title: Identification of hammerhead ribozymes in all domains of life reveals novel structural variations.
abstract: Hammerhead ribozymes are small self-cleaving RNAs that promote strand scission by internal phosphoester transfer. Comparative sequence analysis was used to identify numerous additional representatives of this ribozyme class than were previously known, including the first representatives in fungi and archaea. Moreover, we have uncovered the first natural examples of "type II" hammerheads, and our findings reveal that this permuted form occurs in bacteria as frequently as type I and III architectures. We also identified a commonly occurring pseudoknot that forms a tertiary interaction critical for high-speed ribozyme activity. Genomic contexts of many hammerhead ribozymes indicate that they perform biological functions different from their known role in generating unit-length RNA transcripts of multimeric viroid and satellite virus genomes. In rare instances, nucleotide variation occurs at positions within the catalytic core that are otherwise strictly conserved, suggesting that core mutations are occasionally tolerated or preferred.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Perreault
authors.forename: Zasha
authors.initials: Z
authors.lastname: Weinberg
authors.forename: Adam
authors.initials: A
authors.lastname: Roth
authors.forename: Olivia
authors.initials: O
authors.lastname: Popescu
authors.forename: Pascal
authors.initials: P
authors.lastname: Chartrand
authors.forename: Gerardo
authors.initials: G
authors.lastname: Ferbeyre
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D016960:Agrobacterium tumefaciens / Q000235:genetics; D000818:Animals; D020599:Azorhizobium caulinodans / Q000235:genetics; D001483:Base Sequence; D003013:Clostridium / Q000235:genetics; D019295:Computational Biology; D016678:Genome; D006801:Humans; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics*; D013552:Swine
chemical_list: D012329:RNA, Bacterial; D016337:RNA, Catalytic; C427204:hammerhead ribozyme; D008274:Magnesium