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.

Genetic regulation of biological nitrogen fixation

Key Points

  • Biological nitrogen fixation has an important role in the nitrogen cycle and provides a substantial input of fixed nitrogen into soils. It is widely distributed amongst the Bacteria and Archaea but is not found in eukaryotes. Nitrogen-fixing bacteria are found in a wide variety of habitats including both soil and marine environments and in symbiotic associations with termites, ferns, woody plants and legumes.

  • Nitrogenase, the enzyme that catalyses biological nitrogen fixation, is oxygen sensitive and requires ATP and an electron donor for activity. The enzyme consists of two metalloprotein components — the Fe protein and the MoFe protein — which contain different metal clusters. Electron transfer from the Fe protein to the MoFe protein is ATP-dependent and each step in nitrogen reduction involves an obligatory cycle of association and dissociation of the component proteins. The oxygen sensitivity of nitrogenase and the energetic requirements for nitrogen fixation impose physiological constraints on diazotrophs, necessitating tight regulation of nitrogen fixation (nif) genes in response to the levels of fixed nitrogen, carbon, energy and the external oxygen concentration.

  • Common regulatory components and similar regulatory networks are used to control nitrogen fixation, but there is considerably plasticity in the regulatory networks, which differ from species to species, dependent on host physiology. In the Proteobacteria, most nif genes are activated by the enhancer-binding protein NifA together with the RNA polymerase sigma factor σ54. The expression of NifA and, in many cases its activity, is controlled by regulatory cascades that are responsive to different environmental cues.

  • Four proteins regulate nitrogen fixation in response to oxygen or redox signals. In symbiotic bacteria, FixL (a haemoprotein sensor histidine kinase) and NifA provide a hierarchical response to the oxygen concentration. In other diazotrophs, NifA is not directly responsive to oxygen but its activity is regulated by a partner flavoprotein, NifL, that senses the redox status. The histidine protein kinase RegB and its homologues respond to redox through an active cysteine and might sense the electron flux through a high affinity cbb3-type oxidase.

  • The nitrogen status is communicated to target regulatory proteins by the PII signal-transduction proteins that are covalently modified by uridylylation under nitrogen-limiting conditions. Many bacteria contain more than one homologue of PII, enabling hierarchical regulation in response to the level of fixed nitrogen. In free-living diazotrophic bacteria that have the NifL–NifA regulatory system, the PII-like protein GlnK regulates NifA activity by completely different mechanisms, illustrating the plasticity of protein–protein interactions in these systems.

Abstract

Some bacteria have the remarkable capacity to fix atmospheric nitrogen to ammonia under ambient conditions, a reaction only mimicked on an industrial scale by a chemical process that requires high temperatures, elevated pressure and special catalysts. The ability of microorganisms to use nitrogen gas as the sole nitrogen source and engage in symbioses with host plants confers many ecological advantages, but also incurs physiological penalties because the process is oxygen sensitive and energy dependent. Consequently, biological nitrogen fixation is highly regulated at the transcriptional level by sophisticated regulatory networks that respond to multiple environmental cues.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: Nitrogenase — structure and turnover cycle.
Figure 2: Domain modules found in proteins that mediate transcriptional control of nitrogen fixation (nif) genes.
Figure 3: Comparison of regulatory cascades controlling nif transcription in the free-living diazotroph K. pneumoniae and in the symbiotic diazotrophs S. meliloti and B. japonicum.
Figure 4: Conformational change of the FixL haem-containing PAS domain on oxygen binding.
Figure 5: FixJ structure and activation.
Figure 6: Schematic to illustrate the different mechanisms by which the nitrogen signal is conveyed to regulate the NifL–NifA systems of A. vinelandii and K. pneumoniae.

Similar content being viewed by others

References

  1. Capone, D. G. Marine nitrogen fixation: what's the fuss? Curr. Opin. Microbiol. 4, 341–348 (2001).

    Article  CAS  PubMed  Google Scholar 

  2. Rees, D. C. & Howard, J. B. Nitrogenase: standing at the crossroads. Curr. Opin. Chem. Biol. 4, 559–566 (2000).

    Article  CAS  PubMed  Google Scholar 

  3. Lawson, D. M. & Smith, B. E. in Metal Ions in Biological Systems Vol. 39 (eds Sigel, A. & Sigel, H.) 75–119 (Marcel Dekker, New York, 2002).

    Google Scholar 

  4. Eady, R. R. Structure–function relationships of alternative nitrogenases. Chem. Rev. 96, 3013–3030 (1996).

    Article  CAS  PubMed  Google Scholar 

  5. Einsle, O. et al. Nitrogenase MoFe-protein at 1.16 Å resolution: a central ligand in the FeMo-cofactor. Science 297, 1696–1700 (2002).

    Article  CAS  PubMed  Google Scholar 

  6. Seefeldt, L. C., Dance, I. G. & Dean, D. R. Substrate interactions with nitrogenase: Fe versus Mo. Biochemistry 43, 1401–1409 (2004).

    Article  CAS  PubMed  Google Scholar 

  7. Hageman, R. V. & Burris, R. H. Nitrogenase and nitrogenase reductase associate and dissociate with each catalytic cycle. Proc. Natl Acad. Sci. USA 75, 2699–2702 (1978).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Thornely, R. N. F. & Lowe, D. J. in Molybdenum Enzymes (ed. Spiro, T. G.) 221–284 (John Wiley, New York, 1985).

    Google Scholar 

  9. Lutkenhaus, J. & Sundaramoorthy, M. MinD and role of the deviant Walker A motif, dimerization and membrane binding in oscillation. Mol. Microbiol. 48, 295–303 (2003).

    Article  CAS  PubMed  Google Scholar 

  10. Locher, K. P. et al. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A1. J. Mol. Biol. 307, 297–308 (2001).

    Article  CAS  PubMed  Google Scholar 

  11. Mobitz, H., Friedrich, T. & Boll, M. Substrate binding and reduction of benzoyl-CoA reductase: evidence for nucleotide-dependent conformational changes. Biochemistry 43, 1376–1385 (2004).

    Article  CAS  PubMed  Google Scholar 

  12. Schindelin, H., Kisker, C., Schlessman, J. L., Howard, J. B. & Rees, D. C. Structure of ADP x AIF4-stabilized nitrogenase complex and its implications for signal transduction. Nature 387, 370–376 (1997). Revealed the structure of the nitrogenase complex.

    Article  CAS  PubMed  Google Scholar 

  13. Ribbe, M., Gadkari, D. & Meyer, O. N2 fixation by Streptomyces thermoautotrophicus involves a molybdenum-dinitrogenase and a manganese-superoxide oxidoreductase that couple N2 reduction to the oxidation of superoxide produced from O2 by a molybdenum-CO dehydrogenase. J. Biol. Chem. 272, 26627–26633 (1997). An unusual exception to the rule — an oxygen-insensitive nitrogenase.

    Article  CAS  PubMed  Google Scholar 

  14. Masepohl, B. et al. Regulation of nitrogen fixation in the phototrophic purple bacterium Rhodobacter capsulatus. J. Mol. Microbiol. Biotechnol. 4, 243–248 (2002).

    CAS  PubMed  Google Scholar 

  15. Halbleib, C. M., Zhang, Y. & Ludden, P. W. Regulation of dinitrogenase reductase ADP-ribosyltransferase and dinitrogenase reductase-activating glycohydrolase by a redox-dependent conformational change of nitrogenase Fe protein. J. Biol. Chem. 275, 3493–3500 (2000).

    Article  CAS  PubMed  Google Scholar 

  16. Kaminski, P. A., Mandon, K., Arigoni, F., Desnoues, N. & Elmerich, C. Regulation of nitrogen fixation in Azorhizobium caulinodans: identification of a fixK-like gene, a positive regulator of nifA. Mol. Microbiol. 5, 1983–1991 (1991).

    Article  CAS  PubMed  Google Scholar 

  17. Ratet, P., Pawlowski, K., Schell, J. & de Bruijn, F. J. The Azorhizobium caulinodans nitrogen-fixation regulatory gene, nifA, is controlled by the cellular nitrogen and oxygen status. Mol. Microbiol. 3, 825–838 (1989).

    Article  CAS  PubMed  Google Scholar 

  18. Ho, Y. S., Burden, L. M. & Hurley, J. H. Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor. EMBO J. 19, 5288–5299. (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Little, R. & Dixon, R. The amino-terminal GAF domain of Azotobacter vinelandii NifA binds 2-oxoglutarate to resist inhibition by NifL under nitrogen-limiting conditions. J. Biol. Chem. 278, 28711–28718 (2003).

    Article  CAS  PubMed  Google Scholar 

  20. Arsene, F., Kaminski, P. A. & Elmerich, C. Modulation of NifA activity by PII in Azospirillum brasilense: evidence for a regulatory role of the NifA N-terminal domain. J. Bacteriol. 178, 4830–4838 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Arsene, F., Kaminski, P. A. & Elmerich, C. Control of Azospirillum brasilense NifA activity by P(II): effect of replacing Tyr residues of the NifA N-terminal domain on NifA activity. FEMS Microbiol. Lett. 179, 339–343 (1999).

    Article  CAS  PubMed  Google Scholar 

  22. Martinez-Argudo, I., Little, R., Shearer, N., Johnson, P. & Dixon, R. The NifL–NifA system: a multidomain transcriptional regulatory complex that integrates environmental signals. J. Bacteriol. 186, 601–610 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Barrett, J., Ray, P., Sobczyk, A., Little, R. & Dixon, R. Concerted inhibition of the transcriptional activation functions of the enhancer-binding protein NifA by the anti-activator NifL. Mol. Microbiol. 39, 480–494 (2001).

    Article  CAS  PubMed  Google Scholar 

  24. Martinez-Argudo, I., Little, R. & Dixon, R. Role of the amino-terminal GAF domain of the NifA activator in controlling the response to the anti-activator protein NifL. Mol. Microbiol. 52, 1731–1744 (2004).

    Article  CAS  PubMed  Google Scholar 

  25. Sciotti, M. A., Chanfon, A., Hennecke, H. & Fischer, H. M. Disparate oxygen responsiveness of two regulatory cascades that control expression of symbiotic genes in Bradyrhizobium japonicum. J. Bacteriol. 185, 5639–5642 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Taylor, B. L. & Zhulin, I. B. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63, 479–506 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Gilles-Gonzalez, M. A., Ditta, G. S. & Helinski, D. R. A haemoprotein with kinase activity encoded by the oxygen sensor of Rhizobium meliloti. Nature 350, 170–172 (1991).

    Article  CAS  PubMed  Google Scholar 

  28. Hill, S., Austin, S., Eydmann, T., Jones, T. & Dixon, R. Azotobacter vinelandii NifL is a flavoprotein that modulates transcriptional activation of nitrogen-fixation genes via a redox-sensitive switch. Proc. Natl Acad. Sci. USA. 93, 2143–2148 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Tuckerman, J. R., Gonzalez, G., Dioum, E. M. & Gilles-Gonzalez, M. A. Ligand and oxidation-state specific regulation of the heme-based oxygen sensor FixL from Sinorhizobium meliloti. Biochemistry 41, 6170–6177 (2002).

    Article  CAS  PubMed  Google Scholar 

  30. Hao, B., Isaza, C., Arndt, J., Soltis, M. & Chan, M. K. Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum. Biochemistry 41, 12952–12958 (2002). Discussion of the oxygen-induced conformational change of the FixL haem domain.

    Article  CAS  PubMed  Google Scholar 

  31. Dunham, C. M. et al. A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure. Biochemistry 42, 7701–7708 (2003). Shows the role of Arg220 in the regulatory coupling between FixL haem and protein.

    Article  CAS  PubMed  Google Scholar 

  32. Roche, P., Mouawad, L., Perahia, D., Samama, J. P. & Kahn, D. Molecular dynamics of the FixJ receiver domain: movement of the β4-α4 loop correlates with the in and out flip of Phe101. Protein Sci. 11, 2622–2630 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Birck, C. et al. Conformational changes induced by phosphorylation of the FixJ receiver domain. Structure Fold. Des. 7, 1505–1515 (1999). Structure of the phosphorylated FixJ receiver domain demonstrating major changes in the α4–β5 region involved in the dimerization interface.

    Article  CAS  PubMed  Google Scholar 

  34. Da Re, S. et al. Phosphorylation-induced dimerization of the FixJ receiver domain. Mol. Microbiol. 34, 504–511 (1999).

    Article  CAS  PubMed  Google Scholar 

  35. Dutta, R. & Inouye, M. GHKL, an emergent ATPase/kinase superfamily. Trends Biochem. Sci. 25, 24–28 (2000).

    Article  CAS  PubMed  Google Scholar 

  36. Söderbäck, E. et al. The redox-and fixed nitrogen-responsive regulatory protein NIFL from Azotobacter vinelandii comprises discrete flavin and nucleotide-binding domains. Mol. Microbiol. 28, 179–192 (1998).

    Article  PubMed  Google Scholar 

  37. Klopprogge, K. & Schmitz, R. A. NifL of Klebsiella pneumoniae: redox characterization in relation to the nitrogen source. Biochim. Biophys. Acta 1431, 462–470 (1999).

    Article  CAS  PubMed  Google Scholar 

  38. Macheroux, P. et al. Electron donation to the flavoprotein NifL, a redox-sensing transcriptional regulator. Biochem. J. 332, 413–419 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Grabbe, R. & Schmitz, R. A. Oxygen control of nif gene expression in Klebsiella pneumoniae depends on NifL reduction at the cytoplasmic membrane by electrons derived from the reduced quinone pool. Eur. J. Biochem. 270, 1555–1566 (2003).

    Article  CAS  PubMed  Google Scholar 

  40. Klopprogge, K., Grabbe, R., Hoppert, M. & Schmitz, R. A. Membrane association of Klebsiella pneumoniae NifL is affected by molecular oxygen and combined nitrogen. Arch. Microbiol. 177, 223–234 (2002).

    Article  CAS  PubMed  Google Scholar 

  41. Fischer, H. M. Genetic regulation of nitrogen fixation in rhizobia. Microbiol. Rev. 58, 352–386 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Fischer, H. M., Bruderer, T. & Hennecke, H. Essential and non-essential domains in the Bradyrhizobium japonicum NifA protein: identification of indispensable cysteine residues potentially involved in redox reactivity and/or metal binding. Nucleic Acids Res. 16, 2207–2224 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Elsen, S., Dischert, W., Colbeau, A. & Bauer, C. E. Expression of uptake hydrogenase and molybdenum nitrogenase in Rhodobacter capsulatus is coregulated by the RegB–RegA two-component regulatory system. J. Bacteriol. 182, 2831–2837 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Emmerich, R., Hennecke, H. & Fischer, H. M. Evidence for a functional similarity between the two-component regulatory systems RegSR, ActSR, and RegBA (PrrBA) in α-Proteobacteria. Arch. Microbiol. 174, 307–313 (2000).

    Article  CAS  PubMed  Google Scholar 

  45. Bauer, E., Kaspar, T., Fischer, H. -M. & Hennecke, H. Expression of the fixRnifA operon in Bradyrhizobium japonicum depends on a new response regulator, RegR. J. Bacteriol. 180, 3853–3863 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Swem, L. R. et al. Signal transduction by the global regulator RegB is mediated by a redox-active cysteine. EMBO J. 22, 4699–4708 (2003). Identifies a highly conserved cysteine residue that controls the activity of the sensor kinase RegB by intermolecular disulphide bond formation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Oh, J., Ko, I. & Kaplan, S. Reconstitution of the Rhodobacter sphaeroides cbb 3–PrrBA signal transduction pathway in vitro. Biochemistry 2004 (doi: 10. 1021/bi0496440). Demonstrates that the cbb 3 cytochrome c oxidase inhibits PrrB (a RegB homologue).

  48. Pioszak, A. A., Jiang, P. & Ninfa, A. J. The Escherichia coli PII signal transduction protein regulates the activities of the two-component system transmitter protein NRII by direct interaction with the kinase domain of the transmitter module. Biochemistry 39, 13450–13461 (2000).

    Article  CAS  PubMed  Google Scholar 

  49. He, L., Soupene, E., Ninfa, A. & Kustu, S. Physiological role for the GlnK protein of enteric bacteria: relief of NifL inhibition under nitrogen-limiting conditions. J. Bacteriol. 180, 6661–6667 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Jack, R., De Zamaroczy, M. & Merrick, M. The signal transduction protein GlnK is required for NifL-dependent nitrogen control of nif gene expression in Klebsiella pneumoniae. J. Bacteriol. 181, 1156–1162 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Javelle, A., Severi, E., Thornton, J. & Merrick, M. Ammonium sensing in E. coli: The role of the ammonium transporter AmtB and AmtB-GlnK complex formation. J. Biol. Chem. 279, 8530–8538 (2003).

    Article  PubMed  Google Scholar 

  52. Coutts, G., Thomas, G., Blakey, D. & Merrick, M. Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. EMBO J. 21, 536–545 (2002). Demonstration of the regulated interaction of GlnK with the membrane transporter AmtB.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Meletzus, D., Rudnick, P., Doetsch, N., Green, A. & Kennedy, C. Characterization of the glnKamtB operon of Azotobacter vinelandii. J. Bacteriol. 180, 3260–3264 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Colnaghi, R. et al. Lethality of glnD null mutations in Azotobacter vinelandii is suppressible by prevention of glutamine synthetase adenylylation. Microbiology 147, 1267–1276 (2001).

    Article  CAS  PubMed  Google Scholar 

  55. Contreras, A. et al. The product of the nitrogen fixation regulatory gene nfrX of Azotobacter vinelandii is functionally and structurally homologous to the uridylyltransferase encoded by glnD in enteric bacteria. J. Bacteriol. 173, 7741–7749 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Rudnick, P., Kunz, C., Gunatilaka, M. K., Hines, E. R. & Kennedy, C. Role of GlnK in NifL-mediated regulation of NifA activity in Azotobacter vinelandii. J. Bacteriol. 184, 812–820 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Little, R., Colombo, V., Leech, A. & Dixon, R. Direct interaction of the NifL regulatory protein with the GlnK signal transducer enables the Azotobacter vinelandii NifL–NifA regulatory system to respond to conditions replete for nitrogen. J. Biol. Chem. 277, 15472–15481 (2002).

    Article  CAS  PubMed  Google Scholar 

  58. Money, T., Jones, T., Dixon, R. & Austin, S. Isolation and properties of the complex between the enhancer binding protein NIFA and the sensor NIFL. J. Bacteriol. 181, 4461–4468 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Little, R., Reyes-Ramirez, F., Zhang, Y., van Heeswijk, W. C. & Dixon, R. Signal transduction to the Azotobacter vinelandii NIFL–NIFA regulatory system is influenced directly by interaction with 2-oxoglutarate and the PII regulatory protein. EMBO J. 19, 6041–6050 (2000). Describes unexpected roles for 2-oxoglutarate and PII-like proteins in nif gene regulation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Souza, E. M., Pedrosa, F. O., Drummond, M., Rigo, L. U. & Yates, M. G. Control of Herbaspirillum seropedicae NifA activity by ammonium ions and oxygen. J. Bacteriol. 181, 681–684 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Zhang, Y., Pohlmann, E. L. & Roberts, G. P. Identification of critical residues in GlnB for its activation of NifA activity in the photosynthetic bacterium Rhodospirillum rubrum. Proc. Natl Acad. Sci. USA 101, 2782–2787 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Michel-Reydellet, N. & Kaminski, P. A. Azorhizobium caulinodans PII and GlnK proteins control nitrogen fixation and ammonia assimilation. J. Bacteriol. 181, 2655–2658 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Drepper, T. et al. Role of GlnB and GlnK in ammonium control of both nitrogenase systems in the phototrophic bacterium Rhodobacter capsulatus. Microbiology 149, 2203–2212 (2003).

    Article  CAS  PubMed  Google Scholar 

  64. Pawlowski, A. et al. Yeast two-hybrid studies on interaction of proteins involved in regulation of nitrogen fixation in the phototrophic bacterium Rhodobacter capsulatus. J. Bacteriol. 185, 5240–5247 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Forchhammer, K. Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets,. FEMS Microbiol. Rev. 28, 319–333 (2004).

    Article  CAS  PubMed  Google Scholar 

  66. Zufferey, R., Preisig, O., Hennecke, H. & Thony-Meyer, L. Assembly and function of the cytochrome cbb3 oxidase subunits in Bradyrhizobium japonicum. J. Biol. Chem. 271, 9114–9119 (1996).

    Article  CAS  PubMed  Google Scholar 

  67. Preisig, O., Zufferey, R., Thony-Meyer, L., Appleby, C. A. & Hennecke, H. A high-affinity cbb 3-type cytochrome oxidase terminates the symbiosis-specific respiratory chain of Bradyrhizobium japonicum. J. Bacteriol. 178, 1532–1538 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Buck, M., Gallegos, M. T., Studholme, D. J., Guo, Y. & Gralla, J. D. The bacterial enhancer-dependent σ54N) transcription factor. J. Bacteriol. 182, 4129–4136 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Studholme, D. J. & Dixon, R. Domain architectures of σ54-dependent transcriptional activators. J. Bacteriol. 185, 1757–1767 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Vale, R. D. AAA proteins. Lords of the ring. J. Cell Biol. 150, F13–F19 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Zhang, X. et al. Mechanochemical ATPases and transcriptional activation. Mol. Microbiol. 45, 895–903 (2002).

    Article  CAS  PubMed  Google Scholar 

  72. Bordes, P. et al. The ATP hydrolyzing transcription activator phage shock protein F of Escherichia coli: identifying a surface that binds σ54. Proc. Natl Acad. Sci. USA 100, 2278–2283 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Chaney, M. et al. Binding of transcriptional activators to σ54 in the presence of the transition state analog ADP–aluminum fluoride: insights into activator mechanochemical action. Genes Dev. 15, 2282–2294 (2001). Describes a stable interaction between σ54 and the transcriptional activator protein in the presence of a transition state analogue for ATP hydrolysis.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Lee, S. -Y. et al. Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Genes Dev. 17, 2552–2563 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Arcondéguy, T., Jack, R. & Merrick, M. PII signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol. Mol. Biol. Rev. 65, 80–105 (2001).

    Article  PubMed  PubMed Central  Google Scholar 

  76. Ninfa, A. & Atkinson, M. PII signal transduction proteins. Trends Microbiol. 8, 172–179 (2000).

    Article  CAS  PubMed  Google Scholar 

  77. Schmid, B. et al. Biochemical and structural characterization of the cross-linked complex of nitrogenase: comparison to the ADP–AlF4-stabilized structure. Biochemistry 41, 15557–15565 (2002).

    Article  CAS  PubMed  Google Scholar 

  78. Hefti, M. H., Francoijs, K. J., De Vries, S. C., Dixon, R. & Vervoort, J. The PAS fold. Eur. J. Biochem. 271, 1198–1208 (2004).

    Article  CAS  PubMed  Google Scholar 

  79. Foussard, M. et al. Negative autoregulation of the Rhizobium meliloti fixK gene is indirect and requires a newly identified regulator, FixT. Mol. Microbiol. 25, 27–37 (1997).

    Article  CAS  PubMed  Google Scholar 

  80. Garnerone, A. M., Cabanes, D., Foussard, M., Boistard, P. & Batut, J. Inhibition of the FixL sensor kinase by the FixT protein in Sinorhizobium meliloti. J. Biol. Chem. 274, 32500–32506 (1999).

    Article  CAS  PubMed  Google Scholar 

  81. Arcondeguy, T. et al. The Rhizobium meliloti PII protein, which controls bacterial nitrogen metabolism affects alfalfa nodule development. Genes. Dev. 11, 1194–1206 (1997).

    Article  CAS  PubMed  Google Scholar 

  82. Gong, W., Hao, B. & Chan, M. K. New mechanistic insights from structural studies of the oxygen-sensing domain of Bradyrhizobium japonicum. Biochemistry. 39, 3955–3962 (2000).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

Work in the laboratory of R.D. is supported by the UK Biotechnology and Biosciences Research Council. Work in the laboratory of D.K. is supported by the Centre National de la Recherche Scientifique and the Institut National de la Recherche Agronomique. We thank Michael Chan for the kind gift of images for use in Figure 4. We thank many of our colleagues for helpful discussions and apologise for the multitude of work in this field which is not cited in this article due to space constraints. This review is dedicated to Werner Klipp, who sadly passed away in 2002 and made many contributions to research on gene regulation in nitrogen-fixing bacteria.

Author information

Authors and Affiliations

Authors

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

DATABASES

Entrez

Azotobacter vinelandii

Rhodospirillum rubrum

SwissProt

ArsA

DraG

DraT

FixJ

FixK

FixL

GlnB

GlnK

MinD

NifA

NifL

NtrB

NtrC

The Protein Data Bank

Fe protein

FixJ receiver domain

FixL haem domain

MoFe protein

NtrC1

stabilized complexes

FURTHER INFORMATION

Azotobacter database

Bradyrhizobium japonicum genome project

Sinorhizobium meliloti genome

ProDom

SMART

Ray Dixon's laboratory

Daniel Kahn's laboratory

Glossary

DIAZOTROPHIC ORGANISMS

A nitrogen-fixing organism that is capable of growth on atmospheric nitrogen as the sole nitrogen source.

CHEMOLITHOTROPH

An organism that is capable of using CO, CO2 or carbonates as the sole source of carbon for cell biosynthesis and that derives energy from the oxidation of reduced inorganic compounds.

ACTINORHIZAL

Symbiotic associations of plants that have the capacity to form root nodules with nitrogen-fixing actinomycetes.

TRANSITION-STATE ANALOGUE

A substrate designed to mimic the properties or the geometry of the transition state of a reaction. This is an intermediate state in which the enzyme has reached a geometric and energetic state necessary to overcome the activation energy required for the reaction.

NODULIN

A plant protein that is specifically found, or strongly induced, in root nodules.

BACTEROID

A differentiated intracellular form of a rhizobial cell, specialized in nitrogen fixation.

NITROGEN FIXATION GENES

These are found in both free-living and symbiotic nitrogen-fixing bacteria. They include the structural genes for nitrogenase, genes that are required for nitrogenase biosynthesis and regulatory genes.

UAS

Upstream activator sequences that provide specific recognition sequences for the NifA protein in the vicinity of σ54 -dependent nif promoters.

GAF

A domain that was named after three proteins that contain it: cGMP-stimulated phosphodiesterases, Anabaena adenyl cyclase and Escherichia coli FhlA.

ISOMERIZATION

Describes the step in which the DNA sequence in the RNA polymerase–promoter complex is unwound.

PROTOMER

A subunit from which a larger protein structure is built.

FIX GENES

Genes in addition to nif genes that are required for nitrogen fixation in symbiotic bacteria. Homologues of some of the fix genes are also present in bacteria that do not fix nitrogen.

MICROOXIC

A condition in which oxygen is present at subsaturating concentrations.

PAS

This domain was named after three eukaryotic proteins — PER, ARNT and SIM — in which it is found. In these proteins, the domain detects signals through an associated cofactor.

SURFACE PLASMON RESONANCE

An optical phenomenon that occurs when light is reflected by thin metal films. The technology is used to monitor the progress of biomolecular interactions (for example, protein–protein interactions) in real-time.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dixon, R., Kahn, D. Genetic regulation of biological nitrogen fixation. Nat Rev Microbiol 2, 621–631 (2004). https://doi.org/10.1038/nrmicro954

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro954

This article is cited by

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