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Gene Review

nifD  -  nitrogenase molybdenum-iron protein...

Nostoc sp. PCC 7120

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Disease relevance of nifD

  • The nitrogen fixation gene nifD was completely sequenced from representatives of these genera and analyzed phylogenetically, by using the representatives of other genera of the heterocystous cyanobacteria as outgroups [1].
  • An 11-kilobase-pair element interrupts the nifD gene in vegetative cells of Anabaena sp. strain PCC 7120 [2].
  • The xisA gene was shown to be the only Anabaena gene required for the proper rearrangement in E. coli of a plasmid containing the borders of the nifD element [2].
  • Southern analysis of vegetative cell and heterocyst DNA from A. cylindrica and a Fox+ revertant of Nostoc Mac (isolate R2) showed rearrangement of the nifD and fdxN elements in heterocysts [3].

High impact information on nifD

  • The DNA elements are named after the genes that they interrupt: nifD, fdxN, and hupL [4].
  • In the NtcA-overproducing strain, heterocyst differentiation, induction of NtcA-dependent heterocyst development genes or operons such as devBCA or the cox2 operon, and NtcA-dependent excision of the 11-kb nifD-intervening element only took place under nitrogen deficiency [5].
  • The ntcA mutant was unable to form heterocysts and did not rearrange the nifD or fdxN elements after induction on a medium lacking combined nitrogen [6].
  • Similar inverted repeats are found within each of those three segments, and the sequences of these repeats bear some similarity to the 11-bp direct repeats flanking the 11-kb insertion interrupting the nifD gene of this strain (J. W. Golden, S. J. Robinson, and R. Haselkorn, Nature [London] 314:419-423, 1985) [7].
  • RFLP analyses with Anabaena sp. strain PCC 7120 nifD excision element probes, including an xisA gene probe, detected homologous sequences in DNA extracted from the free-living isolates [8].

Chemical compound and disease context of nifD

  • Alkane-induced expression, substrate binding profile, and immunolocalization of a cytochrome P450 encoded on the nifD excision element of Anabaena 7120 [9].

Biological context of nifD

  • In developing heterocysts the nifD element excises from the chromosome via site-specific recombination between short repeat sequences that flank the element [10].
  • Although the nifD 11-kb and nifS 55-kb rearrangements both occurred under normal aerobic heterocyst-inducing conditions, only the 55-kb excision occurred in argon-bubbled cultures, indicating that the two DNA rearrangements can be regulated differently [11].
  • Some of the expression plasmids resulted in excision of the nifD element in a high proportion of vegetative cells [2].
  • Four open reading frames with the same relative orientation as the nifD element-encoded xisA gene were identified in the sequenced region [10].
  • Developmental rearrangement of cyanobacterial nif genes: nucleotide sequence, open reading frames, and cytochrome P-450 homology of the Anabaena sp. strain PCC 7120 nifD element [10].

Other interactions of nifD

  • The Anabaena strain 7120 xisA gene is located at the nifK-proximal end of the nifD element and is required for excision of the element in heterocysts [12].
  • Sequence analysis revealed regions of DNA that may form stem-loop structures in the intercistronic regions downstream of nifH and nifD [13].


  1. Molecular differentiation of the heterocystous cyanobacteria, Nostoc and Anabaena, based on complete NifD sequences. Henson, B.J., Watson, L.E., Barnum, S.R. Curr. Microbiol. (2002) [Pubmed]
  2. Expression of the Anabaena sp. strain PCC 7120 xisA gene from a heterologous promoter results in excision of the nifD element. Brusca, J.S., Chastain, C.J., Golden, J.W. J. Bacteriol. (1990) [Pubmed]
  3. Two heterocyst-specific DNA rearrangements of nif operons in Anabaena cylindrica and Nostoc sp. strain Mac. Carrasco, C.D., Golden, J.W. Microbiology (Reading, Engl.) (1995) [Pubmed]
  4. Heterocyst-specific excision of the Anabaena sp. strain PCC 7120 hupL element requires xisC. Carrasco, C.D., Holliday, S.D., Hansel, A., Lindblad, P., Golden, J.W. J. Bacteriol. (2005) [Pubmed]
  5. HetR-dependent and -independent expression of heterocyst-related genes in an Anabaena strain overproducing the NtcA transcription factor. Olmedo-Verd, E., Flores, E., Herrero, A., Muro-Pastor, A.M. J. Bacteriol. (2005) [Pubmed]
  6. Anabaena sp. strain PCC 7120 ntcA gene required for growth on nitrate and heterocyst development. Wei, T.F., Ramasubramanian, T.S., Golden, J.W. J. Bacteriol. (1994) [Pubmed]
  7. Characterization of insertion sequence IS892 and related elements from the cyanobacterium Anabaena sp. strain PCC 7120. Cai, Y. J. Bacteriol. (1991) [Pubmed]
  8. Identification of a common cyanobacterial symbiont associated with Azolla spp. through molecular and morphological characterization of free-living and symbiotic cyanobacteria. Gebhardt, J.S., Nierzwicki-Bauer, S.A. Appl. Environ. Microbiol. (1991) [Pubmed]
  9. Alkane-induced expression, substrate binding profile, and immunolocalization of a cytochrome P450 encoded on the nifD excision element of Anabaena 7120. Torres, S., Fjetland, C.R., Lammers, P.J. BMC Microbiol. (2005) [Pubmed]
  10. Developmental rearrangement of cyanobacterial nif genes: nucleotide sequence, open reading frames, and cytochrome P-450 homology of the Anabaena sp. strain PCC 7120 nifD element. Lammers, P.J., McLaughlin, S., Papin, S., Trujillo-Provencio, C., Ryncarz, A.J. J. Bacteriol. (1990) [Pubmed]
  11. Deletion of a 55-kilobase-pair DNA element from the chromosome during heterocyst differentiation of Anabaena sp. strain PCC 7120. Golden, J.W., Carrasco, C.D., Mulligan, M.E., Schneider, G.J., Haselkorn, R. J. Bacteriol. (1988) [Pubmed]
  12. Excision of an 11-kilobase-pair DNA element from within the nifD gene in anabaena variabilis heterocysts. Brusca, J.S., Hale, M.A., Carrasco, C.D., Golden, J.W. J. Bacteriol. (1989) [Pubmed]
  13. Cloning and transcriptional analysis of the nifUHDK genes of Trichodesmium sp. IMS101 reveals stable nifD, nifDK and nifK transcripts. Dominic, B., Chen, Y.B., Zehr, J.P. Microbiology (Reading, Engl.) (1998) [Pubmed]
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