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Cited by 24Bacterial Genetics and BiotechnologyRedox biology and oxidative stressHeat shock proteins research

During Oxidative Stress the Clp Proteins of Escherichia coli Ensure that Iron Pools Remain Sufficient To Reactivate Oxidized Metalloenzymes

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Sen, Ananya, Zhou, Yidan, Imlay, James A.·2020·Journal of Bacteriology
DOI 10.1128/jb.00235-20PMC PMC7925084
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Abstract

Hydrogen peroxide mediates the toxicity of phagocytes, lactic acid bacteria, redox-cycling antibiotics, and photochemistry. The underlying mechanisms all involve its reaction with iron atoms, whether in enzymes or on the surface of DNA. Accordingly, when bacteria perceive toxic H 2 O 2 , they activate defensive tactics that are focused on iron metabolism. In this study, we identify a conundrum: DNA is best protected by the removal of iron from the cytoplasm, but this action impairs the ability of the cell to reactivate its iron-dependent enzymes. The actions of the Clp proteins appear to hedge against the oversequestration of iron by the miniferritin Dps. This buffering effect is important, because E. coli seeks not just to survive H 2 O 2 but to grow in its presence.

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  • Mobilization of stored iron pools often requires reduction, or in some cases proteolysis, and occurs on a time-scale of minutes.

    “Mobilization of these stored iron pools often requires reduction,132 or in some cases proteolysis,127,133 and occurs on a time-scale of minutes.”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [133]

    The Results report that ClpXP proteolyzes the iron-storage protein Dps, and the Discussion gives a 10-minute half-life for Dps in unstressed cells (pages unavailable). This supports proteolysis as a possible route to iron mobilization, but the paper does not establish that stored iron is released on a minutes-long timescale; it also does not support reduction as a mobilization mechanism. (LLM, conf=0.83)

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  1. [1]1. Anbar AD. 2008. Elements and evolution. Science 322:1481-1483. https://doi.org/10.1126/science.1163100. · DOI · Paper page
  2. [2]2. Imlay JA. 2013. The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium. Nat Rev Microbiol 11:443-454. https://doi.org/10.1038/nrmicro3032. · DOI
  3. [3]3. Loew O. 1900. A new enzyme of general occurrence in organismis. Science 11:701-702. https://doi.org/10.1126/science.11.279.701. · DOI
  4. [5]5. Carlioz A, Touati D. 1986. Isolation of superoxide dismutase mutants in Escherichia coli : is superoxide dismutase necessary for aerobic life? EMBO J 5:623-630. https://doi.org/10.1002/j.1460-2075.1986.tb04256.x. · DOI
  5. [8]8. Jang S, Imlay JA. 2007. Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron-sulfur enzymes. J Biol Chem 282:929-937. https://doi.org/10.1074/jbc.M607646200. · DOI
  6. [10]10. Sobota JM, Gu M, Imlay JA. 2014. Intracellular hydrogen peroxide and superoxide poison 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase, the first committed enzyme in the aromatic biosynthetic pathway of Escherichia coli . J Bacteriol 196:1980-1991. https://doi.org/10.1128/JB .01573-14. · DOI
  7. [11]11. Anjem A, Imlay JA. 2012. Mononuclear iron enzymes are primary targets of hydrogen peroxide stress. J Biol Chem 287:15544-15556. https://doi .org/10.1074/jbc.M111.330365. · DOI
  8. [13]13. Korshunov SS, Imlay JA. 2002. A potential role for periplasmic superoxide dismutase in blocking the penetration of external superoxide into the cytosol of phagocytosed bacteria. Mol Microbiol 43:95-106. https://doi .org/10.1046/j.1365-2958.2002.02719.x. · DOI
  9. [14]14. Seaver LC, Imlay JA. 2001. Hydrogen peroxide fluxes and compartmentalization inside growing Escherichia coli . J Bacteriol 183:7182-7189. https://doi.org/10.1128/JB.183.24.7182-7189.2001. · DOI
  10. [15]15. Keyer K, Imlay JA. 1996. Superoxide accelerates DNA damage by elevating free-iron levels. Proc Natl Acad Sci U S A 93:13635-13640. https:// doi.org/10.1073/pnas.93.24.13635. · DOI · Paper page
  11. [16]16. Liu Y, Bauer SC, Imlay JA. 2011. The YaaA protein of the Escherichia coli OxyR regulon lessens hydrogen peroxide toxicity by diminishing the amount of intracellular unincorporated iron. J Bacteriol 193:2186-2196. https://doi.org/10.1128/JB.00001-11. · DOI
  12. [17]17. Woodmansee AL, Imlay JA. 2002. Quantitation of intracellular free iron by electron paramagnetic resonance spectroscopy. Methods Enzymol 349:3-9. https://doi.org/10.1016/s0076-6879(02)49316-0. · DOI
  13. [19]19. Demple B, Halbrook J, Linn S. 1983. Escherichia coli xth mutants are hypersensitive to hydrogen peroxide. J Bacteriol 153:1079-1082. https:// doi.org/10.1128/JB.153.2.1079-1082.1983. · DOI
  14. [20]20. Carlsson J, Carpenter VS. 1980. The recA + gene product is more important that catalase and superoxide dismutase in protecting Escherichia coli against hydrogen peroxide toxicity. J Bacteriol 142:319-321. https:// doi.org/10.1128/JB.142.1.319-321.1980. · DOI
  15. [21]21. Zheng M, Aslund F, Storz G. 1998. Activation of the OxyR transcription factor by reversible disulfide bond formation. Science 279:1718-1721. https://doi.org/10.1126/science.279.5357.1718. · DOI
  16. [23]23. Altuvia S, Almiron M, Huisman G, Kolter R, Storz G. 1994. The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. Mol Microbiol 13:265-272. https://doi.org/10.1111/j .1365-2958.1994.tb00421.x. · DOI
  17. [24]24. Grant RA, Filman DJ, Finkel SE, Kolter R, Hogle JM. 1998. The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat Struct Biol 5:294-303. https://doi.org/10.1038/nsb0498-294. · DOI
  18. [25]25. Ilari A, Ceci P, Ferrari D, Rossi G, Chiancone E. 2002. Iron incorporation into E. coli Dps gives rise to a ferritin-like microcrystalline core. J Biol Chem 277:37619-37623. https://doi.org/10.1074/jbc.M206186200. · DOI
  19. [26]26. Park S, You X, Imlay JA. 2005. Substantial DNA damage from submicromolar intracellular hydrogen peroxide detected in Hpx -mutants of Escherichia coli . Proc Natl Acad Sci U S A 102:9317-9322. https://doi.org/ 10.1073/pnas.0502051102. · DOI
  20. [27]27. Zheng M, Doan B, Schneider TD, Storz G. 1999. OxyR and SoxRS regulation of fur . J Bacteriol 181:4639-4643. https://doi.org/10.1128/JB.181 .15.4639-4643.1999. · DOI
  21. [29]29. Kehres DG, Janakiraman A, Slauch JM, Maguire ME. 2002. Regulation of Salmonella enterica serovar Typhimurium mntH transcription by H 2 O2, Fe 2 + , and Mn 2 + . J Bacteriol 184:3151-3158. https://doi.org/10.1128/jb .184.12.3151-3158.2002. · DOI
  22. [30]30. Lee JH, Yeo WS, Roe JH. 2004. Induction of the sufA operon encoding Fe-S assembly proteins by superoxide generators and hydrogen peroxide: involvement of OxyR, IHF and an unidentified oxidantresponsive factor. Mol Microbiol 51:1745-1755. https://doi.org/10.1111/ j.1365-2958.2003.03946.x.
  23. [31]31. Jang S, Imlay JA. 2010. Hydrogen peroxide inactivates the Escherichia coli Isc iron-sulphur assembly system, and OxyR induces the Suf system to compensate. Mol Microbiol 78:1448-1467. https://doi.org/10.1111/j .1365-2958.2010.07418.x. · DOI
  24. [32]32. Mancini S, Imlay JA. 2015. The induction of two biosynthetic enzymes helps Escherichia coli sustain heme synthesis and activate catalase during hydrogen peroxide stress. Mol Microbiol 96:744-763. https://doi .org/10.1111/mmi.12967. · DOI · Paper page
  25. [33]33. Dougan DA, Reid BG, Horwich AL, Bukau B. 2002. ClpS, a substrate modulator of the ClpAP machine. Mol Cell 9:673-683. https://doi.org/ 10.1016/s1097-2765(02)00485-9. · DOI
  26. [34]34. Sauer RT, Bolon DN, Burton BM, Burton RE, Flynn JM, Grant RA, Hersch GL, Joshi SA, Kenniston JA, Levchenko I, Neher SB, Oakes ES, Siddiqui SM, Wah DA, Baker TA. 2004. Sculpting the proteome with AAA( + ) proteases and disassembly machines. Cell 119:9-18. https://doi.org/10.1016/j.cell .2004.09.020. · DOI
  27. [35]35. Hoskins JR, Kim SY, Wickner S. 2000. Substrate recognition by the ClpA chaperone component of ClpAP protease. J Biol Chem 275: 35361-35367. https://doi.org/10.1074/jbc.M006288200. · DOI
  28. [36]36. Hoskins JR, Wickner S. 2006. Two peptide sequences can function cooperatively to facilitate binding and unfolding by ClpA and degradation by ClpAP. Proc Natl Acad Sci U S A 103:909-914. https://doi.org/10.1073/ pnas.0509154103.
  29. [37]37. Mhammedi-Alaoui A, Pato M, Gama MJ, Toussaint A. 1994. A new component of bacteriophage Mu replicative transposition machinery: the Escherichia coli ClpX protein. Mol Microbiol 11:1109-1116. https:// doi.org/10.1111/j.1365-2958.1994.tb00387.x. · DOI
  30. [38]38. Wawrzynow A, Wojtkowiak D, Marszalek J, Banecki B, Jonsen M, Graves B, Georgopoulos C, Zylicz M. 1995. The ClpX heat-shock protein of Escherichia coli , the ATP-dependent substrate specificity component of the ClpP-ClpX protease, is a novel molecular chaperone. EMBO J 14: 1867-1877. https://doi.org/10.1002/j.1460-2075.1995.tb07179.x. · DOI
  31. [39]39. Wickner S, Gottesman S, Skowyra D, Hoskins J, McKenney K, Maurizi MR. 1994. A molecular chaperone, ClpA, functions like DnaK and DnaJ. Proc Natl Acad Sci U S A 91:12218-12222. https://doi.org/10.1073/pnas.91.25 .12218. · DOI
  32. [40]40. Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G. 2001. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol 183:4562-4570. https://doi .org/10.1128/JB.183.15.4562-4570.2001. · DOI
  33. [41]41. Zheng M, Wang X, Doan B, Lewis KA, Schneider TD, Storz G. 2001. Computation-directed identification of OxyR DNA binding sites in Escherichia coli . J Bacteriol 183:4571-4579. https://doi.org/10.1128/JB.183.15 .4571-4579.2001. · DOI
  34. [43]43. Winterbourn CC, Hampton MB, Livesey JH, Kettle AJ. 2006. Modeling the reactions of superoxide and myeloperoxidase in the neutrophil phagosome. Implications for microbial killing. J Biol Chem 281:39860-39869. https://doi.org/10.1074/jbc.M605898200. · DOI
  35. [44]44. Slauch JM. 2011. How does the oxidative burst of macrophages kill bacteria? Mol Microbiol 80:580-583. https://doi.org/10.1111/j.1365-2958 .2011.07612.x. · DOI
  36. [45]45. Li G-W, Burkhardt D, Gross C, Weissman JS. 2014. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157:624-635. https://doi.org/10.1016/j.cell.2014.02.033. · DOI
  37. [46]46. Park S, Imlay JA. 2003. High levels of intracellular cysteine promote oxidative DNA damage by driving the Fenton reaction. J Bacteriol 185:1942-1950. https://doi.org/10.1128/JB.185.6.1942-1950.2003. · DOI
  38. [47]47. Zhao G, Ceci P, Ilari A, Giangiacomo L, Laue TM, Chiancone E, Chasteen ND. 2002. Iron and hydrogen peroxide detoxification properties of DNA-binding protein from starved cells. A ferritin-like DNA-binding protein of Escherichia coli . J Biol Chem 277:27689-27696. https://doi .org/10.1074/jbc.M202094200. · DOI
  39. [48]48. Martinez A, Kolter R. 1997. Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps. J Bacteriol 179:5188-5194. https://doi.org/10.1128/jb.179.16.5188-5194.1997. · DOI
  40. [49]49. Anjem A, Varghese S, Imlay JA. 2009. Manganese import is a key element of the OxyR response to hydrogen peroxide in Escherichia coli . Mol Microbiol 72:844-858. https://doi.org/10.1111/j.1365-2958.2009.06699.x. · DOI · Paper page
  41. [50]50. Stephani K, Weichart D, Hengge R. 2003. Dynamic control of Dps protein levels by ClpXP and ClpAP proteases in Escherichia coli . Mol Microbiol 49:1605-1614. https://doi.org/10.1046/j.1365-2958.2003.03644.x. · DOI
  42. [51]51. Martin JE, Waters LS, Storz G, Imlay JA. 2015. The Escherichia coli small protein MntS and exporter MntP optimize the intracellular concentration of manganese. PLoS Genet 11:e1004977. https://doi.org/10.1371/journal .pgen.1004977. · DOI
  43. [52]52. Li X, Imlay JA. 2018. Improved measurements of scant hydrogen peroxide enable experiments that define its threshold of toxicity for Escherichia coli . Free Radic Biol Med 120:217-227. https://doi.org/10.1016/j .freeradbiomed.2018.03.025. · DOI
  44. [53]53. Chen L, Helmann JD. 1995. Bacillus subtilis MrgA is a Dps (PexB) homologue: evidence for metalloregulation of an oxidative-stress gene. Mol Microbiol 18:295-300. https://doi.org/10.1111/j.1365-2958.1995.mmi\_18020295.x. · DOI
  45. [54]54. Ezraty B, Henry C, Herisse M, Denamur E, Barras F. 2014. Commercial lysogeny broth culture media and oxidative stress: a cautious tale. Free Radic Biol Med 74:245-251. https://doi.org/10.1016/j.freeradbiomed .2014.07.010. · DOI
  46. [55]55. Khademian M, Imlay JA. 2017. Escherichia coli cytochrome c peroxidase is a respiratory oxidase that enables the use of hydrogen peroxide as a terminal electron acceptor. Proc Natl Acad Sci U S A 114:E6922-E6931. https://doi.org/10.1073/pnas.1701587114. · DOI
  47. [56]56. Rocha AG, Dancis A. 2016. Life without Fe-S clusters. Mol Microbiol 99:821-826. https://doi.org/10.1111/mmi.13273. · DOI
  48. [57]57. Outten FW, Djaman O, Storz G. 2004. A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli . Mol Microbiol 52:861-872. https://doi.org/10.1111/j.1365-2958.2004.04025.x. · DOI
  49. [58]58. Maringanti S, Imlay JA. 1999. An intracellular iron chelator pleiotropically suppresses enzymatic and growth defects of superoxide dismutasedeficient Escherichia coli . J Bacteriol 181:3792-3802. https://doi.org/10 .1128/JB.181.12.3792-3802.1999.
  50. [59]59. Higashitani A, Ishii Y, Kato Y, Koriuchi K. 1997. Functional dissection of a cell-division inhibitor, SulA, of Escherichia coli and its negative regulation by Lon. Mol Gen Genet 254:351-357. https://doi.org/10 .1007/s004380050426.
  51. [60]60. Frank EG, Ennis DG, Gonzalez M, Levine AS, Woodgate R. 1996. Regulation of SOS mutagenesis by proteolysis. Proc Natl Acad Sci U S A 93:10291-10296. https://doi.org/10.1073/pnas.93.19.10291. · DOI
  52. [61]61. Griffith KL, Shah IM, Wolf RE, Jr. 2004. Proteolytic degradation of Escherichia coli transcription activators Sox and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons. Mol Microbiol 51:1801-1816. https://doi .org/10.1046/j.1365-2958.2003.03952.x. · DOI
  53. [62]62. Flynn JM, Neher SB, Kim Y-I, Sauer RT, Baker TA. 2003. Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol Cell 11:671-683. https://doi.org/10 .1016/s1097-2765(03)00060-1.
  54. [63]63. Ninnis RL, Spall SK, Talbo GH, Truscott KN, Dougan DA. 2009. Modification of PATase by L/F-transferase generates a ClpS-dependent N-end rule substrate in Escherichia coli . EMBO J 28:1732-1744. https://doi.org/ 10.1038/emboj.2009.134. · DOI
  55. [64]64. Schmidt R, Zahn R, Bukau B, Mogk A. 2009. ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway. Mol Microbiol 72:506-517. https://doi.org/10.1111/j.1365-2958.2009 .06666.x. · DOI
  56. [65]65. LaBreck CJ, May S, Viola MG, Conti J, Camberg JL. 2017. The protein chaperon ClpX targets native and non-native aggregated substrates for remodeling, disassembly, and degradation with ClpP. Front Mol Biosci 4:1-13. https://doi.org/10.3389/fmolb.2017.00026. · DOI
  57. [66]66. Chai SC, Wang WL, Ye ZQ. 2008. Fe(II) is the native cofactor for Escherichia coli methionine aminopeptidase. J Biol Chem 283:26879-26885. https://doi.org/10.1074/jbc.M804345200. · DOI
  58. [68]68. Datsenko KA, Wanner BL. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640-6645. https://doi.org/10.1073/pnas.120163297. · DOI
  59. [70]70. Haldimann A, Wanner BL. 2001. Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J Bacteriol 183:6384-6393. https://doi.org/10.1128/ JB.183.21.6384-6393.2001.
  60. [71]71. Kohlhaw GB. 1988. Isopropylmalate dehydratase from yeast. Methods Enzymol 166:423-429. https://doi.org/10.1016/s0076-6879(88)66055-1. · DOI
  61. [72]72. Messner KR, Imlay JA. 2002. In vitro quantitation of biological superoxide and hydrogen peroxide generation. Methods Enzymol 349:354-361. https://doi.org/10.1016/s0076-6879(02)49351-2. · DOI

Cited by

Sorted by citations

Authors
Sen, A., Zhou, Y., & Imlay, J. A.
Affiliations
University of Illinois Urbana-Champaign (US)
ORCID
Venue
Journal of Bacteriology
Publisher
American Society for Microbiology
Published
2020-08-25
Volume
202
Issue
18
ISSN
  • 0021-9193 (ISSN-L)
  • 1098-5530
DOI
10.1128/jb.00235-20
PMC
PMC7925084
OpenAlex
W3037177471
Cited by
24
References
4
Citations by year
2026: 2 · 2025: 5 · 2024: 3 · 2023: 6 · 2022: 4 · 2021: 4
FWCI
2.05
Type
journal article
Language
en
Open access
Licence
journals.asm.org/non-commercial-tdm-license (tdm)
Locations
  • Journal of Bacteriology (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Institutes of Health (GM49640)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Redox biology and oxidative stress
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Heat shock proteins research
Keywords
Clp protease, oxidative stress, hydrogen peroxide, iron metabolism, iron sequestration, DNA protection, Escherichia coli, oxidative stress resistance
MeSH terms
Carrier Proteins, Escherichia coli, Hydrogen Peroxide, Iron, Metalloproteins, Oxidative Stress, Escherichia coli Proteins, Endopeptidase Clp

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