메뉴 건너뛰기




Volumn 192, Issue 17, 2010, Pages 4327-4336

Geobacter uraniireducens NikR displays a DNA binding mode distinct from other members of the NikR family

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; GLYCINE; NICKEL; PROTEIN NIKR; SERINE; TETRAMER; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN; DNA BINDING PROTEIN; REPRESSOR PROTEIN;

EID: 77956537744     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00152-10     Document Type: Article
Times cited : (11)

References (49)
  • 1
    • 33646138246 scopus 로고    scopus 로고
    • The metal- and DNA-binding activities of Helicobacter pylori NikR
    • Abraham, L. O., Y. Li, and D. B. Zamble. 2006. The metal- and DNA-binding activities of Helicobacter pylori NikR. J. Inorg. Biochem. 100:1005-1014.
    • (2006) J. Inorg. Biochem. , vol.100 , pp. 1005-1014
    • Abraham, L.O.1    Li, Y.2    Zamble, D.B.3
  • 4
    • 0022254333 scopus 로고
    • Nickel-containing hydrogenase isoenzymes from anaerobically grown Escherichia coli K-12
    • Ballantine, S. P., and D. H. Boxer. 1985. Nickel-containing hydrogenase isoenzymes from anaerobically grown Escherichia coli K-12. J. Bacteriol. 163:454-459.
    • (1985) J. Bacteriol. , vol.163 , pp. 454-459
    • Ballantine, S.P.1    Boxer, D.H.2
  • 5
    • 64049107915 scopus 로고    scopus 로고
    • An intact urease assembly pathway is required to compete with NikR for nickel ions in Helicobacter pylori
    • Benanti, E. L., and P. T. Chivers. 2009. An intact urease assembly pathway is required to compete with NikR for nickel ions in Helicobacter pylori. J. Bacteriol. 191:2405-2408.
    • (2009) J. Bacteriol. , vol.191 , pp. 2405-2408
    • Benanti, E.L.1    Chivers, P.T.2
  • 6
    • 34547130605 scopus 로고    scopus 로고
    • 2+-dependent transcription factor NikR is required for specific DNA binding
    • 2+-dependent transcription factor NikR is required for specific DNA binding. J. Biol. Chem. 282:20365-20375.
    • (2007) J. Biol. Chem. , vol.282 , pp. 20365-20375
    • Benanti, E.L.1    Chivers, P.T.2
  • 7
    • 0034714133 scopus 로고    scopus 로고
    • Interactions of Arg2 in the Mnt N-terminal arm with the central and flanking regions of the Mnt operator
    • Berggrun, A., and R. T. Sauer. 2000. Interactions of Arg2 in the Mnt N-terminal arm with the central and flanking regions of the Mnt operator. J. Mol. Biol. 301:959-973.
    • (2000) J. Mol. Biol. , vol.301 , pp. 959-973
    • Berggrun, A.1    Sauer, R.T.2
  • 8
    • 3543072246 scopus 로고    scopus 로고
    • Metal-selective DNA-binding response of Escherichia coli NikR
    • Bloom, S. L., and D. B. Zamble. 2004. Metal-selective DNA-binding response of Escherichia coli NikR. Biochemistry 43:10029-10038.
    • (2004) Biochemistry , vol.43 , pp. 10029-10038
    • Bloom, S.L.1    Zamble, D.B.2
  • 9
    • 0034730114 scopus 로고    scopus 로고
    • Methyl groups of thymine bases are important for nucleic acid recognition by DtxR
    • Chen, C. S., A. White, J. Love, J. R. Murphy, and D. Ringe. 2000. Methyl groups of thymine bases are important for nucleic acid recognition by DtxR. Biochemistry 39:10397-10407.
    • (2000) Biochemistry , vol.39 , pp. 10397-10407
    • Chen, C.S.1    White, A.2    Love, J.3    Murphy, J.R.4    Ringe, D.5
  • 10
    • 0344393488 scopus 로고    scopus 로고
    • Identification and characterization of the nickel uptake system for urease biogenesis in Streptococcus salivarius 57
    • Chen, Y. Y., and R. A. Burne. 2003. Identification and characterization of the nickel uptake system for urease biogenesis in Streptococcus salivarius 57.I. J. Bacteriol. 185:6773-6779.
    • (2003) I. J. Bacteriol. , vol.185 , pp. 6773-6779
    • Chen, Y.Y.1    Burne, R.A.2
  • 11
    • 0032697047 scopus 로고    scopus 로고
    • NikR is a ribbon-helix-helix DNA-binding protein
    • Chivers, P. T., and R. T. Sauer. 1999. NikR is a ribbon-helix-helix DNA-binding protein. Protein Sci. 8:2494-2500.
    • (1999) Protein Sci. , vol.8 , pp. 2494-2500
    • Chivers, P.T.1    Sauer, R.T.2
  • 12
    • 0036774881 scopus 로고    scopus 로고
    • NikR repressor: High-affinity nickel binding to the C-terminal domain regulates binding to operator DNA
    • Chivers, P. T., and R. T. Sauer. 2002. NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA. Chem. Biol. 9:1141-1148.
    • (2002) Chem. Biol. , vol.9 , pp. 1141-1148
    • Chivers, P.T.1    Sauer, R.T.2
  • 13
    • 0034733505 scopus 로고    scopus 로고
    • 2+-Dependent interaction of NikR with wild-type and mutant operator sites
    • 2+-Dependent interaction of NikR with wild-type and mutant operator sites. J. Biol. Chem. 275:19735-19741.
    • (2000) J. Biol. Chem. , vol.275 , pp. 19735-19741
    • Chivers, P.T.1    Sauer, R.T.2
  • 14
    • 17144395996 scopus 로고    scopus 로고
    • Structure of Pyrococcus horikoshii NikR: Nickel sensing and implications for the regulation of DNA recognition
    • Chivers, P. T., and T. H. Tahirov. 2005. Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition. J. Mol. Biol. 348:597-607.
    • (2005) J. Mol. Biol. , vol.348 , pp. 597-607
    • Chivers, P.T.1    Tahirov, T.H.2
  • 15
    • 0042065267 scopus 로고    scopus 로고
    • Characterization of the roles of NikR, a nickel-responsive pleiotropic autoregulator of Helicobacter pylori
    • DOI 10.1046/j.1365-2958.2003.03621.x
    • Contreras, M., J. M. Thiberge, M. A. Mandrand-Berthelot, and A. Labigne. 2003. Characterization of the roles of NikR, a nickel-responsive pleiotropic autoregulator of Helicobacter pylori. Mol. Microbiol. 49:947-963. (Pubitemid 36981341)
    • (2003) Molecular Microbiology , vol.49 , Issue.4 , pp. 947-963
    • Contreras, M.1    Thiberge, J.-M.2    Mandrand-Berthelot, M.-A.3    Labigne, A.4
  • 16
    • 33845505250 scopus 로고    scopus 로고
    • Helicobacter pylori HP1512 is a nickel-responsive NikR-regulated outer membrane protein
    • Davis, G. S., E. L. Flannery, and H. L. Mobley. 2006. Helicobacter pylori HP1512 is a nickel-responsive NikR-regulated outer membrane protein. Infect. Immun. 74:6811-6820.
    • (2006) Infect. Immun. , vol.74 , pp. 6811-6820
    • Davis, G.S.1    Flannery, E.L.2    Mobley, H.L.3
  • 17
    • 27744481253 scopus 로고    scopus 로고
    • In vitro analysis of protein-operator interactions of the NikR and fur metal-responsive regulators of coregulated genes in Helicobacter pylori
    • DOI 10.1128/JB.187.22.7703-7715.2005
    • Delany, I., R. Ieva, A. Soragni, M. Hilleringmann, R. Rappuoli, and V. Scarlato. 2005. In vitro analysis of protein-operator interactions of the NikR and fur metal-responsive regulators of coregulated genes in Helicobacter pylori. J. Bacteriol. 187:7703-7715. (Pubitemid 41587709)
    • (2005) Journal of Bacteriology , vol.187 , Issue.22 , pp. 7703-7715
    • Delany, I.1    Ieva, R.2    Soragni, A.3    Hilleringmann, M.4    Rappuoli, R.5    Scarlato, V.6
  • 18
    • 0032932493 scopus 로고    scopus 로고
    • Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli
    • De Pina, K., V. Desjardin, M. A. Mandrand-Berthelot, G. Giordano, and L. F. Wu. 1999. Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli. J. Bacteriol. 181:670-674.
    • (1999) J. Bacteriol. , vol.181 , pp. 670-674
    • De Pina, K.1    Desjardin, V.2    Mandrand-Berthelot, M.A.3    Giordano, G.4    Wu, L.F.5
  • 19
    • 33847646219 scopus 로고    scopus 로고
    • Characterization of the Helicobacter pylori NikR-P(ureA) DNA interaction: Metal ion requirements and sequence specificity
    • Dosanjh, N. S., N. A. Hammerbacher, and S. L. Michel. 2007. Characterization of the Helicobacter pylori NikR-P(ureA) DNA interaction: metal ion requirements and sequence specificity. Biochemistry 46:2520-2529.
    • (2007) Biochemistry , vol.46 , pp. 2520-2529
    • Dosanjh, N.S.1    Hammerbacher, N.A.2    Michel, S.L.3
  • 20
    • 59249087478 scopus 로고    scopus 로고
    • Helicobacter pylori NikR's interaction with DNA: A two-tiered mode of recognition
    • Dosanjh, N. S., A. L. West, and S. L. Michel. 2009. Helicobacter pylori NikR's interaction with DNA: a two-tiered mode of recognition. Biochemistry 48:527-536.
    • (2009) Biochemistry , vol.48 , pp. 527-536
    • Dosanjh, N.S.1    West, A.L.2    Michel, S.L.3
  • 21
    • 41149129350 scopus 로고    scopus 로고
    • John Wiley & Sons, Inc., New York, NY. doi:10.1002/0471142727. mb0705s17. [Online.]
    • Eckert, R. L. 2001. DNA sequencing by the chemical method. John Wiley & Sons, Inc., New York, NY. doi:10.1002/0471142727.mb0705s17. [Online.]
    • (2001) DNA Sequencing by the Chemical Method
    • Eckert, R.L.1
  • 22
    • 27744569940 scopus 로고    scopus 로고
    • The nickel-responsive regulator NikR controls activation and repression of gene transcription in Helicobacter pylori
    • Ernst, F. D., E. J. Kuipers, A. Heijens, R. Sarwari, J. Stoof, C. W. Penn, J. G. Kusters, and A. H. van Vliet. 2005. The nickel-responsive regulator NikR controls activation and repression of gene transcription in Helicobacter pylori. Infect. Immun. 73:7252-7258.
    • (2005) Infect. Immun. , vol.73 , pp. 7252-7258
    • Ernst, F.D.1    Kuipers, E.J.2    Heijens, A.3    Sarwari, R.4    Stoof, J.5    Penn, C.W.6    Kusters, J.G.7    Van Vliet, A.H.8
  • 23
    • 33845488317 scopus 로고    scopus 로고
    • NikR mediates nickel-responsive transcriptional repression of the Helicobacter pylori outer membrane proteins FecA3 (HP1400) and FrpB4 (HP1512)
    • Ernst, F. D., J. Stoof, W. M. Horrevoets, E. J. Kuipers, J. G. Kusters, and A. H. van Vliet. 2006. NikR mediates nickel-responsive transcriptional repression of the Helicobacter pylori outer membrane proteins FecA3 (HP1400) and FrpB4 (HP1512). Infect. Immun. 74:6821-6828.
    • (2006) Infect. Immun. , vol.74 , pp. 6821-6828
    • Ernst, F.D.1    Stoof, J.2    Horrevoets, W.M.3    Kuipers, E.J.4    Kusters, J.G.5    Van Vliet, A.H.6
  • 27
    • 34247542510 scopus 로고    scopus 로고
    • Nickel-specific response in the transcriptional regulator, Escherichia coli NikR
    • Leitch, S., M. J. Bradley, J. L. Rowe, P. T. Chivers, and M. J. Maroney. 2007. Nickel-specific response in the transcriptional regulator, Escherichia coli NikR. J. Am. Chem. Soc. 129:5085-5095.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 5085-5095
    • Leitch, S.1    Bradley, M.J.2    Rowe, J.L.3    Chivers, P.T.4    Maroney, M.J.5
  • 28
    • 64849097266 scopus 로고    scopus 로고
    • The pH-responsive DNA-binding activity of Helicobacter pylori NikR
    • Li, Y., and D. Zamble. 2009. The pH-responsive DNA-binding activity of Helicobacter pylori NikR. Biochemistry 48:2486-2496.
    • (2009) Biochemistry , vol.48 , pp. 2486-2496
    • Li, Y.1    Zamble, D.2
  • 31
    • 0038203196 scopus 로고    scopus 로고
    • Nickel uptake and utilization by microorganisms
    • Mulrooney, S. B., and R. P. Hausinger. 2003. Nickel uptake and utilization by microorganisms. FEMS Microbiol. Rev. 27:239-261.
    • (2003) FEMS Microbiol. Rev. , vol.27 , pp. 239-261
    • Mulrooney, S.B.1    Hausinger, R.P.2
  • 32
    • 0027482679 scopus 로고
    • The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel
    • Navarro, C., L. F. Wu, and M. A. Mandrand-Berthelot. 1993. The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel. Mol. Microbiol. 9:1181-1191.
    • (1993) Mol. Microbiol. , vol.9 , pp. 1181-1191
    • Navarro, C.1    Wu, L.F.2    Mandrand-Berthelot, M.A.3
  • 33
    • 34248647893 scopus 로고    scopus 로고
    • TonB-dependent energy transduction between outer and cytoplasmic membranes
    • Postle, K., and R. A. Larsen. 2007. TonB-dependent energy transduction between outer and cytoplasmic membranes. Biometals 20:453-465.
    • (2007) Biometals , vol.20 , pp. 453-465
    • Postle, K.1    Larsen, R.A.2
  • 34
    • 0028147466 scopus 로고
    • Major groove DNA recognition by β-sheets: The ribbon-helix-helix family of gene regulatory proteins
    • Raumann, B. E., B. M. Brown, and R. T. Sauer. 1994. Major groove DNA recognition by β-sheets: the ribbon-helix-helix family of gene regulatory proteins. Curr. Opin. Struct. Biol. 4:36-43.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 36-43
    • Raumann, B.E.1    Brown, B.M.2    Sauer, R.T.3
  • 35
    • 33644894229 scopus 로고    scopus 로고
    • Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: Evidence for a novel group of ATP-binding cassette transporters
    • Rodionov, D. A., P. Hebbeln, M. S. Gelfand, and T. Eitinger. 2006. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. J. Bacteriol. 188:317-327.
    • (2006) J. Bacteriol. , vol.188 , pp. 317-327
    • Rodionov, D.A.1    Hebbeln, P.2    Gelfand, M.S.3    Eitinger, T.4
  • 36
    • 24944576101 scopus 로고    scopus 로고
    • Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escherichia coli
    • Rowe, J. L., G. L. Starnes, and P. T. Chivers. 2005. Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escherichia coli. J. Bacteriol. 187:6317-6323.
    • (2005) J. Bacteriol. , vol.187 , pp. 6317-6323
    • Rowe, J.L.1    Starnes, G.L.2    Chivers, P.T.3
  • 37
    • 0022376555 scopus 로고
    • Differential expression of hydrogenase isoenzymes in Escherichia coli K-12: Evidence for a third isoenzyme
    • Sawers, R. G., S. P. Ballantine, and D. H. Boxer. 1985. Differential expression of hydrogenase isoenzymes in Escherichia coli K-12: evidence for a third isoenzyme. J. Bacteriol. 164:1324-1331.
    • (1985) J. Bacteriol. , vol.164 , pp. 1324-1331
    • Sawers, R.G.1    Ballantine, S.P.2    Boxer, D.H.3
  • 38
    • 33846627273 scopus 로고    scopus 로고
    • Novel nickel transport mechanism across the bacterial outer membrane energized by the TonB/ExbB/ExbD machinery
    • Schauer, K., B. Gouget, M. Carriere, A. Labigne, and H. de Reuse. 2007. Novel nickel transport mechanism across the bacterial outer membrane energized by the TonB/ExbB/ExbD machinery. Mol. Microbiol. 63:1054-1068.
    • (2007) Mol. Microbiol. , vol.63 , pp. 1054-1068
    • Schauer, K.1    Gouget, B.2    Carriere, M.3    Labigne, A.4    De Reuse, H.5
  • 40
    • 33748773334 scopus 로고    scopus 로고
    • NikR-operator complex structure and the mechanism of repressor activation by metal ions
    • Schreiter, E. R., S. C. Wang, D. B. Zamble, and C. L. Drennan. 2006. NikR-operator complex structure and the mechanism of repressor activation by metal ions. Proc. Natl. Acad. Sci. U. S. A. 103:13676-13681.
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 13676-13681
    • Schreiter, E.R.1    Wang, S.C.2    Zamble, D.B.3    Drennan, C.L.4
  • 41
    • 47049094874 scopus 로고    scopus 로고
    • Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation
    • Shelobolina, E. S., H. A. Vrionis, R. H. Findlay, and D. R. Lovley. 2008. Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation. Int. J. Syst. Evol. Microbiol. 58:1075-1078.
    • (2008) Int. J. Syst. Evol. Microbiol. , vol.58 , pp. 1075-1078
    • Shelobolina, E.S.1    Vrionis, H.A.2    Findlay, R.H.3    Lovley, D.R.4
  • 42
    • 0026641755 scopus 로고
    • Crystal structure of the met repressor- operator complex at 2.8 Å resolution reveals DNA recognition by beta-strands
    • Somers, W. S., and S. E. Phillips. 1992. Crystal structure of the met repressor- operator complex at 2.8 Å resolution reveals DNA recognition by beta-strands. Nature 359:387-393.
    • (1992) Nature , vol.359 , pp. 387-393
    • Somers, W.S.1    Phillips, S.E.2
  • 43
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 45
    • 0030738589 scopus 로고    scopus 로고
    • Alternative respiratory pathways of Escherichia coli: Energetics and transcriptional regulation in response to electron acceptors
    • Unden, G., and J. Bongaerts. 1997. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim. Biophys. Acta 1320:217-234.
    • (1997) Biochim. Biophys. Acta , vol.1320 , pp. 217-234
    • Unden, G.1    Bongaerts, J.2
  • 46
    • 66349125424 scopus 로고    scopus 로고
    • The "metallo-specific" response of proteins: A perspective based on the Escherichia coli transcriptional regulator NikR
    • Wang, S. C., A. V. Dias, and D. B. Zamble. 2009. The "metallo- specific" response of proteins: a perspective based on the Escherichia coli transcriptional regulator NikR. Dalton Trans. 2009:2459-2466.
    • (2009) Dalton Trans. , vol.2009 , pp. 2459-2466
    • Wang, S.C.1    Dias, A.V.2    Zamble, D.B.3
  • 47
    • 0032581662 scopus 로고    scopus 로고
    • Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex
    • White, A., X. Ding, J. C. vanderSpek, J. R. Murphy, and D. Ringe. 1998. Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex. Nature 394:502-506.
    • (1998) Nature , vol.394 , pp. 502-506
    • White, A.1    Ding, X.2    VanderSpek, J.C.3    Murphy, J.R.4    Ringe, D.5
  • 48
    • 33750957661 scopus 로고    scopus 로고
    • Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information
    • Yan, B., C. Nunez, T. Ueki, A. Esteve-Nunez, M. Puljic, R. M. Adkins, B. A. Methe, D. R. Lovley, and J. Krushkal. 2006. Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information. Gene 384:73-95.
    • (2006) Gene , vol.384 , pp. 73-95
    • Yan, B.1    Nunez, C.2    Ueki, T.3    Esteve-Nunez, A.4    Puljic, M.5    Adkins, R.M.6    Methe, B.A.7    Lovley, D.R.8    Krushkal, J.9
  • 49
    • 64849111600 scopus 로고    scopus 로고
    • Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
    • Zhang, Y., D. A. Rodionov, M. S. Gelfand, and V. N. Gladyshev. 2009. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics 10:78.
    • (2009) BMC Genomics , vol.10 , pp. 78
    • Zhang, Y.1    Rodionov, D.A.2    Gelfand, M.S.3    Gladyshev, V.N.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.