RNA editing is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within a RNA molecule after it has been generated by RNA polymerase. RNA editing is relatively rare, and common forms of RNA processing (e.g. splicing, 5'-capping and 3'-polyadenylation) are not usually included as editing. Editing events may include the insertion, deletion, and base substitution of nucleotides within the edited RNA molecule.
RNA editing has been observed in some tRNA, rRNA, mRNA or miRNA molecules of eukaryotes and their viruses, archaea and prokaryotes. RNA editing occurs in the cell nucleus and cytosol, as well as within mitochondria and plastids. In vertebrates, editing is rare and usually consists of a small number of changes to the sequence of affected molecules. In other organisms, extensive editing (pan-editing) can occur; in some cases the majority of nucleotides in a mRNA sequence may result from editing.
RNA-editing processes show great molecular diversity, and some appear to be evolutionarily recent acquisitions that arose independently. The diversity of RNA editing phenomena includes nucleobase modifications such as cytidine (C) to uridine (U) and adenosine (A) to inosine (I) deaminations, as well as non-templated nucleotide additions and insertions. RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence.
Editing by insertion or deletion
RNA editing through the addition and deletion of uracil has been found in kinetoplasts from the mitochondria of Trypanosoma brucei Because this may involve a large fraction of the sites in a gene, it is sometimes called "pan-editing" to distinguish it from topical editing of one or a few sites.
Pan-editing starts with the base-pairing of the unedited primary transcript with a guide RNA (gRNA), which contains complementary sequences to the regions around the insertion/deletion points. The newly formed double-stranded region is then enveloped by an editosome, a large multi-protein complex that catalyzes the editing. The editosome opens the transcript at the first mismatched nucleotide and starts inserting uridines. The inserted uridines will base-pair with the guide RNA, and insertion will continue as long as A or G is present in the guide RNA and will stop when a C or U is encountered. The inserted nucleotides cause a frameshift and result in a translated protein that differs from its gene.
The mechanism of the editosome involves an endonucleolytic cut at the mismatch point between the guide RNA and the unedited transcript. The next step is catalyzed by one of the enzymes in the complex, a terminal U-transferase, which adds Us from UTP at the 3’ end of the mRNA. The opened ends are held in place by other proteins in the complex. Another enzyme, a U-specific exoribonuclease, removes the unpaired Us. After editing has made mRNA complementary to gRNA, an RNA ligase rejoins the ends of the edited mRNA transcript. As a consequence, the editosome can edit only in a 3’ to 5’ direction along the primary RNA transcript. The complex can act on only a single guide RNA at a time. Therefore, a RNA transcript requiring extensive editing will need more than one guide RNA and editosome complex.
Editing by deamination
The editing involves cytidine deaminase that deaminates a cytidine base into a uridine base. An example of C-to-U editing is with the apolipoprotein B gene in humans. Apo B100 is expressed in the liver and apo B48 is expressed in the intestines. In the intestines, the mRNA has a CAA sequence edited to be UAA, a stop codon, thus producing the shorter B48 form.
A-to-I editing is the main form of RNA editing in mammals and occurs in regions of double-stranded RNA (dsRNA). Adenosine deaminases acting on RNA (ADARs) are the RNA-editing enzymes involved in the hydrolytic deamination of Adenosine to Inosine (A-to-I editing). A-to-I editing can be specific (a single adenosine is edited within the stretch of dsRNA) or promiscuous (up to 50% of the adenosines are edited). Specific editing occurs within short duplexes (e.g., those formed in an mRNA where intronic sequence base pairs with a complementary exonic sequence), while promiscuous editing occurs within longer regions of duplex (e.g., pre- or pri-miRNAs, duplexes arising from transgene or viral expression, duplexes arising from paired repetitive elements). There are many effects of A-to-I editing, arising from the fact that I behaves as if it is G both in translation and when forming secondary structures. These effects include alteration of coding capacity, altered miRNA or siRNA target populations, heterochromatin formation, nuclear sequestration, cytoplasmic sequestration, endonucleolytic cleavage by Tudor-SN, inhibition of miRNA and siRNA processing, and altered splicing.
RNA editing in plant mitochondria and plastids
It has been shown in previous studies that the only types of RNA editing seen in the plants’ mitochondria and plastids are conversion of C to U and U to C (very rare). RNA-editing sites are found mainly in the coding regions of mRNA, introns, and other non-translated regions. In fact, RNA editing can restore the functionality of tRNA molecules. The editing sites are found primarily upstream of mitochondrial or plastid RNAs. The exact mechanism is unknown, but previous studies have speculated the involvement of gRNA and the editosome complex. The reason behind that specific idea arose from the fact that there are too many editing sites that needed to be changed in those organelles for a deaminase.
RNA editing is essential for the normal functioning of the plant’s translation and respiration activity. Editing can restore the essential base-pairing sequences of tRNAs, restoring functionality. It has also been linked to the production of RNA-edited proteins that are incorporated into the polypeptide complexes of the respiration pathway. Therefore, it is highly probable that polypeptides synthesized from unedited RNAs would not function properly and hinder the activity of both mitochondria and plastids.
RNA editing in viruses
RNA editing in viruses (i.e., measles, mumps, or parainfluenza) are used for stability and generation of protein variants. Viral RNAs are transcribed by a virus-encoded RNA-dependent RNA polymerase, which is prone to pausing and “stuttering” at certain nucleotide combinations. In addition, up to several hundred non-templated As are added by the polymerase at the 3’ end of nascent mRNA. These As help stabilize the mRNA. Furthermore, the pausing and stuttering of the RNA polymerase allows the incorporation of one or two Gs or As upstream of the translational codon. The addition of the non-templated nucleotides shifts the reading frame, which generates a different protein.
Origin and evolution of RNA editing
The RNA-editing system seen in the animal may have evolved from mononucleotide deaminases, which have led to larger gene families that include the apobec-1 and adar genes. These genes share close identity with the bacterial deaminases involved in nucleotide metabolism. The adenosine deaminase of E. coli cannot deaminate a nucleoside in the RNA; the enzyme’s reaction pocket is too small to for the RNA strand to bind to. However, this active site is widened by amino acid changes in the corresponding human analog genes, APOBEC-1 and ADAR, allowing deamination. The gRNA-mediated pan-editing in trypanosome mitochondria, involving templated insertion of U residues, is an entirely different biochemical reaction. The enzymes involved have been shown in other studies to be recruited and adapted from different sources. But, the specificity of nucleotide insertion via the interaction between the gRNA and mRNA are similar to the tRNA editing processes in the animal and Acanthamoeba mithochondria. Eukaryotic ribose methylation of rRNAs by guide RNA molecules is a similar form of modification.
Thus, RNA editing evolved more than once. Several adaptive rationales for editing have been suggested. Editing is often described as a mechanism of correction or repair to compensate for defects in gene sequences. However, in the case of gRNA-mediated editing, this explanation does not seem possible because if a defect happens first, there is no way to generate an error-free gRNA-encoding region, which presumably arises by duplication of the original gene region. This thinking leads to an evolutionary proposal called "constructive neutral evolution" in which the order of steps is reversed, with the gratuitous capacity for editing preceding the "defect". 31
RNA editing may be involved in RNA degradation
A recent study looked at the involvement of RNA editing in RNA degradation. The researchers specifically looked at the interaction between ADAR1 and hUpf1, an enzyme involved in the nonsense-mediated mRNA decay pathway(NMD). They found that ADAR1 and hUpf1 are found within the suprasliceosome and they form a complex that leads to the down-regulation of specific genes. The exact mechanism or the exact pathways that these two are involved in are unknown at this time. The only fact that this research has shown is that they form a complex and down-regulate specific genes.
- Su, AA; Randau, L (August 2011). "A-to-I and C-to-U editing within transfer RNAs.". Biochemistry. Biokhimiia 76 (8): 932–7. doi:10.1134/S0006297911080098. PMID 22022967.
- Brennicke, A., A. Marchfelder, et al. (1999). "RNA editing". FEMS Microbiol Rev 23 (3): 297–316. doi:10.1111/j.1574-6976.1999.tb00401.x. PMID 10371035.
- Benne, R. (1994). "RNA editing in trypanosomes". Eur. J. Biochem 221 (1): 9–23. doi:10.1111/j.1432-1033.1994.tb18710.x. PMID 7513284.
- Arts, G.J. and Benne, R. (1996). "Mechanism and evolution of RNA editing in kinetoplastida". Biochim. Biophys. Acta 1307 (1): 39–54. PMID 8652667.
- Alfonzo, J.D., Thiemann, T. and Simpson, L. (1997). "The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria". Nucleic Acids Res. 25 (19): 3751–3759. doi:10.1093/nar/25.19.3751. PMC 146959. PMID 9380494.
- Blum, B., Bakalara, N. and Simpson, L. (1990). "A model for RNA editing in kinetoplastid mitochondria: `Guide' RNA molecules transcribed from maxicircle DNA provide the edited information". Cell 60 (2): 189–198. doi:10.1016/0092-8674(90)90735-W. PMID 1688737.
- Kable, ML; Heidmann, S; Stuart, KD (1997). "RNA editing : getting U into RNA". Trends Biochem. Sci. 22 (5): 162–166. doi:10.1016/S0968-0004(97)01041-4. PMID 9175474.
- Simpson, L; Thiemann, OH (1995). "Sense from nonsense: RNA editing in mitochondria of kinetoplastid protozoa and slime molds". Cell 81 (6): 837–840. doi:10.1016/0092-8674(95)90003-9. PMID 7781060.
- Stuart, K. (1991). "RNA editing in mitochondrial mRNA of trypanosomatids". Trends Biochem. Sci. 16 (2): 68–72. doi:10.1016/0968-0004(91)90027-S. PMID 1713359.
- Hajduk, S.L. and Sabatini, R.S. (1998). "Mitochondrial mRNA editing in kinetoplastid protozoa". Modification and Editing of RNA (Grosjean, H. and Benne, R., Eds.) (ASM Press, Washington, DC.): 377–394.
- Danecek, P. et al. (2012). "High levels of RNA-editing site conservation amongst 15 laboratory mouse strains". Genome Biology. 13:26 (4). doi:10.1186/gb-2012-13-4-r26. PMC 3446300. PMID 22524474.
- Garrett, S.; Rosenthal, J. J. C. (5 January 2012). "RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses". Science. doi:10.1126/science.1212795.
- Covello, P.S. and Gray, M.W. (1989). "RNA editing in plant mitochondria". Nature 341 (6243): 662–666. doi:10.1038/341662a0. PMID 2552326.
- Gualberto, J.M., Lamattina, L., Bonnard, G., Weil, J.H. and Grienenberger, J.M. (1989). "RNA editing in wheat mitochondria results in the conservation of protein sequences". Nature 341 (6243): 660–662. doi:10.1038/341660a0. PMID 2552325.
- Hiesel, R., Wissinger, B., Schuster, W. and Brennicke, A. (1989). "RNA editing in plant mitochondria". Science 246 (4937): 1632–1634. doi:10.1126/science.2480644. PMID 2480644.
- Hoch, B., Maier, R.M., Appel, K., Igloi, G.L. and Ko« ssel, H. (1991). "Editing of a chloroplast mRNA by creation of an initiation codon". Nature 353 (6340): 178–180. doi:10.1038/353178a0. PMID 1653905.
- Pring, D., Brennicke, A. and Schuster, W. (1993). "RNA editing gives a new meaning to the genetic information in mitochondria and chloroplasts". Plant Mol. Biol. 21 (6): 1163–1170. doi:10.1007/BF00023611. PMID 8490134.
- Wissinger, B., Brennicke, A. and Schuster, W. (1992). "Regeneration good sense: RNA editing and trans splicing in plant mitochondria". Trends Genet. 8 (9): 322–328. doi:10.1016/0168-9525(92)90265-6. PMID 1365399.
- Grienenberger, J.M. (1993). "RNA editing in plant organelles". RNA Editing (Benne, R., Ed.), Ellis Harwood, New York.
- Malek, O., La«ttig, K., Hiesel, R., Brennicke, A. and Knoop, V. (1996). "RNA editing in bryophytes and a molecular phylogeny of land plants". EMBO J. 15 (6): 1403–1411. PMC 450045. PMID 8635473.
- Freyer, R., Kiefer-Meyer, M.C. and Ko« ssel, H. (1997). "Occurrence of plastid RNA editing in all major lineages of land plants". Proc. Natl. Acad. Sci. USA 12: 6285–6296. doi:10.1073/pnas.94.12.6285. PMID 9177209.
- Dietrich, A., Small, I., Cosset, A., Weil, J.H. and Marechal- Drouard, L. (1996). "Editing and import: Strategies for providing plant mitochondria with a complete set of functional transfer RNAs". Biochimie 75: 518–529.
- Bock, R., Hermann, M. and Fuchs, M. (1997). "Identification of critical nucleotide positions for plastid RNA editing site recognition". RNA 3: 1194–1299.
- Gray, M.W. and Covello, P.S. (1993). "RNA editing in plant mitochondria and chloroplasts". FASEB J. 7 (1): 64–71. PMID 8422976.
- Marchfelder, A., Binder, S., Brennicke, A. and Knoop, V. (1998). "Preface". In: Modifcation and Editing of RNA (Grosjean, H. and Benne, R., Eds.) (ASM Press, Washington, DC): 307–323.
- Price, D.H. and Gray, M.W. (1998). "Editing of tRNA". In: Modification and Editing of RNA (Grosjean, H. and Benne, R., Eds.) (ASM Press, Washington, DC): 289–306.
- Curran, J., Boeck, R. and Kolakofsky, D. (1991). "The Sendai virus P gene expresses both an essential protein and an inhibitor of RNA synthesis by shuffling modules via mRNA editing". EMBO J. 10 (10): 3079–3085. PMC 453024. PMID 1655410.
- Zheng, H., Fu, T.B., Lazinski, D. and Taylor, J. (1992). "Editing on the genomic RNA of human hepatitis delta virus". J. Virol. 66 (8): 4693–4697. PMC 241294. PMID 1629949.
- Kolakofsky, D. and Hausmann, S. (1998). "Cotranscriptional paramyxovirus mRNA editing: a contradiction in terms?". In: Modification and Editing of RNA (Grosjean, H. and Benne, R., Eds.) (ASM Press, Washington, DC): 413–420.
- Carter, C.W. (1998). "Nucleoside deaminases for cytidine and adenosine: comparisons with deaminases acting on RNA". In: Modification and Editing of RNA (Grosjean, H. and Benne, R., Eds.) (ASM Press, Washington, DC): 363–376.
- Covello, P.S. and Gray, M.W. (1993). "On the evolution of RNA editing". Trends Genet. 9 (8): 265–268. doi:10.1016/0168-9525(93)90011-6. PMID 8379005.
- Lonergan, K.M. and Gray, M.W. (1993). "Predicted editing of additional transfer RNAs in Acanthamoeba castellanii mitochondria". Nucleic Acids Res. 21 (18): 4402. doi:10.1093/nar/21.18.4402. PMC 310088. PMID 8415006.
- Bachellerie, J.-P. and Cavaille, J. (1998). "Small nucleolar RNAs guide the ribose methylations of eukaryotic rRNAs". In: Modification and Editing of RNA (Grosjean, H. and Benne, R., Eds.) (ASM Press, Washington, DC): 255–272.
- Speijer, D. (March 7, 2011). "Does constructive neutral evolution play an important role in the origin of cellular complexity?: Making sense of the origins and uses of biological complexity". BioEssays 33 (5): n/a–n/a. doi:10.1002/bies.201100010. PMID 21381061.
- Stoltzfus, A. (1999). "On the possibility of constructive neutral evolution". J Mol Evol 49 (2): 169–181. doi:10.1007/PL00006540. PMID 10441669.
- Agranat, L., Raitskin, O., Sperling, J., and Sperling, R. (2008). "The Editing Enzyme ADAR1 and The mRNA Surveillance Protein hUpf1 Interact in the Cell Nucleus". Proc. Natl. Acad. Sci. USA. 105 (13): 5028–5033. doi:10.1073/pnas.0710576105. PMC 2278206. PMID 18362360.
- RNA editing website
- DARNED (DAtabase of RNa EDiting in humans)
- A-I editing website
- C-U Editing Website