Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations

• Published in: PLoS computational biology Vol. 7; no. 5; p. e1002031
• Main Authors: Perreault, Jonathan, Weinberg, Zasha, Roth, Adam, Popescu, Olivia, Chartrand, Pascal, Ferbeyre, Gerardo, Breaker, Ronald R.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.05.2011; Public Library of Science (PLoS)
• Subjects: Abundance; Agrobacterium tumefaciens - genetics; Animals; Archaea; Azorhizobium caulinodans - genetics; Base Sequence; Bioinformatics; Biology; Catalytic RNA; Clostridium - genetics; Computational Biology; Computer applications; Data processing; Fungi; Gene mutations; Genetic transcription; Genome; Genomes; genomics; Humans; Life sciences; Magnesium - chemistry; Medical research; Models, Molecular; Molecular Sequence Data; Mutation; Nucleic Acid Conformation; Nucleotide sequence; Nucleotides; Phylogeny; Physiological aspects; Ribozymes; RNA; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Catalytic - chemistry; RNA, Catalytic - genetics; Satellites; Studies; Swine; Viroids; Canada; United States; Clostridium; Humans; Computational Biology; Agrobacterium tumefaciens; Models, Molecular; Molecular Sequence Data; Phylogeny; RNA, Catalytic; Azorhizobium caulinodans; Animals; Swine; Base Sequence; RNA, Bacterial; Magnesium; Mutation; Genome; Nucleic Acid Conformation
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1002031

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.