1887

Abstract

The gene from HB8 encodes an orthologue of the copper-sensing transcriptional repressor CsoR. X-ray crystal structure analysis of . CsoR indicated that it forms a homotetramer. The structures of the CsoR monomer and dimer are similar to those of CsoR. In the absence of copper ions, . CsoR bound to the promoter region of the copper-sensitive operon --, which encodes the copper chaperone CopZ, CsoR and the copper efflux P-type ATPase CopA, to repress their expression, while in the presence of approximately an equal amount of copper ion, CsoR was released from the DNA, to allow expression of the downstream genes. Both Cu(II) and Cu(I) ions could bind CsoR, and were effective for transcriptional derepression. Additionally, CsoR could also sense various other metal ions, such as Zn(II), Ag(I), Cd(II) and Ni(II), which led to transcriptional derepression. The copper-binding motif of . CsoR contains C-H-H, while those of most orthologues contain C-H-C. The X-ray crystal structure of . CsoR suggests that a histidine residue in the N-terminal domain is also involved in metal-ion binding; that is, the binding motif could be H-C-H-H, like that of RcnR, which binds Ni(II)/Co(II). The non-conserved H70 residue in the metal-binding motif of . CsoR is important for its DNA-binding affinity and metal-ion responsiveness.

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2010-07-01
2020-07-12
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References

  1. Agari Y., Kashihara A., Yokoyama S., Kuramitsu S., Shinkai A.. 2008; Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator. Mol Microbiol70:60–75
    [Google Scholar]
  2. Blackwell L. J., Wang S., Modrich P.. 2001; DNA chain length dependence of formation and dynamics of hMutS α.hMutL α.heteroduplex complexes. J Biol Chem276:33233–33240
    [Google Scholar]
  3. Bolstad B. M., Irizarry R. A., Astrand M., Speed T. P.. 2003; A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics19:185–193
    [Google Scholar]
  4. Brünger A. T., Adams P. D., Clore G. M., DeLano W. L., Gros P., Grosse-Kunstleve R. W., Jiang J. S., Kuszewski J., Nilges M.. other authors 1998; Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr54:905–921
    [Google Scholar]
  5. Cawley S., Bekiranov S., Ng H. H., Kapranov P., Sekinger E. A., Kampa D., Piccolboni A., Sementchenko V., Cheng J.. other authors 2004; Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell116:499–509
    [Google Scholar]
  6. Collaborative Computational Project, Number 4 1994; The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr50:760–763
    [Google Scholar]
  7. Emsley P., Cowtan K.. 2004; Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr60:2126–2132
    [Google Scholar]
  8. Ferraroni M., Myasoedova N. M., Schmatchenko V., Leontievsky A. A., Golovleva L. A., Scozzafava A., Briganti F.. 2007; Crystal structure of a blue laccase from Lentinus tigrinus: evidences for intermediates in the molecular oxygen reductive splitting by multicopper oxidases. BMC Struct Biol7:60
    [Google Scholar]
  9. Gentleman R. C., Carey V. J., Bates D. M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y.. other authors 2004; Bioconductor: open software development for computational biology and bioinformatics. Genome Biol5:R80
    [Google Scholar]
  10. Gouet P., Robert X., Courcelle E.. 2003; ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res31:3320–3323
    [Google Scholar]
  11. Hashimoto Y., Yano T., Kuramitsu S., Kagamiyama H.. 2001; Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker. FEBS Lett506:231–234
    [Google Scholar]
  12. Holm L., Sander C.. 1998; Touring protein fold space with Dali/FSSP. Nucleic Acids Res26:316–319
    [Google Scholar]
  13. Hoseki J., Yano T., Koyama Y., Kuramitsu S., Kagamiyama H.. 1999; Directed evolution of thermostable kanamycin-resistance gene: a convenient selection marker for Thermus thermophilus. J Biochem126:951–956
    [Google Scholar]
  14. Imlay J. A.. 2002; How oxygen damages microbes: oxygen tolerance and obligate anaerobiosis. Adv Microb Physiol46:111–153
    [Google Scholar]
  15. Iwig J. S., Chivers P. T.. 2009; DNA recognition and wrapping by Escherichia coli RcnR. J Mol Biol393:514–526
    [Google Scholar]
  16. Iwig J. S., Rowe J. L., Chivers P. T.. 2006; Nickel homeostasis in Escherichia coli – the rcnR- rcnA efflux pathway and its linkage to NikR function. Mol Microbiol62:252–262
    [Google Scholar]
  17. Iwig J. S., Leitch S., Herbst R. W., Maroney M. J., Chivers P. T.. 2008; Ni(II) and Co(II) sensing by Escherichia coli RcnR. J Am Chem Soc130:7592–7606
    [Google Scholar]
  18. Kabsch W., Sander C.. 1983; Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers22:2577–2637
    [Google Scholar]
  19. Kondo N., Nishikubo T., Wakamatsu T., Ishikawa H., Nakagawa N., Kuramitsu S., Masui R.. 2008; Insights into different dependence of dNTP triphosphohydrolase on metal ion species from intracellular ion concentrations in Thermus thermophilus. Extremophiles12:217–223
    [Google Scholar]
  20. Krissinel E., Henrick K.. 2007; Inference of macromolecular assemblies from crystalline state. J Mol Biol372:774–797
    [Google Scholar]
  21. Kuramitsu S., Hiromi K., Hayashi H., Morino Y., Kagamiyama H.. 1990; Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity. Biochemistry29:5469–5476
    [Google Scholar]
  22. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A.. other authors 2007; clustal w and clustal x version 2.0. Bioinformatics23:2947–2948
    [Google Scholar]
  23. Laskowski R. A., McArthur M. W., Moss D. S., Thornton J. M.. 1993; PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst26:283–291
    [Google Scholar]
  24. LeMaster D. M., Richards F. M.. 1985; 1H-15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry24:7263–7268
    [Google Scholar]
  25. Liu T., Ramesh A., Ma Z., Ward S. K., Zhang L., George G. N., Talaat A. M., Sacchettini J. C., Giedroc D. P.. 2007; CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator. Nat Chem Biol3:60–68
    [Google Scholar]
  26. Lovell S. C., Davis I. W., Arendall W. B. III, de Bakker P. I., Word J. M., Prisant M. G., Richardson J. S., Richardson D. C.. 2003; Structure validation by C α geometry: φ, ψ and C β deviation. Proteins50:437–450
    [Google Scholar]
  27. Ma Z., Cowart D. M., Scott R. A., Giedroc D. P.. 2009a; Molecular insights into the metal selectivity of the copper(I)-sensing repressor CsoR from Bacillus subtilis. Biochemistry48:3325–3334
    [Google Scholar]
  28. Ma Z., Jacobsen F. E., Giedroc D. P.. 2009b; Coordination chemistry of bacterial metal transport and sensing. Chem Rev109:4644–4681
    [Google Scholar]
  29. Oshima T., Imahori K.. 1974; Description of Thermus thermophilus (Yoshida and Oshima) com. nov., a non-sporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol24:102–112
    [Google Scholar]
  30. Otwinowski Z., Minor W.. 1997; Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol276:307–326
    [Google Scholar]
  31. Perrakis A., Harkiolaki M., Wilson K. S., Lamzin V. S.. 2001; ARP/wARP and molecular replacement. Acta Crystallogr D Biol Crystallogr57:1445–1450
    [Google Scholar]
  32. Sanger F., Nicklen S., Coulson A. R.. 1977; DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A74:5463–5467
    [Google Scholar]
  33. Shinkai A., Ohbayashi N., Terada T., Shirouzu M., Kuramitsu S., Yokoyama S.. 2007; Identification of promoters recognized by RNA polymerase- σE holoenzyme from Thermus thermophilus HB8. J Bacteriol189:8758–8764
    [Google Scholar]
  34. Smaldone G. T., Helmann J. D.. 2007; CsoR regulates the copper efflux operon copZA in Bacillus subtilis. Microbiology153:4123–4128
    [Google Scholar]
  35. Storey J. D., Tibshirani R.. 2003; Statistical significance for genomewide studies. Proc Natl Acad Sci U S A100:9440–9445
    [Google Scholar]
  36. Terwilliger T. C., Berendzen J.. 1999; Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr55:849–861
    [Google Scholar]
  37. Touati D.. 2000; Iron and oxidative stress in bacteria. Arch Biochem Biophys373:1–6
    [Google Scholar]
  38. Vassylyeva M. N., Lee J., Sekine S. I., Laptenko O., Kuramitsu S., Shibata T., Inoue Y., Borukhov S., Vassylyev D. G., Yokoyama S.. 2002; Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr58:1497–1500
    [Google Scholar]
  39. Yokoyama S., Hirota H., Kigawa T., Yabuki T., Shirouzu M., Terada T., Ito Y., Matsuo Y., Kuroda Y.. other authors 2000; Structural genomics projects in Japan. Nat Struct Biol7:Suppl.943–945
    [Google Scholar]
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