 360, Issue 3, 2006, Pages 702-714

T-rich DNA Single Strands Bind to a Preformed Site on the Bacterial Cold Shock Protein Bs-CspB

Author keywords

cold shock proteins; cold shock response; DNA binding proteins; RNA chaperone activity; transcription antitermination

Indexed keywords

BACTERIAL PROTEIN; COLD SHOCK PROTEIN; COLD SHOCK PROTEIN B; HEXATHYMIDINE; HYDROGEN; METHYL GROUP; NUCLEIC ACID BASE; PYRIMIDINE DERIVATIVE; SINGLE STRANDED DNA; SOLVENT; SUGAR PHOSPHATE; THYMIDINE DERIVATIVE; THYMINE; UNCLASSIFIED DRUG;

EID: 33745645838     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.05.044     Document Type: Article
Times cited : (61)

References (49)
  • 1
    • 0023186464 scopus 로고
    • Induction of proteins in response to low temperature in Escherichia coli
    • Jones P.G., VanBogelen R.A., and Neidhardt F.C. Induction of proteins in response to low temperature in Escherichia coli. J. Bacteriol. 169 (1987) 2092-2095
    • (1987) J. Bacteriol. , vol.169 , pp. 2092-2095
    • Jones, P.G.1    VanBogelen, R.A.2    Neidhardt, F.C.3
  • 2
    • 0029744180 scopus 로고    scopus 로고
    • Cold shock stress-induced proteins in Bacillus subtilis
    • Graumann P., Schröder K., Schmid R., and Marahiel M.A. Cold shock stress-induced proteins in Bacillus subtilis. J. Bacteriol. 178 (1996) 4611-4619
    • (1996) J. Bacteriol. , vol.178 , pp. 4611-4619
    • Graumann, P.1    Schröder, K.2    Schmid, R.3    Marahiel, M.A.4
  • 3
    • 0030826392 scopus 로고    scopus 로고
    • A family of cold shock proteins in Bacillus subtilis is essential for cellular growth and for efficient protein synthesis at optimal and low temperatures
    • Graumann P., Wendrich T.M., Weber M.H., Schröder K., and Marahiel M.A. A family of cold shock proteins in Bacillus subtilis is essential for cellular growth and for efficient protein synthesis at optimal and low temperatures. Mol. Microbiol. 25 (1997) 741-756
    • (1997) Mol. Microbiol. , vol.25 , pp. 741-756
    • Graumann, P.1    Wendrich, T.M.2    Weber, M.H.3    Schröder, K.4    Marahiel, M.A.5
  • 5
    • 0036855530 scopus 로고    scopus 로고
    • Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response
    • Kaan T., Homuth G., Mader U., Bandow J., and Schweder T. Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response. Microbiology 148 (2002) 3441-3455
    • (2002) Microbiology , vol.148 , pp. 3441-3455
    • Kaan, T.1    Homuth, G.2    Mader, U.3    Bandow, J.4    Schweder, T.5
  • 7
    • 0031658803 scopus 로고    scopus 로고
    • A superfamily of proteins containing the cold shock domain
    • Graumann P.L., and Marahiel M.A. A superfamily of proteins containing the cold shock domain. Trends Biochem. Sci. 23 (1998) 286-290
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 286-290
    • Graumann, P.L.1    Marahiel, M.A.2
  • 9
    • 0043166304 scopus 로고    scopus 로고
    • Transcriptional and post-transcriptional control of cold-shock genes
    • Gualerzi C.O., Giuliodori A.M., and Pon C.L. Transcriptional and post-transcriptional control of cold-shock genes. J. Mol. Biol. 331 (2003) 527-539
    • (2003) J. Mol. Biol. , vol.331 , pp. 527-539
    • Gualerzi, C.O.1    Giuliodori, A.M.2    Pon, C.L.3
  • 10
    • 0033584963 scopus 로고    scopus 로고
    • Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition
    • Lopez M.M., Yutani K., and Makhatadze G.I. Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition. J. Biol. Chem. 274 (1999) 33601-33608
    • (1999) J. Biol. Chem. , vol.274 , pp. 33601-33608
    • Lopez, M.M.1    Yutani, K.2    Makhatadze, G.I.3
  • 11
    • 0035805616 scopus 로고    scopus 로고
    • Interactions of the cold shock protein CspB from Bacillus subtilis with single-stranded DNA. Importance of the T base content and position within the template
    • Lopez M.M., Yutani K., and Makhatadze G.I. Interactions of the cold shock protein CspB from Bacillus subtilis with single-stranded DNA. Importance of the T base content and position within the template. J. Biol. Chem. 276 (2001) 15511-15518
    • (2001) J. Biol. Chem. , vol.276 , pp. 15511-15518
    • Lopez, M.M.1    Yutani, K.2    Makhatadze, G.I.3
  • 12
    • 0037216364 scopus 로고    scopus 로고
    • Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization
    • Zeeb M., and Balbach J. Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization. Protein Sci. 12 (2003) 112-123
    • (2003) Protein Sci. , vol.12 , pp. 112-123
    • Zeeb, M.1    Balbach, J.2
  • 13
    • 0031015217 scopus 로고    scopus 로고
    • CspA, the major cold-shock protein of Escherichia coli, is a RNA chaperone
    • Jiang W., Hou Y., and Inouye M. CspA, the major cold-shock protein of Escherichia coli, is a RNA chaperone. J. Biol. Chem. 272 (1997) 196-202
    • (1997) J. Biol. Chem. , vol.272 , pp. 196-202
    • Jiang, W.1    Hou, Y.2    Inouye, M.3
  • 14
    • 0034608861 scopus 로고    scopus 로고
    • Escherichia coli CspA-family RNA chaperones are transcription antiterminators
    • Bae W., Xia B., Inouye M., and Severinov K. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc. Natl Acad. Sci. USA 97 (2000) 7784-7789
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 7784-7789
    • Bae, W.1    Xia, B.2    Inouye, M.3    Severinov, K.4
  • 15
    • 4944221553 scopus 로고    scopus 로고
    • Genome-wide transcription analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli
    • Phadtare S., and Inouye M. Genome-wide transcription analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli. J. Bacteriol. 186 (2004) 7007-7014
    • (2004) J. Bacteriol. , vol.186 , pp. 7007-7014
    • Phadtare, S.1    Inouye, M.2
  • 16
    • 0032858516 scopus 로고    scopus 로고
    • Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli
    • Phadtare S., and Inouye M. Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli. Mol. Microbiol. 33 (1999) 1004-1014
    • (1999) Mol. Microbiol. , vol.33 , pp. 1004-1014
    • Phadtare, S.1    Inouye, M.2
  • 17
    • 0035682359 scopus 로고    scopus 로고
    • Localization of cold shock proteins to cytosolic spaces surrounding nucleoids in Bacillus subtilis depends on active transcription
    • Weber M.H., Volkov A.V., Fricke I., Marahiel M.A., and Graumann P.L. Localization of cold shock proteins to cytosolic spaces surrounding nucleoids in Bacillus subtilis depends on active transcription. J. Bacteriol. 183 (2001) 6435-6443
    • (2001) J. Bacteriol. , vol.183 , pp. 6435-6443
    • Weber, M.H.1    Volkov, A.V.2    Fricke, I.3    Marahiel, M.A.4    Graumann, P.L.5
  • 18
    • 0034859439 scopus 로고    scopus 로고
    • Specific polar localization of ribosomes in Bacillus subtilis depends on active transcription
    • Mascarenhas J., Weber M.H., and Graumann P.L. Specific polar localization of ribosomes in Bacillus subtilis depends on active transcription. EMBO Rep. 2 (2001) 685-689
    • (2001) EMBO Rep. , vol.2 , pp. 685-689
    • Mascarenhas, J.1    Weber, M.H.2    Graumann, P.L.3
  • 19
    • 0026842808 scopus 로고
    • The Y-box factors: a family of nucleic acid binding proteins conserved from Escherichia coli to man
    • Wolffe A.P., Tafuri S., Ranjan M., and Familari M. The Y-box factors: a family of nucleic acid binding proteins conserved from Escherichia coli to man. New Biol. 4 (1992) 290-298
    • (1992) New Biol. , vol.4 , pp. 290-298
    • Wolffe, A.P.1    Tafuri, S.2    Ranjan, M.3    Familari, M.4
  • 20
    • 0028012282 scopus 로고
    • The major cold shock protein of Bacillus subtilis CspB binds with high affinity to the ATTGG and CCAAT sequences in single stranded oligonucleotides
    • Graumann P.L., and Marahiel M.A. The major cold shock protein of Bacillus subtilis CspB binds with high affinity to the ATTGG and CCAAT sequences in single stranded oligonucleotides. FEBS Letters 338 (1994) 157-160
    • (1994) FEBS Letters , vol.338 , pp. 157-160
    • Graumann, P.L.1    Marahiel, M.A.2
  • 21
    • 0032147094 scopus 로고    scopus 로고
    • Gene regulation by Y-box proteins: coupling control of transcription and translation
    • Matsumoto K., and Wolffe A.P. Gene regulation by Y-box proteins: coupling control of transcription and translation. Trends Cell Biol. 8 (1998) 318-323
    • (1998) Trends Cell Biol. , vol.8 , pp. 318-323
    • Matsumoto, K.1    Wolffe, A.P.2
  • 22
    • 0027296211 scopus 로고
    • Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein
    • Schindelin H., Marahiel M.A., and Heinemann U. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature 364 (1993) 164-168
    • (1993) Nature , vol.364 , pp. 164-168
    • Schindelin, H.1    Marahiel, M.A.2    Heinemann, U.3
  • 23
    • 0028306109 scopus 로고
    • Heinemann Crystal structure of CspA, the major cold shock protein of Escherichia coli
    • Schindelin H., Jiang W., and Inouye M. Heinemann Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc. Natl Acad. Sci. USA 91 (1994) 5119-5123
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 5119-5123
    • Schindelin, H.1    Jiang, W.2    Inouye, M.3
  • 24
    • 0034615784 scopus 로고    scopus 로고
    • Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein
    • Mueller U., Perl D., Schmid F.X., and Heinemann U. Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein. J. Mol. Biol. 297 (2000) 975-988
    • (2000) J. Mol. Biol. , vol.297 , pp. 975-988
    • Mueller, U.1    Perl, D.2    Schmid, F.X.3    Heinemann, U.4
  • 25
    • 0035914470 scopus 로고    scopus 로고
    • Crystal structures of mutant forms of the Bacillus caldolyticus cold shock protein differing in thermal stability
    • Delbrück H., Mueller U., Perl D., Schmid F.X., and Heinemann U. Crystal structures of mutant forms of the Bacillus caldolyticus cold shock protein differing in thermal stability. J. Mol. Biol. 313 (2001) 359-369
    • (2001) J. Mol. Biol. , vol.313 , pp. 359-369
    • Delbrück, H.1    Mueller, U.2    Perl, D.3    Schmid, F.X.4    Heinemann, U.5
  • 27
    • 0034844324 scopus 로고    scopus 로고
    • Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima
    • Kremer W., Schuler B., Harrieder S., Geyer M., Gronwald W., Welker C., et al. Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima. Eur. J. Biochem. 268 (2001) 2527-2539
    • (2001) Eur. J. Biochem. , vol.268 , pp. 2527-2539
    • Kremer, W.1    Schuler, B.2    Harrieder, S.3    Geyer, M.4    Gronwald, W.5    Welker, C.6
  • 28
    • 0038473989 scopus 로고    scopus 로고
    • OB fold: growing bigger with functional consistancy
    • Agrawal V., and Radha Kishan K.V. OB fold: growing bigger with functional consistancy. Curr. Protein Peptide Sci. 4 (2003) 195-206
    • (2003) Curr. Protein Peptide Sci. , vol.4 , pp. 195-206
    • Agrawal, V.1    Radha Kishan, K.V.2
  • 29
    • 0029078286 scopus 로고
    • Mutational analysis of the putative nucleic acid-binding surface of the cold-shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single-stranded DNA containing the Y-box motif
    • Schröder K., Graumann P., Schnuchel A., Holak T.A., and Marahiel M.A. Mutational analysis of the putative nucleic acid-binding surface of the cold-shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single-stranded DNA containing the Y-box motif. Mol. Microbiol. 16 (1995) 699-708
    • (1995) Mol. Microbiol. , vol.16 , pp. 699-708
    • Schröder, K.1    Graumann, P.2    Schnuchel, A.3    Holak, T.A.4    Marahiel, M.A.5
  • 30
    • 0032032172 scopus 로고    scopus 로고
    • Surface-exposed phenylalanines in the RNP1/RNP2 motif stabilize the cold-shock protein CspB from Bacillus subtilis
    • Schindler T., Perl D., Graumann P., Sieber V., Marahiel M.A., and Schmid F.X. Surface-exposed phenylalanines in the RNP1/RNP2 motif stabilize the cold-shock protein CspB from Bacillus subtilis. Proteins: Struct. Funct. Genet. 30 (1998) 401-406
    • (1998) Proteins: Struct. Funct. Genet. , vol.30 , pp. 401-406
    • Schindler, T.1    Perl, D.2    Graumann, P.3    Sieber, V.4    Marahiel, M.A.5    Schmid, F.X.6
  • 31
    • 0036295228 scopus 로고    scopus 로고
    • The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1
    • Kloks C.P., Spronk C.A., Lasonder E., Hoffmann A., Vuister G.W., Grzesiek S., and Hilbers C.W. The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1. J. Mol. Biol. 316 (2002) 317-326
    • (2002) J. Mol. Biol. , vol.316 , pp. 317-326
    • Kloks, C.P.1    Spronk, C.A.2    Lasonder, E.3    Hoffmann, A.4    Vuister, G.W.5    Grzesiek, S.6    Hilbers, C.W.7
  • 32
    • 2442664066 scopus 로고    scopus 로고
    • Structural basis of single-stranded RNA recognition
    • Messias A., and Sattler M. Structural basis of single-stranded RNA recognition. Acc. Chem. Res. 37 (2004) 279-287
    • (2004) Acc. Chem. Res. , vol.37 , pp. 279-287
    • Messias, A.1    Sattler, M.2
  • 33
    • 33750008214 scopus 로고    scopus 로고
    • Zeeb, M., Max, K., Weininger, U., Löw, C., Sticht, H. & Balbach, J. (2006). Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution. Nucl. Acids Res. In then press.
  • 34
    • 0030915704 scopus 로고    scopus 로고
    • Improved R-factors for diffraction analysis in macromolecular crystallography
    • Diederichs K., and Karplus P.A. Improved R-factors for diffraction analysis in macromolecular crystallography. Nature Struct. Biol. 4 (1997) 269-275
    • (1997) Nature Struct. Biol. , vol.4 , pp. 269-275
    • Diederichs, K.1    Karplus, P.A.2
  • 37
    • 0018121584 scopus 로고
    • Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications
    • Holbrook S.R., Sussman J.L., Warrant R.W., and Kim S.-H. Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J. Mol. Biol. 123 (1978) 631-660
    • (1978) J. Mol. Biol. , vol.123 , pp. 631-660
    • Holbrook, S.R.1    Sussman, J.L.2    Warrant, R.W.3    Kim, S.-H.4
  • 38
    • 0029762372 scopus 로고    scopus 로고
    • The role of the 5′-end untranslated region of the mRNA for CspA, the major cold-shock protein of Escherichia coli, in cold-shock adaptation
    • Jiang W., Fang L., and Inouye M. The role of the 5′-end untranslated region of the mRNA for CspA, the major cold-shock protein of Escherichia coli, in cold-shock adaptation. J. Bacteriol. 178 (1996) 4919-4925
    • (1996) J. Bacteriol. , vol.178 , pp. 4919-4925
    • Jiang, W.1    Fang, L.2    Inouye, M.3
  • 39
    • 0026642589 scopus 로고
    • Overproduction, crystallization, and preliminary X-ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB
    • Schindelin H., Herrler M., Willimsky G., Marahiel M.A., and Heinemann U. Overproduction, crystallization, and preliminary X-ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB. Proteins: Struct. Funct. Genet. 14 (1992) 120-124
    • (1992) Proteins: Struct. Funct. Genet. , vol.14 , pp. 120-124
    • Schindelin, H.1    Herrler, M.2    Willimsky, G.3    Marahiel, M.A.4    Heinemann, U.5
  • 40
    • 0029049321 scopus 로고
    • Extremely rapid folding in the absence of intermediates: The cold-shock protein from Bacillus subtilis
    • Schindler T., Herrler M., Marahiel M.A., and Schmid F.X. Extremely rapid folding in the absence of intermediates: The cold-shock protein from Bacillus subtilis. Nature Struct. Biol. 2 (1995) 663-673
    • (1995) Nature Struct. Biol. , vol.2 , pp. 663-673
    • Schindler, T.1    Herrler, M.2    Marahiel, M.A.3    Schmid, F.X.4
  • 41
    • 16544383242 scopus 로고    scopus 로고
    • Single-stranded DNA bound to bacterial cold-shock proteins: preliminary crystallographic and Raman analysis
    • Bienert R., Zeeb M., Dostal L., Feske A., Magg C., Max K., et al. Single-stranded DNA bound to bacterial cold-shock proteins: preliminary crystallographic and Raman analysis. Acta Crystallog. sect. D 60 (2004) 755-757
    • (2004) Acta Crystallog. sect. D , vol.60 , pp. 755-757
    • Bienert, R.1    Zeeb, M.2    Dostal, L.3    Feske, A.4    Magg, C.5    Max, K.6
  • 42
    • 0037349370 scopus 로고    scopus 로고
    • Facilities and methods for the high-throughput crystal structure analysis of human proteins
    • Heinemann U., Büssow K., Mueller U., and Heinemann U. Facilities and methods for the high-throughput crystal structure analysis of human proteins. Acc. Chem. Res. 36 (2003) 157-163
    • (2003) Acc. Chem. Res. , vol.36 , pp. 157-163
    • Heinemann, U.1    Büssow, K.2    Mueller, U.3    Heinemann, U.4
  • 43
    • 0027879008 scopus 로고
    • Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants
    • Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallog. 26 (1993) 795-800
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 795-800
    • Kabsch, W.1
  • 44
    • 84920325457 scopus 로고
    • AMoRe: an automated package for molecular replacement
    • Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A 50 (1994) 157-163
    • (1994) Acta Crystallog. sect. A , vol.50 , pp. 157-163
    • Navaza, J.1
  • 45
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
    • (1997) Acta Crystallog. sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 47
    • 0026351773 scopus 로고
    • Thermodynamic methods for modelindependent determination of equilibrium binding isotherms for protein-DNA interactions: Spectroscopic approaches to monitor binding
    • Lohman T.M., and Bujalowski W. Thermodynamic methods for modelindependent determination of equilibrium binding isotherms for protein-DNA interactions: Spectroscopic approaches to monitor binding. Methods Enzymol. 208 (1991) 258-290
    • (1991) Methods Enzymol. , vol.208 , pp. 258-290
    • Lohman, T.M.1    Bujalowski, W.2
  • 48
    • 0030956737 scopus 로고    scopus 로고
    • Fluorescence methods for studying equilibrium macromolecule-ligand interactions
    • Eftink M.R. Fluorescence methods for studying equilibrium macromolecule-ligand interactions. Methods Enzymol. 278 (1997) 221-257
    • (1997) Methods Enzymol. , vol.278 , pp. 221-257
    • Eftink, M.R.1
  • 49
    • 0025398721 scopus 로고
    • WHAT IF: a molecular modelling and drug design program
    • Vriend G. WHAT IF: a molecular modelling and drug design program. J. Mol. Graph. 8 (1990) 52-56
    • (1990) J. Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1


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