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Nucleic Acids Research 2004 32(13):3947-3956; doi:10.1093/nar/gkh734
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Published online 27 July 2004

Nucleic Acids Research, Vol. 32 No. 13 © Oxford University Press 2004; all rights reserved

Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species

Karen L. Posey, Vassiliki Koufopanou1, Austin Burt1 and Frederick S. Gimble*

Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, 2121 W. Holcombe Blvd, Houston, TX 77030, USA and 1 Department of Biological Sciences, Imperial College, Silwood Park, Ascot, Berkshire, SL5 7PY, UK

* To whom correspondence should be addressed. Tel: +1 713 677 7605; Fax: +1 713 677 7689; Email: fgimble{at}ibt.tamhsc.edu

Received April 29, 2004; Revised July 2, 2004; Accepted July 12, 2004

Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. Several yeast species contain the VMA1 HEG that encodes the intein-associated VMA1-derived endonuclease (VDE). The evolutionary state of VDEs from 12 species was assessed by assaying their endonuclease activities. Only two enzymes are active, PI-ZbaI from Zygosaccharomyces bailii and PI-ScaI from Saccharomyces cariocanus. PI-ZbaI cleaves the Z.bailii recognition sequence significantly faster than the Saccharomyces cerevisiae site, which differs at six nucleotide positions. A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI between Gln-55 and nucleotides +9/+10. PI-ZbaI cleaves the Z.bailii substrate primarily due to a single base-pair substitution (A/T+5 -> T/A+5). Structural modeling of the PI-ZbaI/DNA complex suggests that Arg-331, which is absent in PI-SceI, contacts T/A+5, and the reduced activity observed in a PI-ZbaI R331A mutant provides evidence for this interaction. These data illustrate that homing endonucleases evolve altered specificity as they adapt to recognize alternative target sites.


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