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Gene Review:

nifD - nitrogenase molybdenum-iron protein...

Bradyrhizobium diazoefficiens USDA 110

Parker, M.A. et al., Noti, J.D. et al., Yun, A.C. et al., Wang, S.Z. et al., Masterson, R.V. et al., et al.

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Disease relevance of nifD

DNA fragments containing either the nifD or nifH promoter and 5' structural gene sequences from Bradyrhizobium japonicum I110 were fused in frame to the lacZ gene [1].
A total of 96 independent Tn5 insertions within a 39-kilobase-pair (kbp) segment of chromosomal DNA containing the three structural genes for nitrogenase (nifH, nifD, and nifK) from Bradyhizobium japonicum I110 were obtained in Escherichia coli and transferred to the wild-type strain by marker exchange [2].
Structural genes (nifD and nifK) encoding alpha and beta subunits of the MoFe protein of Clostridium pasteurianum (Cp) have been cloned and sequenced [3].
The DNA sequence was determined for the cloned Thiobacillus ferrooxidans nifH and part of the nifD genes [4].

High impact information on nifD

We investigated the interaction of NifA with the nifD promoter region by using in vivo dimethyl sulfate footprinting [5].
This is in clear contrast to the situation with nifH and nifD promoters [6].
Slow-growing R. japonicum strains do not harbor structural nif genes, homologous to nifD and nifH, on large plasmids (100 to 200 megadaltons) [7].
No evidence for any gene duplication of nifD was found by Southern hybridization analysis on a subset of the strains, so unrecognized paralogy is not likely to be responsible for the discrepancy between 16S rRNA and nifD tree topologies [8].
These results are consistent with a model whereby geographic areas were initially colonized by several diverse 16S rRNA lineages, with subsequent horizontal gene transfer of nifD leading to increased nifD sequence homogeneity within each regional population [8].

Biological context of nifD

Isolates that were closely related or identical in gene sequence at one locus often had divergent sequences at the other locus and a partition homogeneity test indicated that the 16S rRNA and nifD phylogenies were significantly incongruent [8].

Other interactions of nifD

The nifD gene (coding for the beta-subunit of dinitrogenase) and nifE are linked, and separated by 95 nucleotides [9].

References

Nitrogenase promoter-lacZ fusion studies of essential nitrogen fixation genes in Bradyrhizobium japonicum I110. Yun, A.C., Noti, J.D., Szalay, A.A. J. Bacteriol. (1986) [Pubmed]
Organization and characterization of genes essential for symbiotic nitrogen fixation from Bradyrhizobium japonicum I110. Noti, J.D., Folkerts, O., Turken, A.N., Szalay, A.A. J. Bacteriol. (1986) [Pubmed]
Distinct structural features of the alpha and beta subunits of nitrogenase molybdenum-iron protein of Clostridium pasteurianum: an analysis of amino acid sequences. Wang, S.Z., Chen, J.S., Johnson, J.L. Biochemistry (1988) [Pubmed]
Nucleotide sequence of the gene encoding the nitrogenase iron protein of Thiobacillus ferrooxidans. Pretorius, I.M., Rawlings, D.E., O'Neill, E.G., Jones, W.A., Kirby, R., Woods, D.R. J. Bacteriol. (1987) [Pubmed]
Influence of oxygen on DNA binding, positive control, and stability of the Bradyrhizobium japonicum NifA regulatory protein. Morett, E., Fischer, H.M., Hennecke, H. J. Bacteriol. (1991) [Pubmed]
Regulation of the fixA gene and fixBC operon in Bradyrhizobium japonicum. Gubler, M., Hennecke, H. J. Bacteriol. (1988) [Pubmed]
Nitrogen fixation (nif) genes and large plasmids of Rhizobium japonicum. Masterson, R.V., Russell, P.R., Atherly, A.G. J. Bacteriol. (1982) [Pubmed]
Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium. Parker, M.A., Lafay, B., Burdon, J.J., van Berkum, P. Microbiology (Reading, Engl.) (2002) [Pubmed]
The nifEN genes participating in FeMo cofactor biosynthesis and genes encoding dinitrogenase are part of the same operon in Bradyrhizobium species. Aguilar, O.M., Taormino, J., Thöny, B., Ramseier, T., Hennecke, H., Szalay, A.A. Mol. Gen. Genet. (1990) [Pubmed]

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