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Gene Review

nifH  -  nitrogenase reductase

Sinorhizobium meliloti 1021

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Disease relevance of nifH

  • 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 [1].
  • The 5'-regulatory region and amino-terminal end of the first open reading frame of the mos locus are highly homologous to the 5'-regulatory region and amino-terminal portion of the Rhizobium meliloti nifH gene [2].
  • These phages had mutations within the nifH promoter that decreased the affinity of the promoter for E sigma54 [3].
  • When a Salmonella typhimurium strain that overexpressed sigma54 was infected with these challenge phages, E sigma54 bound to the nifH promoter and repressed transcription of the ant gene as seen by the increased frequency of lysogeny [3].
  • However, nifH sequences, most similar to those of Sinorhizobium meliloti, were detected within strains related to the genera Microbacterium, Agromyces, Starkeya and Phyllobacterium [4].

High impact information on nifH

  • In the R. meliloti nifH and K. pneumoniae nifL promoters, in which the transcription initiation sites have been determined, the consensus sequence is situated in the -15 region [5].
  • IHF fails to stimulate activation of transcription from this promoter by another activator of sigma 54-holoenzyme, NTRC (nitrogen regulatory protein C), which lacks a specific binding site in the nifH promoter region [6].
  • Reverse transcription-PCR with RNA isolated from mature alfalfa nodules yielded no products for rhbF or rhtA at a time when the nifH gene was strongly expressed, indicating that siderophore biosynthesis and transport genes are not strongly expressed when nitrogenase is being formed in root nodules [7].
  • The efficient nitrogen fixation is a result of the higher expression level of the nifH gene, encoding one of the subunits of the nitrogenase enzyme, and nifA, the transcriptional regulator of the nif operon [8].
  • Following mutagenesis of challenge phages that carried the R. meliloti nifH promoter, mutant phages that could form plaques on an S. typhimurium strain that overexpressed sigma54 were isolated [3].

Chemical compound and disease context of nifH

  • Unlike wild-type sigma(54), holoenzymes assembled with the R383A or R383K mutants could not form activator-independent, heparin-stable complexes on heteroduplex Sinorhizobium meliloti nifH DNA mismatched next to the GC [9].

Biological context of nifH


Associations of nifH with chemical compounds

  • Furthermore, we show that both repeats bound dctD protein and that together they resulted in succinate-sensitive transcription when placed upstream of another sigma 54 consensus promoter, that of R. meliloti nifH [13].

Other interactions of nifH

  • The diversity of the symbiotic genes was then assessed by PCR-RFLP of nodC and nifH genes [14].

Analytical, diagnostic and therapeutic context of nifH

  • A 12.1-kilobase PstI fragment from Rhizobium japonicum, which contains homology to both the Klebsiella pneumoniae and the Rhizobium meliloti nifH genes, was cloned into vector pHE3 . The nifH -homologous region was localized on the restriction enzyme cleavage map by Southern blot hybridization experiments [10].
  • A cultivation-independent approach was used to identify potentially nitrogen-fixing endophytes in seven sweet potato varieties collected in Uganda and Kenya. Nitrogenase reductase genes (nifH) were amplified by PCR, and amplicons were cloned in Escherichia coli [11].
  • We have attempted to visualize the arrangement of proteins on DNA fragments carrying the nifH promoter-regulatory region of K. pneumoniae by electron microscopy [6].


  1. A Rhizobium meliloti symbiotic regulatory gene. Szeto, W.W., Zimmerman, J.L., Sundaresan, V., Ausubel, F.M. Cell (1984) [Pubmed]
  2. Synthesis of an opine-like compound, a rhizopine, in alfalfa nodules is symbiotically regulated. Murphy, P.J., Heycke, N., Trenz, S.P., Ratet, P., de Bruijn, F.J., Schell, J. Proc. Natl. Acad. Sci. U.S.A. (1988) [Pubmed]
  3. Genetic analysis of the Rhizobium meliloti nifH promoter, using the P22 challenge phage system. Ashraf, S.I., Kelly, M.T., Wang, Y.K., Hoover, T.R. J. Bacteriol. (1997) [Pubmed]
  4. Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya. Zakhia, F., Jeder, H., Willems, A., Gillis, M., Dreyfus, B., de Lajudie, P. Microb. Ecol. (2006) [Pubmed]
  5. 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]
  6. Role of integration host factor in stimulating transcription from the sigma 54-dependent nifH promoter. Santero, E., Hoover, T.R., North, A.K., Berger, D.K., Porter, S.C., Kustu, S. J. Mol. Biol. (1992) [Pubmed]
  7. Genetic organization of the region encoding regulation, biosynthesis, and transport of rhizobactin 1021, a siderophore produced by Sinorhizobium meliloti. Lynch, D., O'Brien, J., Welch, T., Clarke, P., Cuív, P.O., Crosa, J.H., O'Connell, M. J. Bacteriol. (2001) [Pubmed]
  8. Mutation in the ntrR gene, a member of the vap gene family, increases the symbiotic efficiency of Sinorhizobium meliloti. Oláh, B., Kiss, E., Györgypál, Z., Borzi, J., Cinege, G., Csanádi, G., Batut, J., Kondorosi, A., Dusha, I. Mol. Plant Microbe Interact. (2001) [Pubmed]
  9. In vitro roles of invariant helix-turn-helix motif residue R383 in sigma(54) (sigma(N)). Wigneshweraraj, S.R., Ishihama, A., Buck, M. Nucleic Acids Res. (2001) [Pubmed]
  10. Rhizobium japonicum nitrogenase Fe protein gene (nifH). Fuhrmann, M., Hennecke, H. J. Bacteriol. (1984) [Pubmed]
  11. Endophytic nifH gene diversity in African sweet potato. Reiter, B., Bürgmann, H., Burg, K., Sessitsch, A. Can. J. Microbiol. (2003) [Pubmed]
  12. nifH promoter activity is regulated by DNA supercoiling in Sinorhizobium meliloti. Liu, Y.J., Hu, B., Zhu, J.B., Shen, S.J., Yu, G.Q. Acta Biochim. Biophys. Sin. (Shanghai) (2005) [Pubmed]
  13. Rhizobium meliloti and Rhizobium leguminosarum dctD gene products bind to tandem sites in an activation sequence located upstream of sigma 54-dependent dctA promoters. Ledebur, H., Gu, B., Sojda, J., Nixon, B.T. J. Bacteriol. (1990) [Pubmed]
  14. Salt-tolerant rhizobia isolated from a Tunisian oasis that are highly effective for symbiotic N(2)-fixation with Phaseolus vulgaris constitute a novel biovar (bv. mediterranense) of Sinorhizobium meliloti. Mnasri, B., Mrabet, M., Laguerre, G., Aouani, M.E., Mhamdi, R. Arch. Microbiol. (2007) [Pubmed]
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