Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Building Fe–S proteins: bacterial strategies

Nature Reviews Microbiology volume 8, pages 436–446 (2010)Cite this article

Subjects

Key Points

  • Fe–S clusters are among the most conserved cofactors in prokaryotes and eukaryotes. Fe–S proteins participate in a wide array of cellular processes, from metabolism to gene regulation and DNA replication.

  • Fe–S clusters are highly unstable and, upon destabilization, they can lead to oxidative stress via Fenton chemistry. Dedicated systems have therefore evolved for building, protecting and inserting these clusters into apoproteins.

  • The components required for Fe–S cluster biogenesis have been identified in the model systems Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana and exhibit structural and functional homologies. They constitute the so-called Fe–S cluster (Isc) and sulphur mobilization (Suf) systems. In eukaryotes, the Isc system is located in the mitochondria and the Suf system in chloroplasts. E. coli also has both systems.

  • Both in vitro and in vivo analyses have revealed that Fe–S biogenesis comprises two steps: a 'building' step, during which iron and sulphur are collected and assembled into a cluster, and a 'delivery' step, during which the cluster is transported to the apoprotein targets.

  • The origin of the sulphur is L-cysteine, and the way in which cysteine desulphurase mobilizes sulphur for Fe–S cluster formation is well understood. The origin of the iron remains unclear, and several sources are likely to be used.

  • A key step in Fe–S cluster biogenesis is catalysed by a scaffold protein, which can accept both iron and sulphur, allowing them to form a cluster that is eventually transferred either to downstream components in the Fe–S cluster biogenesis process or, under certain conditions, directly to apoproteins.

  • In vivo approaches have revealed the existence of a complex trafficking step, in which ready-made clusters can use different routes to reach their final targets. So-called A-type transporters (ATC) are required for this step.

  • Genetic studies in E. coli allowed the existence of seemingly redundant ATCs to be rationalized: environmental conditions, gene regulation and preferential partnerships seem to control the route that a cluster takes from its site of building to its final destination.

  • Several Fe–S cluster biogenesis factors that do not belong to either the Isc system or the Suf system have been identified; their roles and how they cooperate with the Isc and Suf systems remain to be clarified.

Abstract

The broad range of cellular activities carried out by Fe–S proteins means that they have a central role in the life of most organisms. At the interface between biology and chemistry, studies of bacterial Fe–S protein biogenesis have taken advantage of the specific approaches of each field and have begun to reveal the molecular mechanisms involved. The multiprotein systems that are required to build Fe–S proteins have been identified, but the in vivo roles of some of the components remain to be clarified. The way in which cellular Fe–S cluster trafficking pathways are organized remains a key issue for future studies.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Fe–S clusters: structure and function.
Figure 2: Fe–S proteins and oxidative stress.
Figure 3: The main steps in the Escherichia coli Fe–S cluster biogenesis pathway.
Figure 4: The source of sulphur.
Figure 5: Model for Fe–S cluster assembly on Fe–S cluster protein U (IscU) and subsequent transfer to apoproteins.

Similar content being viewed by others

References

  1. Beinert, H. Iron-sulfur proteins: ancient structures, still full of surprises. J. Biol. Inorg. Chem. 5, 2–15 (2000). A review from a pioneer in the Fe–S protein field.

    Article  CAS  PubMed  Google Scholar 

  2. Fontecave, M. Iron-sulfur clusters: ever-expanding roles. Nature Chem. Biol. 2, 171–174 (2006).

    Article  CAS  Google Scholar 

  3. Kiley, P. J. & Beinert, H. The role of Fe-S proteins in sensing and regulation in bacteria. Curr. Opin. Microbiol. 6, 181–185 (2003).

    Article  CAS  PubMed  Google Scholar 

  4. Ayala-Castro, C., Saini, A. & Outten, F. W. Fe-S cluster assembly pathways in bacteria. Microbiol. Mol. Biol. Rev. 72, 110–125 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Fontecave, M., Py, B., Ollagnier de Choudens, S. & Barras, F. From iron and cysteine to iron-sulfur clusters: the biogenesis protein machineries. Ecosal [online] (2008).

  6. Xu, X. M. & Møller, S. G. Iron-sulfur cluster biogenesis systems and their crosstalk. Chembiochem. 9, 2355–2362 (2008).

    Article  CAS  PubMed  Google Scholar 

  7. Lill, R. & Mühlenhoff, U. Maturation of iron-sulfur proteins in eukaryotes: mechanisms, connected processes, and diseases. Annu. Rev. Biochem. 77, 669–700 (2008).

    Article  CAS  PubMed  Google Scholar 

  8. Rouault, T. A. & Tong, W. H. Iron-sulfur cluster biogenesis and human disease. Trends Genet. 24, 398–407 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kessler, D. & Papenbrock, J. Iron-sulfur cluster biosynthesis in photosynthetic organisms. Photosynth. Res. 86, 391–407 (2005).

    Article  CAS  PubMed  Google Scholar 

  10. Balk, J. & Lobréaux, S. Biogenesis of iron-sulfur proteins in plants. Trends Plant. Sci. 10, 324–331 (2005).

    Article  CAS  PubMed  Google Scholar 

  11. Imlay, J. A. Iron-sulphur clusters and the problem with oxygen. Mol. Microbiol. 59, 1073–1082 (2006). A perspective on the use of Fe–S proteins in relation to the evolution of Earth's atmosphere.

    Article  PubMed  Google Scholar 

  12. Kuo, C. F., Mashino, T. & Fridovich, I. α,β-Dihydroxyisovalerate dehydratase. A superoxide-sensitive enzyme. J. Biol. Chem. 262, 4724–4727 (1987). A seminal paper on the relationship between oxidative stress and Fe–S proteins.

    CAS  PubMed  Google Scholar 

  13. Flint, D. H., Tuminello, J. F. & Emptage, M. H. The inactivation of Fe-S cluster containing hydrolyases by superoxide. J. Biol. Chem. 268, 22369–22376 (1993).

    CAS  PubMed  Google Scholar 

  14. Keyer, K. & Imlay, J. A. Inactivation of dehydratase [4Fe-4S] clusters and disruption of iron homeostasis upon cell exposure to peroxynitrite. J. Biol. Chem. 272, 27652–27659 (1997).

    Article  CAS  PubMed  Google Scholar 

  15. Jang, S. & Imlay, J. A. Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron-sulfur enzymes. J. Biol. Chem. 282, 929–937 (2007).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  17. Mello Filho, A. C., Hoffmann, M. E. & Meneghini, R. Cell killing and DNA damage by hydrogen peroxide are mediated by intracellular iron. Biochem. J. 218, 273–275 (1984).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Imlay, J. A., Chin, S. M. & Linn., S. Toxic DNA damage by hydrogen peroxide through the Fenton reaction in vivo and in vitro. Science 240, 640–642 (1988).

    Article  CAS  PubMed  Google Scholar 

  19. Kohanski, M. A., Dwyer, D. J., Hayete, B., Lawrence, C. A. & Collins, J. J. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130, 797–810 (2007).

    Article  CAS  PubMed  Google Scholar 

  20. Jacobson, M. R. et al. Biochemical and genetic analysis of the nifUSVWZM cluster from Azotobacter vinelandii. Mol. Gen. Genet. 219, 49–57 (1989). A landmark article signalling the start of the research into bacterial Fe–S cluster biogenesis.

    Article  CAS  PubMed  Google Scholar 

  21. Zheng, L., Cash, V. L., Flint, D. H. & Dean, D. R. Assembly of iron-sulfur clusters. Identification of an iscSUA-hscBA-fdx gene cluster from Azotobacter vinelandii. J. Biol. Chem. 273, 13264–13272 (1998). This paper reports the identification of the Isc system.

    Article  CAS  PubMed  Google Scholar 

  22. Patzer, S. I. & Hantke, K. SufS is a NifS-like protein, and SufD is necessary for stability of the [2Fe-2S] FhuF protein in Escherichia coli. J. Bacteriol. 181, 3307–3309 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Nachin, L., El Hassouni, M., Loiseau, L., Expert, D. & Barras, F. SoxR-dependent response to oxidative stress and virulence of Erwinia chrysanthemi: the key role of SufC, an orphan ABC ATPase. Mol. Microbiol. 39, 960–972 (2001).

    Article  CAS  PubMed  Google Scholar 

  24. Takahashi, Y. & Tokumoto, U. A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids. J. Biol. Chem. 277, 28380–28383 (2002). This paper reports the identification of the Suf system.

    Article  CAS  PubMed  Google Scholar 

  25. Outten, F. W., Djaman, O. & Storz, G. A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli. Mol. Microbiol. 52, 861–872 (2004).

    Article  CAS  PubMed  Google Scholar 

  26. Johnson, D. C., Unciuleac, M. C. & Dean, D. R. Controlled expression and functional analysis of iron-sulfur cluster biosynthetic components within Azotobacter vinelandii. J. Bacteriol. 188, 7551–7561 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Olson, J. W., Agar, J. N., Johnson, M. K. & Maier, R. J. Characterization of the NifU and NifS Fe-S cluster formation proteins essential for viability in Helicobacter pylori. Biochemistry 39, 16213–16219 (2000).

    Article  CAS  PubMed  Google Scholar 

  28. Takahashi, Y. & Nakamura, M. Functional assignment of the ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 gene cluster involved in the assembly of Fe-S clusters in Escherichia coli. J. Biochem. 126, 917–926 (1999).

    Article  CAS  PubMed  Google Scholar 

  29. Tokumoto, U. & Takahashi, Y. Genetic analysis of the isc operon in Escherichia coli involved in the biogenesis of cellular iron-sulfur proteins. J. Biochem. 130, 63–71 (2001).

    Article  CAS  PubMed  Google Scholar 

  30. Rincon-Enriquez, G., Crété, P., Barras, F. & Py, B. Biogenesis of Fe/S proteins and pathogenicity: IscR plays a key role in allowing Erwinia chrysanthemi to adapt to hostile conditions. Mol. Microbiol. 67, 1257–1273 (2008).

    Article  CAS  PubMed  Google Scholar 

  31. Huet, G., Daffé, M. & Saves, I. Identification of the Mycobacterium tuberculosis SUF machinery as the exclusive mycobacterial system of [Fe-S] cluster assembly: evidence for its implication in the pathogen's survival. J. Bacteriol. 187, 6137–6146 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Mihara, H. & Esaki, N. Bacterial cysteine desulfurases: their function and mechanisms. Appl. Microbiol. Biotechnol. 60, 12–23 (2002).

    Article  CAS  PubMed  Google Scholar 

  33. Zheng, L., White, R. H., Cash, V. L., Jack, R. F. & Dean, D. R. Cysteine desulfurase activity indicates a role for NIFS in metallocluster biosynthesis. Proc. Natl Acad. Sci. USA 90, 2754–2758 (1993). The first identification of the source and the mechanism of sulphur mobilization for Fe–S cluster formation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Flint, D. H. Escherichia coli contains a protein that is homologous in function and N-terminal sequence to the protein encoded by the nifS gene of Azotobacter vinelandii and that can participate in the synthesis of the Fe-S cluster of dihydroxy-acid dehydratase. J. Biol. Chem. 271, 16068–16074 (1996).

    Article  CAS  PubMed  Google Scholar 

  35. Mihara, H., Kurihara, T., Yoshimura, T. & Esaki, N. Kinetic and mutational studies of three NifS homologs from Escherichia coli: mechanistic difference between L-cysteine desulfurase and L-selenocysteine lyase reactions. J. Biochem. 127, 559–567 (2000).

    Article  CAS  PubMed  Google Scholar 

  36. Schwartz, C. J., Djaman, O., Imlay, J. A. & Kiley, P. J. The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli. Proc. Natl Acad. Sci. USA 97, 9009–9014 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Mueller, E. G. Trafficking in persulfides: delivering sulfur in biosynthetic pathways. Nature Chem. Biol. 2, 185–194 (2006).

    Article  CAS  Google Scholar 

  38. Ikeuchi, Y., Shigi, N., Kato, J., Nishimura, A. & Suzuki, T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol. Cell 21, 97–108 (2006).

    Article  CAS  PubMed  Google Scholar 

  39. Nilsson, K, Lundgren, H. K., Hagervall, T. G. & Björk, G. R. The cysteine desulfurase IscS is required for synthesis of all five thiolated nucleosides present in tRNA from Salmonella enterica serovar typhimurium. J. Bacteriol. 184, 6830–6835 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Lauhon, C. T. Requirement for IscS in biosynthesis of all thionucleosides in Escherichia coli. J. Bacteriol. 184, 6820–6829 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Nachin, L., Loiseau, L., Expert, D. & Barras, F. SufC: an unorthodox cytoplasmic ABC/ATPase required for [Fe-S] biogenesis under oxidative stress. EMBO J. 22, 427–437 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Lee, J. H., Yeo, W. S. & Roe, J. H. Induction of the sufA operon encoding Fe-S assembly proteins by superoxide generators and hydrogen peroxide: involvement of OxyR, IHF and an unidentified oxidant-responsive factor. Mol. Microbiol. 51, 1745–1755 (2004).

    Article  CAS  PubMed  Google Scholar 

  43. Yeo, W. S., Lee, J. H., Lee, K. C. & Roe, J. H. IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins. Mol. Microbiol. 61, 206–218 (2006).

    Article  CAS  PubMed  Google Scholar 

  44. Lee, K. C., Yeo, W. S. & Roe, J. H. Oxidant-responsive induction of the suf operon, encoding a Fe-S assembly system, through Fur and IscR in Escherichia coli. J. Bacteriol. 190, 8244–8247 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Tokumoto, U., Kitamura, S., Fukuyama, K. & Takahashi, Y. Interchangeability and distinct properties of bacterial Fe-S cluster assembly systems: functional replacement of the isc and suf operons in Escherichia coli with the nifSU-like operon from Helicobacter pylori. J. Biochem. 136, 199–209 (2004).

    Article  CAS  PubMed  Google Scholar 

  46. Loiseau, L. et. al. Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting Fe-S cluster biogenesis in Escherichia coli. J. Biol. Chem. 280, 26760–26769 (2005).

    Article  CAS  PubMed  Google Scholar 

  47. Trotter, V. et al. The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein. Mol. Microbiol. 74, 1527–1542 (2009).

    Article  CAS  PubMed  Google Scholar 

  48. Urbina, H. D., Silberg, J. J., Hoff, K. G. & Vickery, L. E. Transfer of sulfur from IscS to IscU during Fe/S cluster assembly. J. Biol. Chem. 276, 44521–44526 (2001).

    Article  CAS  PubMed  Google Scholar 

  49. Smith, A. D. et al. Sulfur transfer from IscS to IscU: the first step in iron-sulfur cluster biosynthesis. J. Am. Chem. Soc. 123, 11103–11104 (2001).

    Article  CAS  PubMed  Google Scholar 

  50. Loiseau, L., Ollagnier de Choudens, S., Nachin, L., Fontecave, M. & Barras, F. Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE form a new type of cysteine desulfurase. J. Biol. Chem. 278, 38352–38359 (2003).

    Article  CAS  PubMed  Google Scholar 

  51. Ollagnier de Choudens, S. et al. Mechanistic studies of the SufS-SufE cysteine desulfurase: evidence for sulfur transfer from SufS to SufE. FEBS Lett. 555, 263–267 (2003).

    Article  CAS  PubMed  Google Scholar 

  52. Outten, F. W., Wood, M. J., Munoz, F. M. & Storz, G. The SufE protein and the SufBCD complex enhance SufS cysteine desulfurase activity as part of a sulfur transfer pathway for Fe-S cluster assembly in Escherichia coli. J. Biol. Chem. 278, 45713–45719 (2003).

    Article  CAS  PubMed  Google Scholar 

  53. Layer, G. et al.SufE transfers sulfur from SufS to SufB for iron-sulfur cluster assembly. J. Biol. Chem. 282, 13342–13350 (2007). The first evidence for the identification of SufBCD as the scaffold in the Suf system.

    Article  CAS  PubMed  Google Scholar 

  54. Sendra, M., Ollagnier de Choudens, S., Lascoux, D., Sanakis, Y. & Fontecave, M. The SUF iron-sulfur cluster biosynthetic machinery: sulfur transfer from the SUFS-SUFE complex to SUFA. FEBS Lett. 581, 1362–1368 (2007).

    Article  CAS  PubMed  Google Scholar 

  55. Layer, G., Ollagnier de Choudens, S., Sanakis, Y. & Fontecave, M. Iron-sulfur cluster biosynthesis: characterization of Escherichia coli CyaY as an iron donor for the assembly of [2Fe-2S] clusters in the scaffold IscU. J. Biol. Chem. 281, 16256–16263 (2006).

    Article  CAS  PubMed  Google Scholar 

  56. Adinolfi, S. et al. Bacterial frataxin CyaY is the gatekeeper of iron-sulfur cluster formation catalyzed by IscS. Nature Struct. Mol. Biol. 16, 390–396 (2009).

    Article  CAS  Google Scholar 

  57. Shi, R. et al. Structural basis for Fe–S cluster assembly and tRNA thiolation mediated by IscS protein–protein interactions. PLoS Biol. 8, e1000354 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Pandolfo, M. & Pastore, A. The pathogenesis of Friedreich ataxia and the structure and function of frataxin. J. Neurol. 256, 9–17 (2009).

    Article  CAS  PubMed  Google Scholar 

  59. Bou-Abdallah, F., Adinolfi, S., Pastore, A., Laue, T. M. & Chasteen, D. N. Iron binding and oxidation kinetics in frataxin CyaY of Escherichia coli. J. Mol. Biol. 341, 605–615 (2004).

    Article  CAS  PubMed  Google Scholar 

  60. Pastore, C., Franzese, M., Sica, F., Temussi, P. & Pastore, A. Understanding the binding properties of an unusual metal-binding protein-a study of bacterial frataxin. FEBS J. 274, 4199–4210 (2007).

    Article  CAS  PubMed  Google Scholar 

  61. Nair, M. et al. Solution structure of the bacterial frataxin ortholog, CyaY: mapping the iron binding sites. Structure 12, 2037–2048 (2004).

    Article  CAS  PubMed  Google Scholar 

  62. Li, D. S., Ohshima, K., Jiralerspong, S., Bojanowski, M. W. & Pandolfo, M. Knock-out of the cyaY gene in Escherichia coli does not affect cellular iron content and sensitivity to oxidants. FEBS Lett. 456, 13–16 (1999).

    Article  CAS  PubMed  Google Scholar 

  63. Vivas, E., Skovran, E. & Downs, D. M. Salmonella enterica strains lacking the frataxin homolog CyaY show defects in Fe-S cluster metabolism in vivo. J. Bacteriol. 188, 1175–1179 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Thorgersen, M. P. & Downs, D. M. Oxidative stress and disruption of labile iron generate specific auxotrophic requirements in Salmonella enterica. Microbiology 155, 295–304 (2009).

    Article  CAS  PubMed  Google Scholar 

  65. Ding, H. & Clark, R. J. Characterization of iron binding in IscA, an ancient iron-sulphur cluster assembly protein. Biochem. J. 379, 433–440 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Ding, H., Harrison, K. & Lu, J. Thioredoxin reductase system mediates iron binding in IscA and iron delivery for the iron-sulfur cluster assembly in IscU. J. Biol. Chem. 280, 30432–30437 (2005).

    Article  CAS  PubMed  Google Scholar 

  67. Yang, J., Bitoun, J. P. & Ding, H. Interplay of IscA and IscU in biogenesis of iron-sulfur clusters. J. Biol. Chem. 281, 27956–27963 (2006).

    Article  CAS  PubMed  Google Scholar 

  68. Lu, J., Yang, J., Tan, G. & Ding, H. Complementary roles of SufA and IscA in the biogenesis of iron-sulfur clusters in Escherichia coli. Biochem. J. 409, 535–543 (2008).

    Article  CAS  PubMed  Google Scholar 

  69. Djaman, O., Outten, F. W. & Imlay, J. A. Repair of oxidized iron-sulfur clusters in Escherichia coli. J. Biol. Chem. 279, 44590–44599 (2004). A rigorous testing of the hypothesis that an Fe–S cluster repair system exists.

    Article  CAS  PubMed  Google Scholar 

  70. Bitoun, J. P., Wu, G. & Ding, H. Escherichia coli FtnA acts as an iron buffer for re-assembly of iron-sulfur clusters in response to hydrogen peroxide stress. Biometals 21, 693–703 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Velayudhan, J., Castor, M., Richardson, A., Main-Hester, K. L. & Fang, F. C. The role of ferritins in the physiology of Salmonella enterica sv. Typhimurium: a unique role for ferritin B in iron-sulphur cluster repair and virulence. Mol. Microbiol. 63, 1495–1507 (2007).

    Article  CAS  PubMed  Google Scholar 

  72. Expert, D., Boughammoura, A. & Franza, T. Siderophore-controlled iron assimilation in the enterobacterium Erwinia chrysanthemi: evidence for the involvement of bacterioferritin and the Suf iron-sulfur cluster assembly machinery. J. Biol. Chem. 283, 36564–36572 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Dean, D. R. & Brigle, K. E. Azotobacter vinelandii nifD- and nifE-encoded polypeptides share structural homology. Proc. Natl Acad. Sci. USA 82, 5720–5723 (1985).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Goodwin, P. J. et al. The Azotobacter vinelandii NifEN complex contains two identical [4Fe-4S] clusters. Biochemistry 37, 10420–10428 (1998).

    Article  CAS  PubMed  Google Scholar 

  75. Bandyopadhyay, S., Chandramouli, K. & Johnson, M. K. Iron-sulfur cluster biosynthesis. Biochem. Soc. Trans. 36, 1112–1119 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Raulfs, E. C., O'Carroll, I. P., Dos Santos, P. C., Unciuleac, M. C. & Dean, D. R. In vivo iron-sulfur cluster formation. Proc. Natl Acad. Sci. USA 105, 8591–8596 (2008). A genetic analysis supporting the existence of the scaffold.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Agar, J. N. et al. IscU as a scaffold for iron-sulfur cluster biosynthesis: sequential assembly of [2Fe-2S] and [4Fe-4S] clusters in IscU. Biochemistry 39, 7856–7862 (2000). Spectroscopy-based evidence for the occurrence of multiple forms of IscU.

    Article  CAS  PubMed  Google Scholar 

  78. Chandramouli, K. et al. Formation and properties of [4Fe-4S] clusters on the IscU scaffold protein. Biochemistry 46, 6804–6811 (2007).

    Article  CAS  PubMed  Google Scholar 

  79. Kato, S. et al. Cys-328 of IscS and Cys-63 of IscU are the sites of disulfide bridge formation in a covalently bound IscS/IscU complex: implications for the mechanism of iron-sulfur cluster assembly. Proc. Natl Acad. Sci. USA 99, 5948–5952 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Unciuleac, M. C. et al. In vitro activation of apo-aconitase using a [4Fe-4S] cluster-loaded form of the IscU [Fe-S] cluster scaffolding protein. Biochemistry 46, 6812–6821 (2007).

    Article  CAS  PubMed  Google Scholar 

  81. Shimomura, Y., Wada, K., Fukuyama, K. & Takahashi, Y. The asymmetric trimeric architecture of [2Fe-2S] IscU: implications for its scaffolding during iron-sulfur cluster biosynthesis. J. Mol. Biol. 383, 133–143 (2008).

    Article  CAS  PubMed  Google Scholar 

  82. Vickery, L. E. & Cupp-Vickery, J. R. Molecular chaperones HscA/Ssq1 and HscB/Jac1 and their roles in iron-sulfur protein maturation. Crit. Rev. Biochem. Mol. Biol. 42, 95–111 (2007). An account of the studies of co-chaperones in Fe–Scluster biogenesis by prominent contributors in the field.

    Article  CAS  PubMed  Google Scholar 

  83. Chandramouli, K. & Johnson, M. K. HscA and HscB stimulate [2Fe-2S] cluster transfer from IscU to apoferredoxin in an ATP-dependent reaction. Biochemistry 45, 11087–11095 (2006).

    Article  CAS  PubMed  Google Scholar 

  84. Bonomi, F., Iametti, S., Morleo, A., Ta, D. & Vickery, L. E. Studies on the mechanism of catalysis of iron-sulfur cluster transfer from IscU[2Fe2S] by HscA/HscB chaperones. Biochemistry 47, 12795–12801 (2008).

    Article  CAS  PubMed  Google Scholar 

  85. Petrovic, A. et al. Hydrodynamic characterization of the SufBC and SufCD complexes and their interaction with fluorescent adenosine nucleotides. Protein Sci. 17, 1264–1274 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Wada, K. et al. Molecular dynamism of Fe-S cluster biosynthesis implicated by the structure of the SufC2-SufD2 complex. J. Mol. Biol. 387, 245–258 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Chahal, H. K, Dai, Y., Saini, A., Ayala-Castro, C. & Outten, F. W. The SufBCD Fe-S scaffold complex interacts with SufA for Fe-S cluster transfer. Biochemistry 48, 10644–10653 (2009).

    Article  CAS  PubMed  Google Scholar 

  88. Eccleston, J. F., Petrovic, A., Davis, C. T., Rangachari, K. & Wilson, R. J. The kinetic mechanism of the SufC ATPase: the cleavage step is accelerated by SufB. J. Biol. Chem. 281, 8371–8378 (2006).

    Article  CAS  PubMed  Google Scholar 

  89. Vinella, D., Brochier-Armanet, C., Loiseau, L., Talla, E. & Barras, F. Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers. PLoS Genet. 5, e1000497 (2009). An in vivo analysis of the specificities and redundancies of A-type proteins.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Krebs, C. et al. IscA, an alternate scaffold for Fe-S cluster biosynthesis. Biochemistry 40, 14069–14680 (2001).

    Article  CAS  PubMed  Google Scholar 

  91. Ollagnier de Choudens, S. et al. SufA from Erwinia chrysanthemi. Characterization of a scaffold protein required for iron-sulfur cluster assembly. J. Biol. Chem. 278, 17993–18001 (2003).

    Article  CAS  PubMed  Google Scholar 

  92. Loiseau, L. et al. ErpA, an iron sulfur (Fe S) protein of the A-type essential for respiratory metabolism in Escherichia coli. Proc. Natl Acad. Sci. USA 104, 13626–13631 (2007). This paper reports the first case of in vivo specificity between an A-type protein and a target apoprotein.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Gupta, V. et al. Native Escherichia coli SufA, coexpressed with SufBCDSE, purifies as a [2Fe-2S] protein and acts as an Fe-S transporter to Fe-S target enzymes. J. Am. Chem. Soc. 131, 6149–6153 (2009). A demonstration that, in vivo , IscA binds to Fe–S clusters.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Zeng, J. et al. The IscA from Acidithiobacillus ferrooxidans is an iron-sulfur protein, which assembles the [4Fe-4S] cluster with intracellular iron and sulfur. Arch. Biochem. Biophys. 463, 237–244 (2007).

    Article  CAS  PubMed  Google Scholar 

  95. Ollagnier de Choudens, S., Sanakis, Y. & Fontecave, M. SufA/IscA: reactivity studies of a class of scaffold proteins involved in [Fe-S] cluster assembly. J. Biol. Inorg. Chem. 9, 828–838 (2004).

    Article  CAS  PubMed  Google Scholar 

  96. Mettert, E. L., Outten, F. W., Wanta, B. & Kiley, P. J. The impact of O2 on the Fe-S. cluster biogenesis requirements of Escherichia coli FNR. J. Mol. Biol. 384, 798–811 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Tan, G., Lu, J., Bitoun, J. P., Huang, H. & Ding, H. IscA/SufA paralogues are required for the [4Fe-4S] cluster assembly in enzymes of multiple physiological pathways in Escherichia coli under aerobic growth conditions. Biochem. J. 420, 463–472 (2009).

    Article  CAS  PubMed  Google Scholar 

  98. Angelini, S. et al. NfuA, a new factor required for maturing Fe/S proteins in Escherichia coli under oxidative stress and iron starvation conditions. J. Biol. Chem. 283, 14084–14091 (2008).

    Article  CAS  PubMed  Google Scholar 

  99. Bandyopadhyay, S. et al. A proposed role for the Azotobacter vinelandii NfuA protein as an intermediate iron-sulfur cluster carrier. J. Biol. Chem. 283, 14092–14099 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Balasubramanian, R., Shen, G., Bryant, D. A. & Golbeck, J. H. Regulatory roles for IscA and SufA in iron homeostasis and redox stress responses in the cyanobacterium Synechococcus sp. strain PCC 7002. J. Bacteriol. 188, 3182–3191 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Jin, Z. et al. Biogenesis of iron-sulfur clusters in photosystem I: holo-NfuA from the cyanobacterium Synechococcus sp. PCC 7002 rapidly and efficiently transfers [4Fe-4S] clusters to apo-PsaC in vitro. J. Biol. Chem. 283, 28426–28435 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Agar, J. N. et al. Modular organization and identification of a mononuclear iron-binding site within the NifU protein. J. Biol. Inorg. Chem. 5, 167–177 (2000).

    Article  CAS  PubMed  Google Scholar 

  103. Boyd, J. M., Sondelski, J. L. & Downs, D. M. Bacterial ApbC protein has two biochemical activities that are required for in vivo function. J. Biol. Chem. 284, 110–118 (2009). An important contribution to the understanding of the role of one of the most conserved proteins in all living organisms.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Boyd, J. M., Pierik, A. J., Netz, D. J., Lill, R. & Downs, D. M. Bacterial ApbC can bind and effectively transfer iron-sulfur clusters. Biochemistry 47, 8195–81202 (2008).

    Article  CAS  PubMed  Google Scholar 

  105. Boyd, J. M., Lewis, J. A., Escalante-Semerena, J. C. & Downs, D. M. Salmonella enterica requires ApbC function for growth on tricarballylate: evidence of functional redundancy between ApbC and IscU. J. Bacteriol. 190, 4596–4602 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Bych, K. et al. The iron-sulphur protein Ind1 is required for effective complex I assembly. EMBO J. 27, 1736–1746 (2008). An example of the use of in vivo labelling to elucidate the position of an Fe–S cluster biogenesis factor in a pathway.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Justino, M. C., Baptista, J. M. & Saraiva, L. M. Di-iron proteins of the Ric family are involved in iron-sulfur cluster repair. Biometals 22, 99–108 (2009).

    Article  CAS  PubMed  Google Scholar 

  108. Overton, T. W. et al. Widespread distribution in pathogenic bacteria of di-iron proteins that repair oxidative and nitrosative damage to iron-sulfur centers. J. Bacteriol. 190, 2004–2013 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Harrington, J. C. et al. Resistance of Haemophilus influenzae to reactive nitrogen donors and gamma interferon-stimulated macrophages requires the formate-dependent nitrite reductase regulator-activated ytfE gene. Infect. Immun. 77, 1945–1958 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Vine, C. E., Justino, M. C., Saraiva, L. M. & Cole, J. Detection by whole genome microarrays of a spontaneous 126-gene deletion during construction of a ytfE mutant: confirmation that a ytfE mutation results in loss of repair of iron-sulfur centres in proteins damaged by oxidative or nitrosative stress. J. Microbiol. Methods. 81, 77–79 (2010)

    Article  CAS  PubMed  Google Scholar 

  111. Justino, M. C., Vicente, J. B., Teixeira, M. & Saraiva, L. M. New genes implicated in the protection of anaerobically grown Escherichia coli against nitric oxide. J. Biol. Chem. 280, 2636–2643 (2005).

    Article  CAS  PubMed  Google Scholar 

  112. Justino, M. C., Almeida, C. C., Gonçalves, V. L., Teixeira, M. & Saraiva, L. M. Escherichia coli YtfE is a di-iron protein with an important function in assembly of iron-sulphur clusters. FEMS Microbiol. Lett. 257, 278–284 (2006).

    Article  CAS  PubMed  Google Scholar 

  113. Todorovic, S. et al. Iron-sulfur repair YtfE protein from Escherichia coli: structural characterization of the di-iron center. J. Biol. Inorg. Chem. 13, 765–770 (2008).

    Article  CAS  PubMed  Google Scholar 

  114. Gralnick, J. & Downs, D. Protection from superoxide damage associated with an increased level of the YggX protein in Salmonella enterica. Proc. Natl Acad. Sci. USA 98, 8030–8035 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Tucker, N. P. et al. The transcriptional repressor protein NsrR senses nitric oxide directly via a [2Fe-2S] cluster. PLoS ONE 3, e3623 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Schwartz, C. J. et al. 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, 14895–14900 (2001). The proposal that an autoregulatory system allows bacterial cells to sense Fe–S cluster homeostasis.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Giel, J. L., Rodionov, D., Liu, M., Blattner, F. R. & Kiley, P. J. IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli. Mol. Microbiol. 60, 1058–1075 (2006). This paper shows that IscR regulates a broad range of genes.

    Article  CAS  PubMed  Google Scholar 

  118. Wu, Y. & Outten, F. W. IscR controls iron-dependent biofilm formation in Escherichia coli by regulating type I fimbria expression. J. Bacteriol. 191, 1248–1257 (2009).

    Article  CAS  PubMed  Google Scholar 

  119. Nesbit, A. D., Giel, J. L., Rose, J. C. & Kiley, P. J. Sequence-specific binding to a subset of IscR-regulated promoters does not require IscR Fe-S cluster ligation. J. Mol. Biol. 387, 28–41 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Shen, G. et al. SufR coordinates two [4Fe-4S]2+, 1+ clusters and functions as a transcriptional repressor of the sufBCDS operon and an autoregulator of sufR in cyanobacteria. J. Biol. Chem. 282, 31909–31919 (2007). Adescription of the Fe–S cluster biogenesis strategy in cyanobacteria.

    Article  CAS  PubMed  Google Scholar 

  121. Butland, G. et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531–537 (2005).

    Article  CAS  PubMed  Google Scholar 

  122. Arifuzzaman, M. et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16, 686–691 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Butland, G. et al. eSGA: E. coli synthetic genetic array analysis. Nature Methods 5, 789–795 (2008).

    Article  CAS  PubMed  Google Scholar 

  124. Bandyopadhyay, S. et al. Chloroplast monothiol glutaredoxins as scaffold proteins for the assembly and delivery of [2Fe-2S] clusters. EMBO J. 27, 1122–1133 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Mandrand-Berthelot, M. A., Couchoux-Luthaud, G., Santini, C. L. & Giordano, G. Mutants of Escherichia coli specifically deficient in respiratory formate dehydrogenase activity. J. Gen. Microbiol. 134, 3129–3139 (1988).

    CAS  PubMed  Google Scholar 

  126. Ote, T. et al. Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation. Mol. Microbiol. 59, 265–275 (2006).

    Article  CAS  PubMed  Google Scholar 

  127. Seaton, B. L. & Vickery, L. E. A gene encoding a DnaK/hsp70 homolog in Escherichia coli. Proc. Natl Acad. Sci. USA 91, 2066–2070 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Lelivelt, M. J. & Kawula, T. H. Hsc66, an Hsp70 homolog in Escherichia coli, is induced by cold shock but not by heat shock. J. Bacteriol. 177, 4900–4907 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Desnoyers, G., Morissette, A., Prévost, K. & Massé, E. Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA. EMBO J. 28, 1551–1561 (2009). The first example of a role for small-RNA-mediated regulation in Fe–S cluster homeostasis.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors apologize to all colleagues whose studies could not be referred to owing to space constraints. The authors acknowledge past and present colleagues who contributed to Fe–S cluster studies in the F.B. group: S. Angélini, L. Loiseau, L. Nachin, V. Trotter and D. Vinella. Thanks are due to M. Ansaldi for careful reading of the manuscript and to M. Fontecave and S. Ollagnier de Choudens for a warm and efficient collaboration. Financial support is provided by the Centre National de la Recherche Scientifique, the Université de la Méditerranée and the Agence Nationale de la Recherche (ANR-07-BLAN-0101-02).

Author information

Authors and Affiliations

  1. Laboratoire de Chimie Bactérienne, UPR-CNRS 9043, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, 31 Chemin Joseph Aiguier, Marseille, 13009, France

    Béatrice Py & Frédéric Barras

Authors
  1. Béatrice Py
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Frédéric Barras
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Frédéric Barras.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Related links

Related links

DATABASES

Entrez Genome Project

Arabidopsis thaliana

Azotobacter vinelandii

Bacillus subtilis

Erwinia chrysanthemi

Escherichia coli

Haemophilus influenzae

Helicobacter pylori

Mycobacterium tuberculosis

Saccharomyces cerevisiae

Salmonella enterica

Synechococcus sp. PCC7002

Synechocystis sp. PCC 6803

FURTHER INFORMATION

Frédéric Barras's homepage

Rights and permissions

Reprints and permissions

About this article

Cite this article

Py, B., Barras, F. Building Fe–S proteins: bacterial strategies. Nat Rev Microbiol 8, 436–446 (2010). https://doi.org/10.1038/nrmicro2356

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro2356

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing