Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species.
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.
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.
Karen L
KL
Posey
Vassiliki
V
Koufopanou
Austin
A
Burt
Frederick S
FS
Gimble
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D005075:Biological Evolution; D004251:DNA Transposable Elements; D004271:DNA, Fungal / Q000737:chemistry* / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D004720:Endonucleases / Q000737:chemistry / Q000378:metabolism*; D006180:Proton-Translocating ATPases / Q000378:metabolism; D012440:Saccharomyces / Q000201:enzymology; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D004718:Saccharomycetales / Q000201:enzymology* / Q000235:genetics; D016415:Sequence Alignment; D013379:Substrate Specificity; D020068:Zygosaccharomyces / Q000201:enzymology
D000596:Amino Acids; D004251:DNA Transposable Elements; D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D004720:Endonucleases; C047020:endodeoxyribonuclease ScaI; D015252:Deoxyribonucleases, Type II Site-Specific; D006180:Proton-Translocating ATPases; C081687:VMA1 protein, S cerevisiae