Widespread occurrence of self-cleaving ribozymes.
Hepatitis delta virus (HDV) and cytoplasmic polyadenylation element-binding protein 3 (CPEB3) ribozymes form a family of self-cleaving RNAs characterized by a conserved nested double-pseudoknot and minimal sequence conservation. Secondary structure-based searches were used to identify sequences capable of forming this fold, and their self-cleavage activity was confirmed in vitro. Active sequences were uncovered in several marine organisms, two nematodes, an arthropod, a bacterium, and an insect virus, often in multiple sequence families and copies. Sequence searches based on identified ribozymes showed that plants, fungi, and a unicellular eukaryote also harbor the ribozymes. In Anopheles gambiae, the ribozymes were found differentially expressed and self-cleaved at basic developmental stages. Our results indicate that HDV-like ribozymes are abundant in nature and suggest that self-cleaving RNAs may play a variety of biological roles.
Webb
Chiu-Ho T
CH
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 USA.
Riccitelli
Nathan J
NJ
Ruminski
Dana J
DJ
Lupták
Andrej
A
D000818:Animals; D000852:Anopheles / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D001483:Base Sequence; D002384:Catalysis; D056890:Eukaryota / Q000201:enzymology / Q000235:genetics*; D020224:Expressed Sequence Tags; D003698:Hepatitis Delta Virus / Q000201:enzymology / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*
D016337:RNA, Catalytic