title: New classes of self-cleaving ribozymes revealed by comparative genomics analysis.
abstract: Enzymes made of RNA catalyze reactions that are essential for protein synthesis and RNA processing. However, such natural ribozymes are exceedingly rare, as evidenced by the fact that the discovery rate for new classes has dropped to one per decade from about one per year during the 1980s. Indeed, only 11 distinct ribozyme classes have been experimentally validated to date. Recently, we recognized that self-cleaving ribozymes frequently associate with certain types of genes from bacteria. Herein we exploited this association to identify divergent architectures for two previously known ribozyme classes and to discover additional noncoding RNA motifs that are self-cleaving RNA candidates. We identified three new self-cleaving classes, which we named twister sister, pistol and hatchet, from this collection, suggesting that even more ribozymes remain hidden in modern cells.
authors.affiliation: 1] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA. [2] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
authors.forename: Zasha
authors.initials: Z
authors.lastname: Weinberg
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
authors.forename: Peter B
authors.initials: PB
authors.lastname: Kim
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
authors.forename: Tony H
authors.initials: TH
authors.lastname: Chen
authors.affiliation: 1] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA. [2] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
authors.forename: Sanshu
authors.initials: S
authors.lastname: Li
authors.affiliation: 1] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA. [2] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
authors.forename: Kimberly A
authors.identifier: 0000000330285863
authors.initials: KA
authors.lastname: Harris
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
authors.forename: Christina E
authors.identifier: 0000000228261734
authors.initials: CE
authors.lastname: Lünse
authors.affiliation: 1] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA. [2] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA. [3] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000201:enzymology / Q000235:genetics*; D001419:Bacteria / Q000201:enzymology / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D014176:Protein Biosynthesis; D059748:Proteolysis; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D016337:RNA, Catalytic