Catalysis and Gene Regulation

Part of the Biological Magnetic Resonance book series (BIMR, volume 29)


This chapter deals with the border territory between protein and molecular biology. Nature has found use for the “corpse” of an enzyme that normally deals with energy transformation, for directing mRNA use in the cytoplasm: the iron-regulatory protein “IRP,” which simply is cytoplasmic aconitase without the main constituent of its active site, the [4Fe–4S] cluster. The remaining protein, now known as “IRP1,” shows affinity for up to ten mRNAs in animal cells. The first mRNA discovered to be targets for IRP1 binding were the two subunits of the iron storage protein ferritin and the mRNA encoding transferrin receptor 1 (TfR1), required for iron uptake by most animal cells. When the supply of iron is adequate, IRP1 is converted to c-aconitase and any excess iron can be stored in ferritin while uptake of iron by TfR1 is diminished; when however, the iron supply declines, the cluster in c-aconitase is disassembled and IRP1 now binds to ferritin and TfR mRNA, which decreases iron storage and increases cellular iron uptake. In what follows, we will provide more of the background on which the described processes are made possible. We then proceed to illustrate related control systems, such as the global microbial control system, based on the FNR protein, in which again a sensitive Fe–S cluster is the active control device. The cluster of FNR decays from the [4Fe–4S] to the [2Fe–2S] state in the presence of oxygen, which provides the signal for microbes to switch from using oxygen as oxidant to compounds such as fumarate and nitrate as, albeit less effective, oxidizing agents. Related systems, based on the sensitivity of Fe–S clusters, are also mentioned. The use of EPR in analysis of these regulatory systems will be referred to when relevant. The application of electron paramagnetic resonance (EPR) to analyzing regulatory proteins is based on the observation of EPR signals from the various cluster types containing [2Fe–2S], [3Fe–4S], or [4Fe–4S] and eventually superclusters, such as those occurring in nitrogen-fixing systems. The signals are found for the one-electron reduced states with [2Fe–2S] and [4Fe–4S] clusters and for the oxidized form of the [3Fe–4S] cluster and of highpotential Fe–S proteins.


Electron Paramagnetic Resonance Dinitrosyl Iron Dinitrosyl Iron Complex Cellular Iron Uptake Iron Storage Protein Ferritin 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Rouault TA, Stout CD, Kaptain S, Harford JB, Klausner RD. 1991. Structural relationship between an iron-regulated RNA-binding protein (IRE–BP) and aconitase: functional implications. Cell 64(5):881–883.CrossRefPubMedGoogle Scholar
  2. 2.
    Hentze MW, Argos P. 1991. Homology between IRE–BP, a regulatory RNA-binding protein, aconitase, and isopropylmalate isomerase. Nucleic Acids Res 19(8):1739–1740.CrossRefPubMedGoogle Scholar
  3. 3.
    Beinert H, Kennedy MC, Stout CD. 1996. Aconitase as iron–sulfur protein, enzyme, and iron-regulatory protein. Chem Rev 96(7):2335–2374.CrossRefPubMedGoogle Scholar
  4. 4.
    Dupuy J, Volbeda A, Carpentier P, Darnault C, Moulis JM, Fontecilla-Camps JC. 2006. Crystal structure of human iron regulatory protein 1 as cytosolic aconitase. Structure 14(1):129–139.CrossRefPubMedGoogle Scholar
  5. 5.
    Kennedy MC, Antholine WE, Beinert H. 1997. An EPR investigation of the products of the reaction of cytosolic and mitochondrial aconitases with nitric oxide. J Biol Chem 272(33):20340–20347.CrossRefPubMedGoogle Scholar
  6. 6.
    Drapier JC, Hibbs JB, Jr. 1986. Murine cytotoxic activated macrophages inhibit aconitase in tumor cells: inhibition involves the iron-sulfur prosthetic group and is reversible. J Clin Invest 78(3):790–797.CrossRefPubMedGoogle Scholar
  7. 7.
    Drapier JC, Pellat C, Henry Y. 1991. Generation of EPR-detectable nitrosyl-iron complexes in tumor target cells cocultured with activated macrophages. J Biol Chem 266(16):10162–10167.PubMedGoogle Scholar
  8. 8.
    Drapier JC, Hirling H, Wietzerbin J, Kaldy P, Kühn LC. 1993. Biosynthesis of nitric oxide activates iron regulatory factor in macrophages. Embo J 12(9):3643–3649.PubMedGoogle Scholar
  9. 9.
    Weiss G, Goossen B, Doppler W, Fuchs D, Pantopoulos K, Werner-Felmayer G, Wachter H, Hentze MW. 1993. Translational regulation via iron-responsive elements by the nitric oxide/NO-synthase pathway. Embo J 12(9):3643–3649.Google Scholar
  10. 10.
    Castro L, Rodriguez M, Radi R. 1994. Aconitase is readily inactivated by peroxynitrite, but not by its precursor, nitric oxide. J Biol Chem 269(47):29409–29415.PubMedGoogle Scholar
  11. 11.
    Hausladen A, Fridovich I. 1994. Superoxide and peroxynitrite inactivate aconitases, but nitric oxide does not. J Biol Chem 269(47):29405–29408.PubMedGoogle Scholar
  12. 12.
    Soum E, Brazzolotto X, Goussias C, Bouton C, Moulis JM, Mattioli TA, Drapier JC. 2003. Peroxynitrite and nitric oxide differently target the iron–sulfur cluster and amino acid residues of human iron regulatory protein 1. Biochemistry 42(25):7648–7654.CrossRefPubMedGoogle Scholar
  13. 13.
    Soum E, Drapier JC. 2003. Nitric oxide and peroxynitrite promote complete disruption of the [4Fe–4S] cluster of recombinant human iron regulatory protein 1. J Biol Inorg Chem 8(1–2):226–232.PubMedGoogle Scholar
  14. 14.
    Bouton C, Hirling H, Drapier JC. 1997. Redox modulation of iron regulatory proteins by peroxynitrite. J Biol Chem 272(32):19969–19975.CrossRefPubMedGoogle Scholar
  15. 15.
    Cairo G, Ronchi R, Recalcati S, Campanella A, Minotti G. 2002. Nitric oxide and peroxynitrite activate the iron regulatory protein-1 of J774A.1 macrophages by direct disassembly of the Fe–S cluster of cytoplasmic aconitase. Biochemistry 41(23):7435–7442.CrossRefPubMedGoogle Scholar
  16. 16.
    Demple B, Ding H, Jorgensen M. 2002. Escherichia coli SoxR protein: sensor/transducer of oxidative stress and nitric oxide. Methods Enzymol 348:355–364.CrossRefPubMedGoogle Scholar
  17. 17.
    Green J, Scott C, Guest JR. 2001. Functional versatility in the CRP–FNR superfamily of transcription factors: FNR and FLP. Adv Microb Physiol 44:1–34.CrossRefPubMedGoogle Scholar
  18. 18.
    Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR. 2005. Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187(3):1135–1160.CrossRefPubMedGoogle Scholar
  19. 19.
    Kiley PJ, Beinert H. 1998. Oxygen sensing by the global regulator, FNR: the role of the iron–sulfur cluster. FEMS Microbiol Rev 22(5):341–352.CrossRefPubMedGoogle Scholar
  20. 20.
    Kiley PJ, Beinert H. 2003. The role of Fe–S proteins in sensing and regulation in bacteria. Curr Opin Microbiol 6(2):181–185.CrossRefPubMedGoogle Scholar
  21. 21.
    Lazazzera BA, Bates DM, Kiley PJ. 1993. The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state. Genes Dev 7(10):1993–2005.CrossRefPubMedGoogle Scholar
  22. 22.
    Lazazzera BA, Beinert H, Khoroshilova N, Kennedy MC, Kiley PJ. 1996. DNA binding and dimerization of the Fe–S-containing FNR protein from Escherichia coli are regulated by oxygen. J Biol Chem 271(5):2762–2768.CrossRefPubMedGoogle Scholar
  23. 23.
    Moore LJ, Kiley PJ. 2001. Characterization of the dimerization domain in the FNR transcription factor. J Biol Chem 276(49):45744–45750.CrossRefPubMedGoogle Scholar
  24. 24.
    Crack J, Green J, Thomson AJ. 2004. Mechanism of oxygen sensing by the bacterial transcription factor fumarate–nitrate reduction (FNR). J Biol Chem 279(10):9278–9286.CrossRefPubMedGoogle Scholar
  25. 25.
    Green J, Bennett B, Jordan P, Ralph ET, Thomson AJ, Guest JR. 1996. Reconstitution of the [4Fe–4S] cluster in FNR and demonstration of the aerobic–anaerobic transcription switch in vitro. Biochem J 316(Pt 3):887–892.PubMedGoogle Scholar
  26. 26.
    Khoroshilova N, Popescu C, Münck E, Beinert H, Kiley PJ. 1997. Iron–sulfur cluster disassembly in the FNR protein of Escherichia coli by O2: [4Fe–4S] to [2Fe–2S] conversion with loss of biological activity. Proc Natl Acad Sci USA 94(12):6087–6092.CrossRefPubMedGoogle Scholar
  27. 27.
    Popescu CV, Bates DM, Beinert H, Münck E, Kiley PJ. 1998. Mössbauer spectroscopy as a tool for the study of activation/inactivation of the transcription regulator FNR in whole cells of Escherichia coli. Proc Natl Acad Sci USA 95(23):13431–13435.CrossRefGoogle Scholar
  28. 28.
    Sutton VR, Mettert EL, Beinert H, Kiley PJ. 2004. Kinetic analysis of the oxidative conversion of the [4Fe–4S]2+ cluster of FNR to a [2Fe–2S]2+ cluster. J Bacteriol 186(23):8018–8025.CrossRefPubMedGoogle Scholar
  29. 29.
    Mühlenhoff U, Lill R. 2000. Biogenesis of iron–sulfur proteins in eukaryotes: a novel task of mitochondria that is inherited from bacteria. Biochim Biophys Acta 1459(2–3):370–382.PubMedGoogle Scholar
  30. 30.
    Smith AD, Jameson GN, Dos Santos PC, Agar JN, Naik S, Krebs C, Frazzon J, Dean DR, Huynh BH, Johnson MK. 2005. NifS-mediated assembly of [4Fe–4S] clusters in the N- and C-terminal domains of the NifU scaffold protein. Biochemistry 44(39):12955–12969.CrossRefPubMedGoogle Scholar
  31. 31.
    Yoon T, Cowan JA. 2003. Iron–sulfur cluster biosynthesis: characterization of frataxin as an iron donor for assembly of [2Fe–2S] clusters in ISU-type proteins. J Am Chem Soc 125(20):6078–6084.CrossRefPubMedGoogle Scholar
  32. 32.
    Schwartz CJ, Giel JL, Patschkowski T, Luther C, Ruzicka FJ, Beinert H, Kiley PJ. 2001. IscR, an Fe–S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe–S cluster assembly proteins. Proc Natl Acad Sci USA 98(26):14895–14900.CrossRefPubMedGoogle Scholar
  33. 33.
    Nachin L, Loiseau L, Expert D, Barras F. 2003. SufC: an unorthodox cytoplasmic ABC/ATPase required for [Fe–S] biogenesis under oxidative stress. Embo J 22(3):427–437.CrossRefPubMedGoogle Scholar
  34. 34.
    Takahashi Y, Tokumoto U. 2002. A third bacterial system for the assembly of iron–sulfur clusters with homologs in archaea and plastids. J Biol Chem 277(32):28380–28383.CrossRefPubMedGoogle Scholar
  35. 35.
    Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ. 2006. IscR-dependent gene expression links iron–sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli. Mol Microbiol 60(4):1058–1075.CrossRefPubMedGoogle Scholar
  36. 36.
    Woodmansee AN, Imlay JA. 2002. Quantitation of intracellular free iron by electron paramagnetic resonance spectroscopy. Methods Enzymol 349:3–9.CrossRefPubMedGoogle Scholar
  37. 37.
    Yavin E, Boal AK, Stemp ED, Boon EM, Livingston AL, O'Shea VL, David SS, Barton JK. 2005. Protein-DNA charge transport: redox activation of a DNA repair protein by guanine radical. Proc Natl Acad Sci USA 102(10):3546–3551.CrossRefPubMedGoogle Scholar
  38. 38.
    Yavin E, Stemp ED, O'Shea VL, David SS, Barton JK. 2006. Electron trap for DNA-bound repair enzymes: a strategy for DNA-mediated signaling. Proc Natl Acad Sci USA 103(10):3610–3614.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Centre for Magnetic ResonanceThe University of QueenslandSt. LuciaAustralia

Personalised recommendations