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Gene Review

nifA  -  Fis family transcriptional regulator

Sinorhizobium meliloti 1021

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Disease relevance of nifA

  • We report the discovery of two genes from Rhizobium meliloti, fixL and fixJ, which are positive regulators of symbiotic expression of diverse nitrogen fixation (nif and fix) genes. nif gene regulation is shown to consist of a cascade: the fixLJ genes activate nifA, which in turn activates nifHDK and fixABCX [1].
  • The R. meliloti regulatory gene hybridizes to E. coli ntrC(glnG) and, to a lesser extent, to K. pneumoniae nifA DNA [2].
  • Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins [3].
  • The pleiotropic nature of symbiotic regulatory mutants: Bradyrhizobium japonicum nifA gene is involved in control of nif gene expression and formation of determinate symbiosis [4].
  • In both Klebsiella pneumoniae and Azotobacter vinelandii the nifL gene, which encodes a negative regulator of nitrogen fixation, lies immediately upstream of nifA [5].

High impact information on nifA

  • The nifH and P2 promoters can be activated in free-living cultures of R. meliloti containing plasmids that produce the Escherichia coli ntrC(glnG) or the Klebsiella pneumoniae nifA regulatory gene products constitutively [2].
  • In addition fixK negatively regulates expression of the nif-specific activator nifA as well as its own expression by autoregulation [6].
  • This extension encodes a putative DNA-binding domain strongly homologous to the Rhizobium meliloti nifA protein and to some extent to the ntrC protein [3].
  • Site-directed insertion and deletion/replacement mutagenesis revealed that nifA is probably the promoter-distal cistron within an operon [4].
  • Promoter deletion analysis has shown that although an extensive upstream DNA sequence 9160 bp) is required for full heterologous activation of the R. meliloti nifHDK promoter by the Klebsiella pneumoniae nifA protein in Escherichia coli, this region is not required for expression of R [7].

Chemical compound and disease context of nifA

  • The expression under microaerobic conditions of the Rhizobium meliloti nifA and consequently the nifHDK genes was found to be negatively regulated by ammonia and nitrate [8].

Biological context of nifA

  • Here we use an in vitro transcription system to prove that FixJ is a transcriptional activator of both nifA and fixK and that phosphorylation of FixJ markedly increases its activity [9].
  • This use of atmospheric oxygen to control nifA transcription in vitro represents a reconstitution of a bacterial two-component signal transduction system in its entirety, from effector to ultimate target, by the use of purified components [9].
  • Lastly, we were able to show that anaerobiosis, in the presence of FixL* and ATP, greatly stimulates FixJ activity at the nifA promoter with either Escherichia coli or R. meliloti RNA polymerase [9].
  • Promoters regulated by the glnG (ntrC) and nifA gene products share a heptameric consensus sequence in the -15 region [10].
  • The R. leguminosarum bv. viciae nifA gene is expressed independently of FixL and FixK under aerobic and microaerobic conditions, whereas fixL gene expression is induced under microaerobiosis [11].

Associations of nifA with chemical compounds

  • AICAR, a purine-related metabolite, was recently shown to inhibit respiratory and nifA gene expression in Sino-rhizobium meliloti [12].
  • In our efforts to understand the mechanisms involved, in this work, we have found that the observed enhancement on nodulation competitiveness by IncQ derivatives carrying K. pneumoniae nifA was not dependent on the plasmid-borne nifA activity but on the sensitivity of nonresistant strains to the streptomycin carried over from growth cultures [13].

Regulatory relationships of nifA


Other interactions of nifA

  • Transcriptome profiles of a nifA and a fixK mutant showed that NifA activates a limited number of genes, all specific to the symbiotic state, whereas FixK controls more than 90 genes, involved in free-living and/or symbiotic life [17].
  • The nifA gene has been identified between the fixX and nifB genes in the clover microsymbiont Rhizobium leguminosarum biovar trifolii (R.I. bv. trifolii) strain ANU843 [18].
  • Broad-host-range plasmids carrying translational fusions of Rhizobium meliloti nifH, fixA and nifA promoters were constructed [19].

Analytical, diagnostic and therapeutic context of nifA


  1. Cascade regulation of nif gene expression in Rhizobium meliloti. David, M., Daveran, M.L., Batut, J., Dedieu, A., Domergue, O., Ghai, J., Hertig, C., Boistard, P., Kahn, D. Cell (1988) [Pubmed]
  2. A Rhizobium meliloti symbiotic regulatory gene. Szeto, W.W., Zimmerman, J.L., Sundaresan, V., Ausubel, F.M. Cell (1984) [Pubmed]
  3. Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins. Drummond, M., Whitty, P., Wootton, J. EMBO J. (1986) [Pubmed]
  4. The pleiotropic nature of symbiotic regulatory mutants: Bradyrhizobium japonicum nifA gene is involved in control of nif gene expression and formation of determinate symbiosis. Fischer, H.M., Alvarez-Morales, A., Hennecke, H. EMBO J. (1986) [Pubmed]
  5. Sequence and molecular analysis of the nifL gene of Azotobacter vinelandii. Blanco, G., Drummond, M., Woodley, P., Kennedy, C. Mol. Microbiol. (1993) [Pubmed]
  6. fixK, a gene homologous with fnr and crp from Escherichia coli, regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti. Batut, J., Daveran-Mingot, M.L., David, M., Jacobs, J., Garnerone, A.M., Kahn, D. EMBO J. (1989) [Pubmed]
  7. Deletion analysis of Rhizobium meliloti symbiotic promoters. Better, M., Ditta, G., Helinski, D.R. EMBO J. (1985) [Pubmed]
  8. Ammonia regulation of the Rhizobium meliloti nitrogenase structural and regulatory genes under free-living conditions: involvement of the fixL gene product? Noonan, B., Motherway, M., O'Gara, F. Mol. Gen. Genet. (1992) [Pubmed]
  9. Oxygen regulation of nifA transcription in vitro. Agron, P.G., Ditta, G.S., Helinski, D.R. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  10. Promoters regulated by the glnG (ntrC) and nifA gene products share a heptameric consensus sequence in the -15 region. Ow, D.W., Sundaresan, V., Rothstein, D.M., Brown, S.E., Ausubel, F.M. Proc. Natl. Acad. Sci. U.S.A. (1983) [Pubmed]
  11. Rhizobium leguminosarum bv. viciae contains a second fnr/fixK-like gene and an unusual fixL homologue. Patschkowski, T., Schlüter, A., Priefer, U.B. Mol. Microbiol. (1996) [Pubmed]
  12. The fixM flavoprotein modulates inhibition by AICAR or 5'AMP of respiratory and nitrogen fixation gene expression in Sinorhizobium meliloti. Cosseau, C., Garnerone, A.M., Batut, J. Mol. Plant Microbe Interact. (2002) [Pubmed]
  13. Multicopy vectors carrying the Klebsiella pneumoniae nifA gene do not enhance the nodulation competitiveness of Sinorhizobium meliloti on alfalfa. van Dillewijn, P., Martínez-Abarca, F., Toro, N. Mol. Plant Microbe Interact. (1998) [Pubmed]
  14. Autophosphorylation and phosphatase activities of the oxygen-sensing protein FixL of Rhizobium meliloti are coordinately regulated by oxygen. Lois, A.F., Weinstein, M., Ditta, G.S., Helinski, D.R. J. Biol. Chem. (1993) [Pubmed]
  15. Rhizobium meliloti regulatory gene fixJ activates transcription of R. meliloti nifA and fixK genes in Escherichia coli. Hertig, C., Li, R.Y., Louarn, A.M., Garnerone, A.M., David, M., Batut, J., Kahn, D., Boistard, P. J. Bacteriol. (1989) [Pubmed]
  16. The Rhizobium meliloti fdxN gene encoding a ferredoxin-like protein is necessary for nitrogen fixation and is cotranscribed with nifA and nifB. Klipp, W., Reiländer, H., Schlüter, A., Krey, R., Pühler, A. Mol. Gen. Genet. (1989) [Pubmed]
  17. FixJ: a major regulator of the oxygen limitation response and late symbiotic functions of Sinorhizobium meliloti. Bobik, C., Meilhoc, E., Batut, J. J. Bacteriol. (2006) [Pubmed]
  18. The nifA gene product from Rhizobium leguminosarum biovar trifolii lacks the N-terminal domain found in other NifA proteins. Iismaa, S.E., Watson, J.M. Mol. Microbiol. (1989) [Pubmed]
  19. Expression and quantification of firefly luciferase under control of Rhizobium meliloti symbiotic promoters. Cebolla, A., Ruiz-Berraquero, F., Palomares, A.J. J. Biolumin. Chemilumin. (1991) [Pubmed]
  20. Genetic characterization and sequence analysis of the duplicated nifA/nifB gene region of Rhodobacter capsulatus. Masepohl, B., Klipp, W., Pühler, A. Mol. Gen. Genet. (1988) [Pubmed]
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