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Gene Review

xisA  -  nifD element site-specific recombinase

Nostoc sp. PCC 7120

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Disease relevance of xisA

  • Site-directed inactivation of the Anabaena xisA gene blocked rearrangement of the 11-kilobase element and nitrogen fixation, but did not affect rearrangement of the 55-kilobase element, heterocyst differentiation, or heterocyst pattern formation [1].
  • Shuttle vectors containing the Escherichia coli tac consensus promoter fused to various 5' deletions of the xisA gene were constructed and conjugated into Anabaena sp. strain PCC 7120 cells [2].
  • These conserved regions include the flanking 3' and 5' regions, the xisA gene, and a small open reading frame known as ORF2 in Nostoc sp. Strain PCC 7120 [3].

High impact information on xisA

  • Genome rearrangement and nitrogen fixation in Anabaena blocked by inactivation of xisA gene [1].
  • The xisA gene, located on the nifD 11-kilobase DNA element, was inactivated by recombination between the chromosome and a copy of the xisA gene that was mutated by inserting an antibiotic gene cassette [1].
  • We have identified a second DNA-binding activity (factor 2) that interacts with rbcL and xisA upstream regions [4].
  • The factor 2 binding site on xisA was localized to a 68-bp region that showed considerable overlap with the BifA binding sites [4].
  • 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 [5].

Biological context of xisA

  • DNase footprinting and deletion analysis of the xisA binding site mapped the binding to a 66-base-pair region containing three repeats of the consensus recognition sequence ACATT [6].
  • Four open reading frames with the same relative orientation as the nifD element-encoded xisA gene were identified in the sequenced region [7].
  • Excision of the element required deletion of an xisA 5' regulatory region which presumably blocks expression in Anabaena sp. strain PCC 7120 vegetative cells but not in E. coli [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].


  1. Genome rearrangement and nitrogen fixation in Anabaena blocked by inactivation of xisA gene. Golden, J.W., Wiest, D.R. Science (1988) [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. Characterization of a 4 kb variant of the nifD element in Anabaena sp. strain ATCC 33047. Henson, B.J., Watson, L.E., Barnum, S.R. Curr. Microbiol. (2005) [Pubmed]
  4. Two Anabaena sp. strain PCC 7120 DNA-binding factors interact with vegetative cell- and heterocyst-specific genes. Ramasubramanian, T.S., Wei, T.F., Golden, J.W. J. Bacteriol. (1994) [Pubmed]
  5. 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]
  6. A sequence-specific DNA-binding factor (VF1) from Anabaena sp. strain PCC 7120 vegetative cells binds to three adjacent sites in the xisA upstream region. Chastain, C.J., Brusca, J.S., Ramasubramanian, T.S., Wei, T.F., Golden, J.W. J. Bacteriol. (1990) [Pubmed]
  7. 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]
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