Excision of the nifD element in the heterocystous cyanobacteria
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ORIGINAL PAPER
Excision of the nifD element in the heterocystous cyanobacteria B. J. Henson · L. E. Pennington · L. E. Watson · S. R. Barnum
Received: 8 March 2007 / Revised: 17 October 2007 / Accepted: 2 November 2007 / Published online: 19 February 2008 © Springer-Verlag 2008
Abstract Heterocyst diVerentiation 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-speciWc recombination during the latter stages of diVerentiation. 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 Xanking regions of the nifD element in an E. coli host. Using PCR directed mutagenesis, nucleotides in the nifD element Xanking regions in substrate plasmids were altered and the eVect 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 aVected recombination. Our results also indicated that the
Communicated by Jack Meeks. Electronic supplementary material The online version of this article (doi:10.1007/s00203-007-0326-6) contains supplementary material, which is available to authorized users. B. J. Henson Graduate School of Public Health, Department of Human Genetics, University of Pittsburgh, 315 Paran Hall, 130 De Soto St, Pittsburgh, PA 15261, USA L. E. Pennington · L. E. Watson · S. R. Barnum (&) Department of Botany, Miami University, 314 Pearson Hall, 700 East High St, Oxford, OH 45056, USA e-mail: [email protected]
site of excision and branch migration occurs in a 6 bp region within the direct repeats. Keywords nifD Element · xisA · Developmentally regulated DNA rearrangement · Site-speciWc recombination
Introduction Homologous recombination involves the exchange of genetic information between two molecules of DNA that contain long stretches of sequence similarity. Site-speciWc recombination diVers in that the exchange occurs between DNA molecules with short stretches of sequence similarity (i.e., direct repeats or inverted repeats). The enzymes that perform these reactions are classiWed as site-speciWc recombinases, and they catalyze a number of reactions including integrations (insertions), inversions, or excisions (deletions). Site-speciWc recombinases are currently divided into the serine family (resolvases/invertases) and the tyrosine family (phage integrases), and the two are evolutionarily and functionally unrelated (Nunes-Düby et al. 1998; Smith and Thorpe 2002). Within the serine family, resolvases typically only recognize direct repeats and excise the DNA between them, whereas the invertases recognize inverted repeats and invert the DNA between them. In addition the invertases also require a FIS (factor f
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