RNA editing
The term RNA editing describes those molecular processes in which the information content in an RNA molecule is altered through a chemical change in the base makeup. To date, such changes have been observed in tRNA, rRNA, and mRNA molecules of eukaryotes but not prokaryotes. RNA editing occurs in the cell nucleus and cytosol, as well as in mitochondria and plastids, which are thought to have evolved from prokaryotic-like endosymbionts.
Most of the RNA-editing processes, however, appear to be evolutionarily recent acquisitions that arose independently. The diversity of RNA editing mechanisms includes nucleoside 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[1].
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[2-4, 5-10]. Editing of the RNA 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[3, 4]. 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[5,6]. 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[7]. 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[8,10].
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
C-U editing
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. The B100 form has a CAA sequence that is edited to UAA, a stop codon, in the intestines. It is unedited in the liver.
A-I editing
A-to-I editing 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 plants
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)[11-23]. RNA-editing sites are found mainly in the coding regions of mRNA, introns, and other non-translated regions [13]. In fact, RNA editing can restore the functionality of tRNA molecules[15, 16]. The editing sites are found primarily upstream of mitochondrial or plastid RNAs[39]. 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[21]. Editing can restore the essential base-pairing sequences of tRNAs, restoring functionality[24]. 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 animals
The first observation of RNA editing in the animal mitochondrion was polyA addition[25]. Polyadenylation is responsible for the derivation of the 3’ termini of numerous mRNAs in animals. The 3’ termini are generated by processing of the 5’ ends of downstream tRNAs followed by limited polyadenylation of the mRNAs. In fact, some of the nascent mRNA 3’ termini do not contain a stop codon to end translation and may end with a U (after the last codon). The U is extended to generate a UAA stop codon by 3’ addition via a polyA polymerase. However, if these incomplete mRNA transcripts were not edited, translation would be terminated and the ribosome would dissociate. RNA editing is essential in the completion of some transcripts and ensures the proper synthesis of proteins in the mitochondria of animals.
RNA editing in viruses
RNA editing in viruses (i.e., measles, mumps, or parainfluenza) are used for stability and generation of protein variants[26,27]. 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[28]. 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[28]. 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[29, 30].
The insertional editing seen in the trypanosome mitochondria has no relation with the nucleoside conversion process. The enzymes involved have been shown in other studies to be recruited and adapted from different sources[3,31]. 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[32]. Furthermore, the eukaryotic ribose methylation of rRNAs by guide RNA molecules may provide another link between RNA editing and modification[33].
As a consequence, the numerous studies suggest that RNA editing may have evolved in specific lineages of speciation, due to the subtle differences in their mechanism. The data does not support the existence of RNA editing in the RNA world, since its mechanism is not linked to any hypothesized process that may have existed at that time. Therefore, RNA editing appears to have evolved at a later time to compensate for the changes in gene sequences and to increase variation.
RNA editing may be involved in RNA degradation
A recent study looked at the involvement of RNA editing in RNA degradation[34]. 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 lead 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.
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