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

• Published in: Nucleic acids research 2004-01, Vol.32 (13), p.3947-4956
• Main Authors: Posey, K.L, Koufopanou, V, Burt, A, Gimble, F.S
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino Acids - chemistry; Base Pairing; Base Sequence; Binding Sites; Biological Evolution; Deoxyribonucleases, Type II Site-Specific - metabolism; DNA; DNA Transposable Elements; DNA, Fungal - chemistry; DNA, Fungal - metabolism; endodeoxyribonucleases; Endonucleases - chemistry; Endonucleases - metabolism; enzyme activity; mutants; mutation; Proton-Translocating ATPases - metabolism; Saccharomyces; Saccharomyces - enzymology; Saccharomyces cariocanus; Saccharomyces cerevisiae; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism; Saccharomycetales; Saccharomycetales - enzymology; Saccharomycetales - genetics; Sequence Alignment; Substrate Specificity; VMA1-derived endonuclease; yeasts; Zygosaccharomyces; Zygosaccharomyces - enzymology; Zygosaccharomyces bailii
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkh734

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.