Letter | Published:

The PerR transcription factor senses H2O2 by metal-catalysed histidine oxidation

Nature volume 440, pages 363367 (16 March 2006) | Download Citation

Subjects

Abstract

The sensing of reactive oxygen species is essential for cellular responses to oxidative stress1. The sensing of peroxides is typically mediated by redox-active cysteines in sensors such as the bacterial OxyR, OhrR, and Hsp33 proteins2,3. Bacillus subtilis PerR is the prototype for a widespread family of metal-dependent peroxide sensors that regulate inducible peroxide-defence genes4. Here we show that PerR senses peroxides by metal-catalysed oxidation. PerR contains two metal-binding sites: a structural Zn2+ site and a regulatory divalent metal ion site that preferentially binds Fe2+ or Mn2+ (ref. 5). Protein oxidation, catalysed by a bound ferrous ion, leads to the rapid and direct incorporation of one oxygen atom into histidine 37 (H37) or H91, two of the residues that coordinate the bound Fe2+. This mechanism accounts for the ability of PerR to sense low levels of hydrogen peroxide in vivo. The reduction of hydrogen peroxide by metal ions to generate highly reactive hydroxyl radicals underlies the genotoxic effects of peroxides1, and has been shown to contribute to enzyme inactivation, but has not previously been shown to provide a regulatory mechanism for peroxide sensing.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    Pathways of oxidative damage. Annu. Rev. Microbiol. 57, 395–418 (2003)

  2. 2.

    & Exploiting thiol modifications. PLoS Biol. 2, e400 (2004)

  3. 3.

    , , & Microbial H2O2 sensors as archetypical redox signaling modules. Trends Biochem. Sci. 29, 351–357 (2004)

  4. 4.

    & Regulation of inducible peroxide stress responses. Mol. Microbiol. 45, 9–15 (2002)

  5. 5.

    & Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA. Mol. Microbiol. 41, 849–859 (2001)

  6. 6.

    et al. The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors. J. Bacteriol. 185, 243–253 (2003)

  7. 7.

    , , & Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible. J. Bacteriol. 184, 3276–3286 (2002)

  8. 8.

    The role of cysteine residues as redox-sensitive regulatory switches. Curr. Opin. Struct. Biol. 14, 679–686 (2004)

  9. 9.

    , , , & H2O2-sensitive Fur-like repressor CatR regulating the major catalase gene in Streptomyces coelicolor. J. Biol. Chem. 275, 38254–38260 (2000)

  10. 10.

    , & Amino acid residues involved in reversible thiol formation and zinc ion binding in the Streptomyces reticuli redox regulator FurS. Mol. Genet. Genomics 268, 618–627 (2003)

  11. 11.

    et al. Architecture of a protein central to iron homeostasis: crystal structure and spectroscopic analysis of the ferric uptake regulator. Mol. Microbiol. 47, 903–915 (2003)

  12. 12.

    , & Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions. Proc. Natl Acad. Sci. USA 92, 8190–8194 (1995)

  13. 13.

    et al. Redox regulation of OxyR requires specific disulfide bond formation involving a rapid kinetic reaction path. Nat. Struct. Mol. Biol. 11, 1179–1185 (2004)

  14. 14.

    & Identification of oxidized histidine generated at the active site of Cu,Zn-superoxide dismutase exposed to H2O2. Selective generation of 2-oxo-histidine at the histidine 118. J. Biol. Chem. 269, 2405–2410 (1994)

  15. 15.

    & 2-Oxo-histidine as a novel biological marker for oxidatively modified proteins. FEBS Lett. 332, 208–210 (1993)

  16. 16.

    Mechanisms of metal-catalyzed oxidation of histidine to 2-oxo-histidine in peptides and proteins. J. Pharm. Biomed. Anal. 21, 1093–1097 (2000)

  17. 17.

    , , , & A new look at a time-worn system: oxidation of CuZn-SOD by H2O2. Free Radic. Biol. Med. 26, 905–918 (1999)

  18. 18.

    et al. A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli Ada. Mol. Cell 20, 117–129 (2005)

  19. 19.

    et al. Crystal structure of LexA: a conformational switch for regulation of self-cleavage. Cell 106, 585–594 (2001)

  20. 20.

    , & Mitochondria, oxidants, and aging. Cell 120, 483–495 (2005)

  21. 21.

    Role of oxidative carbonylation in protein quality control and senescence. EMBO J. 24, 1311–1317 (2005)

  22. 22.

    et al. Lifespan and mitochondrial control of neurodegeneration. Nature Genet. 36, 1153–1158 (2004)

  23. 23.

    & Cu(II)-catalyzed oxidation of beta-amyloid peptide targets His13 and His14 over His6: Detection of 2-Oxo-histidine by HPLC-MS/MS. Chem. Res. Toxicol. 15, 717–722 (2002)

  24. 24.

    , , , & Antioxidant activity of Ferrozine-iron-amino acid complexes. Proc. Natl Acad. Sci. USA 98, 451–456 (2001)

  25. 25.

    , & Construction and application of epitope- and green fluorescent protein-tagging integration vectors for Bacillus subtilis. Appl. Environ. Microbiol. 68, 2624–2628 (2002)

  26. 26.

    , & Plasmids for ectopic integration in Bacillus subtilis. Gene 180, 57–61 (1996)

  27. 27.

    , , & SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 31, 3381–3385 (2003)

Download references

Acknowledgements

We thank M. Fuangthong and S. Soonsanga for their initial analyses of functionally altered perR variants, E. Madsen for help with the anaerobic experiments, S. Zhang and R. Sherwood for assistance with mass spectrometry, and G. Storz, P. Kiley, J. Imlay, and C. M. Moore for comments. This work was supported by grants from the NSF and NIH. Author Contributions: J.-W.L. performed all experimental work, J.-W.L. and J.D.H. analysed results and co-wrote the paper.

Author information

Affiliations

  1. Department of Microbiology, Cornell University, Ithaca, New York 14853, USA

    • Jin-Won Lee
    •  & John D. Helmann

Authors

  1. Search for Jin-Won Lee in:

  2. Search for John D. Helmann in:

Competing interests

Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Corresponding author

Correspondence to John D. Helmann.

Supplementary information

PDF files

  1. 1.

    Supplementary Figures

    This file contains Supplementary Figures 1–8 and their legends.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature04537

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.