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Protein polymorphism generated by differential RNA editing of a plant mitochondrial rps12 gene.

The rps12 gene transcripts encoding mitochondrial ribosomal protein S12 are partially edited in petunia mitochondria. Different petunia lines were found vary in the extent of rps12 transcript editing. To test whether multiple forms of RPS12 proteins are produced in petunia mitochondria as a result of partial editing, we probed mitochondrial proteins with specific antibodies against edited and unedited forms of a 13-amino-acid RPS12 peptide spanning two amino acids affected by RNA editing. Both antibodies reacted with mitochondrial proteins at the expected size for RPS12 proteins. The amounts of unedited RPS12 protein in different petunia lines correlate with the abundance of unedited transcripts in these plants. Unedited rps12 translation products are also detected in other plant species, indicating that polymorphism in mitochondrial rps12 expression is widespread. Moreover, we show that RPS12 proteins recognized by both edited-specific and unedited-specific antibodies are present in a petunia mitochondrial ribosome fraction. These results demonstrate that partially edited transcripts can be translated and that the protein product can accumulate to detectable levels. Therefore, genes exhibiting incompletely edited transcripts can encode more than one gene product in plant mitochondria.

Amino Acid Sequence↗

RNA editing and mitochondrial genomic organization in the cryptobiid kinetoplastid protozoan Trypanoplasma borreli.

The bodonids and cryptobiids represent an early diverged sister group to the trypanosomatids among the kinetoplastid protozoa. The trypanosome type of uridine insertion-deletion RNA editing was found to occur in the cryptobiid fish parasite Trypanoplasma borreli. A pan-edited ribosomal protein, S12, and a novel 3'- and 5'-edited cytochrome b, in addition to an unedited cytochrome oxidase III gene and an apparently unedited 12S rRNA gene, were found in a 6-kb fragment of the 80- to 90-kb mitochondrial genome. The gene order differs from that in trypanosomatids, as does the organization of putative guide RNA genes; guide RNA-like molecules are transcribed from tandemly repeated 1-kb sequences organized in 200- and 170-kb molecules instead of minicircles. The presence of pan-editing in this lineage is consistent with an ancient evolutionary origin of this process.

Animals↗

RNA editing at the Q/R site for the glutamate receptor subunits GLUR2, GLUR5, and GLUR6 in hippocampus and temporal cortex from epileptic patients.

Posttranscriptional editing of mRNA is a phenomenon that generates molecular heterogeneity and functional variety. With the intention to test if RNA editing plays a role in pathological processes, which contribute to seizure maintenance, we examined the ratio of the unedited (Q) to edited (R) form of the AMPA receptor subunit GluR2 and kainate receptor subunits GluR5 and GluR6 in the hippocampus and temporal cerebral cortex, both excised from patients with pharmacoresistant temporal lobe epilepsies. We compared the data with samples from nonepileptic human control tissue (autopsy tissue). The ratio of Q/R editing was analyzed by means of reverse transcription-polymerase chain reaction followed by a restriction enzyme assay. We found that the editing efficiency for the kainate receptor subunits GluR5 and GluR6 was significantly higher in temporal cortex than in normal controls. The alteration in GluR5 and GluR6 mRNA editing in the neocortical tissue may reflect an adaptive reaction of ongoing seizure activity to prevent excessive Ca(2+) influx.

Adolescent↗

Three distinct RNA sequence elements are required for efficient apolipoprotein B (apoB) RNA editing in vitro.

Apolipoprotein B (apoB) mRNA is edited in rat liver and intestine to convert a CAA glutamine codon to a UAA translational stop codon by the direct conversion of cytidine to uridine at nucleotide 6666. We have proposed the 'mooring sequence' model for apoB RNA editing, in which editing complexes (editosomes) assemble on specific apoB mRNA flanking sequences to direct this site-specific editing event. One sequence element (approx. nts 6671-81, the presumed 'mooring sequence') has been previously identified as necessary for editing. We have identified two additional sequence elements which are necessary for efficient editing: (1) a 5' 'Regulator' region which modulates editing efficiency and (2) a 'Spacer' region between the editing site and the 3' mooring sequence, whose distance is critical for efficient editing. Utilizing this data, we have induced editing at a cryptic site and have defined a 22 nucleotide 'cassette' of specific apoB sequence which is sufficient to support wild-type levels of editing in vitro in a background of distal apoB RNA sequence.

Animals↗

Evolutionary analysis of RNA editing enzymes.

This article focuses on the evolution of apolipoprotein B (apoB) mRNA editing. We review the tools commonly used in homology search and phylogenetic analysis and demonstrate their use in the analysis of RNA-editing enzymes. The ultimate goal is to apply these tools to answer two questions: How did apoB mRNA editing come about? How might it be related to other base substitution editing in the course of evolution.

APOBEC-1 Deaminase↗

RNA editing intermediates of cox2 transcripts in maize mitochondria.

Eighteen cytidines are changed to uridines in the coding sequence of transcripts for cytochrome c oxidase subunit 2 (cox2) in maize mitochondria. The temporal relationship of editing and splicing was examined in cox2 transcripts by sequence analysis of spliced and unspliced cDNAs. Cloned cDNAs of unspliced cox2 transcripts ranged from clones with no edited nucleotides to completely edited forms, while spliced cDNAs were nearly completely edited. Incompletely edited transcripts in the nascent pool of unspliced transcripts represent intermediates of the editing process. These results indicate that editing proceeds without a strong directional bias and suggest that RNA editing is a posttranscriptional process.

Amino Acid Sequence↗

RNA editing: a novel mechanism for regulating lipid transport from the intestine.

Human apolipoprotein (apo)-B mRNA undergoes a novel tissue specific editing reaction which replaces a genomically templated cytidine with uridine. This substitution converts codon 2153 from glutamine (CAA) in apo-B100 mRNA to a stop codon (UAA) in apo-B48 mRNA. This novel RNA editing process is responsible for the generation of hepatic apo-B100 and intestinal apo-B48. We have established the following concerning this process: (1) by transfection of a series of deletion mutants into the rat hepatoma cell line McArdle 7777, which makes both apo-B100 and apo-B48, we have defined a minimum sequence of 26 nucleotides that is required for apo-B mRNA editing. The sequence containing the modified nucleotide forms a 26 nucleotide highly conserved stem loop with the modified nucleotide occurring in an 8-base loop. (2) Conversion in vitro of apo-B mRNA has been established, using cell free S100 cytoplasmic extract and synthetic RNA templates. Activity was abolished by protease treatment. (3) Transgenic mice were created which expressed a human apo-B construct spanning the stop codon. Apo-B mRNA was found in all tissues examined and this was shown to undergo editing. (4) In the rat liver, which produces apo B-100 and apo-B48, modulation of the relative proportion of these proteins by thyroxine was demonstrated to be mediated at the level of the RNA editing mechanism. It is concluded that apo-B mRNA is edited by a generally expressed protein and editing is highly regulated.

Animals↗

Regulation of alternative splicing by RNA editing.

The enzyme ADAR2 is a double-stranded RNA-specific adenosine deaminase which is involved in the editing of mammalian messenger RNAs by the site-specific conversion of adenosine to inosine. Here we identify several rat ADAR2 mRNAs produced as a result of two distinct alternative splicing events. One such splicing event uses a proximal 3' acceptor site, adding 47 nucleotides to the ADAR2 coding region, changing the predicted reading frame of the mature ADAR2 transcript. Nucleotide-sequence analysis of ADAR2 genomic DNA revealed the presence of adenosine-adenosine (AA) and adenosine-guanosine (AG) dinucleotides at these proximal and distal alternative 3' acceptor sites, respectively. Use of the proximal 3' acceptor depends upon the ability of ADAR2 to edit its own pre-mRNA, converting the intronic AA to an adenosine-inosine (AI) dinucleotide which effectively mimics the highly conserved AG sequence normally found at 3' splice junctions. Our observations indicate that RNA editing can serve as a mechanism for regulating alternative splicing and they suggest a novel strategy by which ADAR2 can modulate its own expression.

Adenosine↗

Internal frameshifts within the mitochondrial genes for cytochrome oxidase subunit II and maxicircle unidentified reading frame 3 of Leishmania tarentolae are corrected by RNA editing: evidence for translation of the edited cytochrome oxidase subunit II mRNA.

The Leishmania tarentolae cytochrome oxidase (EC 1.9.3.1) subunit II (COII) and maxicircle unidentified reading frame 3 (MURF3) mRNAs are edited internally by the addition of four and five uridine residues, respectively, which eliminate -1 and +1 reading frameshifts in the gene sequences. The editing events in COII are conserved in three kinetoplastid species, and those in MURF3 are conserved in two species. A primer extension assay showed that the ratio of edited to unedited RNA differed for each gene: 89% of the COII and 36% of the MURF3 transcripts are edited. Preliminary evidence was obtained for translation of the edited COII transcript into protein: antibodies generated against a synthetic peptide with the predicted carboxyl-terminal amino acid sequence reacted with a polypeptide of the correct molecular weight in immunoblots of a mitochondrial lysate.

Amino Acid Sequence↗

RNA-editing terminal uridylyl transferase 1: identification of functional domains by mutational analysis.

The catalytic, RNA-binding and oligomerization domains of the RNA-editing terminal uridylyl transferase 1 (RET1) from Leishmania tarentolae mitochondria were characterized by mutational analysis. Significant N- and C-terminal portions of the protein were found to be dispensable for UTP polymerization in vitro. Changes of conserved amino acids in the active site demonstrated a general similarity of sugar-phosphate moiety recognition of the incoming ribonucleotide triphosphate by RET1 and eukaryotic poly(A) polymerases. Overlapping RNA-binding and oligomerization regions were mapped to the C-terminal region, which is conserved only among trypanosomatid RET1 enzymes. In the absence of an RNA primer, RET1 can use UTP itself to initiate nucleotide transfer and produce poly(U) molecules of several hundred nucleotides. An N-terminal zinc finger motif is essential for enzyme activity; deletion of this motif or chelation of zinc inhibits activity.

Amino Acid Motifs↗

Recombinant measles viruses defective for RNA editing and V protein synthesis are viable in cultured cells.

The measles virus (MV) phosphoprotein (P) gene encodes three proteins, P, C, and V. The V protein is synthesized by pseudo-templated transcription, also designated as RNA editing: during P gene transcription one G residue is inserted at a defined position in about 50% of the mRNAs. To study the importance of sequence elements for the nontemplated G insertion, we generated recombinant MVs in which six different mutations were introduced within the region where editing occurs (3' UUUUUCCC, template strand). These viruses were then analyzed for their ability to edit their P mRNA and to produce V protein. Single U to C changes within the U stretch abolished editing. Extending the template by three C residues at the site of G insertion resulted in a less precise editing phenotype and overproduction of V. None of these mutants were impaired in their multiplication behavior when analyzed in cultured cells. However, the syncytia of a recombinant MV overproducing V protein were in general smaller and lysed 1 to 2 days later than usual.

Animals↗

Variation in sequence and RNA editing within core domains of mitochondrial group II introns among plants.

The 3' regions of several group II introns within the mitochondrial genes nad1 and nad7 show unexpected sequence divergence among flowering plants, and the core domains 5 and 6 are predicted to have weaker helical structure than those in self-splicing group II introns. To assess whether RNA editing improves helical stability by the conversion of A-C mispairs to A-U pairs, we sequenced RT-PCR amplification products derived from excised intron RNAs or partially spliced precursors. Only in some cases was editing observed to strengthen the predicted helices. Moreover, the editing status within nad1 intron 1 and nad7 intron 4 was seen to differ among plant species, so that homologous intron sequences shared lower similarity at the RNA level than at the DNA level. Plant-specific variation was also seen in the length of the linker joining domains 5 and 6 of nad7 intron 3; it ranged from 4 nt in wheat to 11 nt in soybean, in contrast to the 2-4 nt length typical of classical group II introns. However, this intron is excised as a lariat structure with a domain 6 branchpoint adenosine. Our observations suggest that the core structures and sequences of these plant mitochondrial introns are subject to less stringent evolutionary constraints than conventional group II introns.

Alternative Splicing↗

Effect of RNA editing and subunit co-assembly single-channel properties of recombinant kainate receptors.

1. Patch-clamp methods have been used to examine single-channel properties of recombinant GluR5 and GluR6 kainate-preferring glutamate receptors which differ in a single amino acid residue as a result of RNA editing at the Q/R (glutamine/arginine) site. Subunits were expressed alone or in combination with the high-affinity kainate receptor subunit KA - 2 in transfected human embryonic kidney (HEK-293) cells. 2. In outside-out patches, unedited homomeric GluR6(Q) receptors exhibited directly resolved domoate-activated single-channel conductances of 8, 15 and 25 pS. Variance analysis of GluR6(Q) responses gave a mean conductance of 5.4 pS, while the edited isoform GluR6(R) had an unusually low channel conductance (225 fS). 3. Homomeric channels composed of GluR5(Q) subunits exhibited three conductance states of 5, 9 and 14 pS characterized by prolonged burst activations in the presence of domoate. In contrast, the GluR5(R) subunit, which has not previously been reported to form functional homomeric receptors, had an extremely low conductance (< 200 fS). 4. Heteromeric GluR6(Q)/KA-2 kainate receptors gave single-channel events indistinguishible from homomeric GluR6(Q) channels. Conversely, openings produced by GluR5(Q)KA-2 and GluR5(Q) receptors differed from each other in their kinetic properties. The primary effect of co-expression of KA-2 with GluR5(Q) was a dramatic shortening in channel burst length. 5. Spectral and variance analyses were used to estimate mean single-channel conductances of heteromeric edited receptor-channels; channel conductances were 950 fS for GluR5(R)KA-2 receptors and 700 fS for GluR6(R)/KA-2 receptors. Both receptor types had significantly higher conductances than the respective homomeric channels, GluR5(R) and GluR6(R). 6. We conclude that Q/R site editing dramatically reduces single-channel conductance. Furthermore, we find similarity between the kainate receptor-channels described in sensory neurones and the recombinant GluR5(Q) homomeric channel. Characterization of recombinant single-channel properties could therefore aid identification of the native kainate receptors.

Action Potentials↗

Mitochondrial RNA editing of cytochrome c oxidase subunit II (coxII) in the primitive vascular plant Psilotum nudum.

A 634-nucleotide tract, including primers, was amplified via the polymerase chain reaction within a mitochondrial coxII gene of the primitive vascular plant Psilotum nudum and sequenced. Alignment with homologous coxII gene sequences from diverse plant species having known RNA editing sites which restore amino acid sequence consensus was used to infer eight sites of C-to-U transitions in Psilotum. In every case, the predicted editing event would confer the selective advantage of conserving the amino acid residue at a site where amino acid sequence divergence has not been observed in other plant species. The plant mitochondrial editing machinery is shown for the first time to extend to one of the deepest branches of vascular plant phylogeny.

Amino Acid Sequence↗

Mitochondrial RNA editing truncates a chimeric open reading frame associated with S male-sterility in maize.

Adjacent mitochondrial open reading frames orf355 and orf77 are associated with S cytoplasmic male sterility (CMS-S) in maize, but the mechanisms leading to collapse of developing CMS-S pollen are unknown. Sequence similarity between orf77 and the mitochondrial ATP synthase subunit 9 (atp9) locus led us to examine RNA editing in orf77 and atp9 transcripts of pre-collapse CMS-S microspores. Editing of atp9 was not influenced by the presence of orf77 transcripts. Sequence analysis of cDNA clones demonstrated that atp9 transcripts are fully edited in CMS-S microspores. Orf77 nucleotides corresponding to edited nucleotides in atp9 were either not edited or edited inefficiently within the context of orf77, perhaps due to limited conservation of flanking sequences between orf77 and atp9. However, eight of ten orf77 cDNA clones carried an unexpected terminating edit that truncated orf77 to predict a peptide of 17 amino acids (ORF17) sharing significant identity with the C-terminal transmembrane domain of the ATP9 protein.

Amino Acid Sequence↗