title: Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers.
abstract: Hammerhead ribozymes represent the most common of the 9 natural classes of self-cleaving RNAs. The hammerhead catalytic core includes 11 highly-conserved nucleotides located largely within the unpaired regions of a junction formed by stems I, II and III. The vast majority of previously reported examples carry an additional pseudoknot or other tertiary interactions between nucleotides that precede stem I and nucleotides in the loop of stem II. These extra contacts are critical for high-speed RNA catalysis. Herein, we report the discovery of ∼150,000 additional variant hammerhead representatives that exhibit diminished stem III substructures. These variants are frequently associated with Penelope-like retrotransposons, which are a type of mobile genetic element. Kinetic analyses indicate that these RNAs form dimers to cleave RNA.
authors.affiliation: a Department of Molecular , Cellular and Developmental Biology, Yale University , New Haven , CT , USA.
authors.forename: Christina E
authors.initials: CE
authors.lastname: Lünse
authors.affiliation: a Department of Molecular , Cellular and Developmental Biology, Yale University , New Haven , CT , USA.|b Howard Hughes Medical Institute (HHMI), Yale University , New Haven , CT , USA.
authors.forename: Zasha
authors.initials: Z
authors.lastname: Weinberg
authors.affiliation: a Department of Molecular , Cellular and Developmental Biology, Yale University , New Haven , CT , USA.|b Howard Hughes Medical Institute (HHMI), Yale University , New Haven , CT , USA.|c Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , CT , USA.
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D055162:Biocatalysis; D020134:Catalytic Domain; D019281:Dimerization; D020049:Isoptera / Q000737:chemistry; D007700:Kinetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D059367:RNA Cleavage; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D016053:RNA, Protozoan / Q000235:genetics / Q000378:metabolism; D018626:Retroelements; D012987:Soil / Q000737:chemistry; D014561:Urochordata / Q000737:chemistry
chemical_list: D016337:RNA, Catalytic; D016053:RNA, Protozoan; D018626:Retroelements; D012987:Soil; C427204:hammerhead ribozyme; D012313:RNA
keywords: Penelope-like retrotransposon; Phosphoester transfer; self-cleaving