Chemistry and Biology of Self-Cleaving Ribozymes
- PMID: 26481500
- PMCID: PMC4630146
- DOI: 10.1016/j.tibs.2015.09.001
Chemistry and Biology of Self-Cleaving Ribozymes
Abstract
Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure, with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be used as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered.
Keywords: aptazymes; retrotransposon; riboregulation; riboswitch; ribozyme; self-scission.
Copyright © 2015 Elsevier Ltd. All rights reserved.
Figures




Similar articles
-
Kinetic Parameters of trans Scission by Extended HDV-like Ribozymes and the Prospect for the Discovery of Genomic trans-Cleaving RNAs.Biochemistry. 2018 Mar 6;57(9):1440-1450. doi: 10.1021/acs.biochem.7b00789. Epub 2018 Feb 13. Biochemistry. 2018. PMID: 29388767
-
Biochemical analysis of pistol self-cleaving ribozymes.RNA. 2015 Nov;21(11):1852-8. doi: 10.1261/rna.052514.115. Epub 2015 Sep 18. RNA. 2015. PMID: 26385507 Free PMC article.
-
Catalytic strategies of self-cleaving ribozymes.Acc Chem Res. 2008 Aug;41(8):1027-35. doi: 10.1021/ar800050c. Epub 2008 Jul 25. Acc Chem Res. 2008. PMID: 18652494 Review.
-
Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs.Genome Biol. 2016 Jun 23;17(1):135. doi: 10.1186/s13059-016-1002-4. Genome Biol. 2016. PMID: 27339130 Free PMC article.
-
HDV family of self-cleaving ribozymes.Prog Mol Biol Transl Sci. 2013;120:123-71. doi: 10.1016/B978-0-12-381286-5.00004-4. Prog Mol Biol Transl Sci. 2013. PMID: 24156943 Review.
Cited by
-
Allosteric Modulation of the Faecalibacterium prausnitzii Hepatitis Delta Virus-like Ribozyme by Glucosamine 6-Phosphate: The Substrate of the Adjacent Gene Product.Biochemistry. 2017 Nov 14;56(45):6006-6014. doi: 10.1021/acs.biochem.7b00879. Epub 2017 Nov 3. Biochemistry. 2017. PMID: 29045794 Free PMC article.
-
The case of the missing allosteric ribozymes.Nat Chem Biol. 2021 Apr;17(4):375-382. doi: 10.1038/s41589-020-00713-2. Epub 2021 Jan 25. Nat Chem Biol. 2021. PMID: 33495645 Free PMC article. Review.
-
Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes From Comparative Analysis of Active Sites.ACS Catal. 2018 Jan 5;8(1):314-327. doi: 10.1021/acscatal.7b02976. Epub 2017 Dec 8. ACS Catal. 2018. PMID: 32547833 Free PMC article.
-
Ribocentre: a database of ribozymes.Nucleic Acids Res. 2023 Jan 6;51(D1):D262-D268. doi: 10.1093/nar/gkac840. Nucleic Acids Res. 2023. PMID: 36177882 Free PMC article.
-
The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes.RNA. 2021 Sep;27(9):1017-1024. doi: 10.1261/rna.078813.121. Epub 2021 Jun 15. RNA. 2021. PMID: 34131025 Free PMC article.
References
-
- Lai MM. The molecular biology of hepatitis delta virus. Annu Rev Biochem. 1995;64:259–286. - PubMed
-
- Taylor JM. Hepatitis delta virus. Intervirology. 1999;42:173–178. - PubMed
-
- Salehi-Ashtiani K, Luptak A, Litovchick A, Szostak JW. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science. 2006;313:1788–1792. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources