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Arch Microbiol. 2008 Apr;189(4):357-66. doi: 10.1007/s00203-007-0326-6. Epub 2008 Feb 19.

Excision of the nifD element in the heterocystous cyanobacteria.

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Graduate School of Public Health, Department of Human Genetics, University of Pittsburgh, 315 Paran Hall, 130 De Soto St, Pittsburgh, PA 15261, USA.


Heterocyst differentiation in cyanobacteria is accompanied by developmentally regulated DNA rearrangements that occur within the nifD, fdxN, and hupL genes. These genetic elements are excised from the genome by site-specific recombination during the latter stages of differentiation. The nifD element is excised by the recombinase, XisA, located within the element. Our objective was to examine the XisA-mediated excision of the nifD element. To accomplish this, we observed the ability of XisA to excise substrate plasmids that contained the flanking regions of the nifD element in an E. coli host. Using PCR directed mutagenesis, nucleotides in the nifD element flanking regions in substrate plasmids were altered and the effect on recombination was determined. Results indicate that only certain nucleotides within and surrounding the direct repeats are involved in excision. In some nucleotide positions, the presence of a purine versus a pyrimidine greatly affected recombination. Our results also indicated that the site of excision and branch migration occurs in a 6 bp region within the direct repeats.

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