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PubMed1991

Cycles of progressive realignment of gRNA with mRNA in RNA editing.

We characterized numerous partially edited NADH dehydrogenase 7 and ATPase 6 cDNAs. Most of these have a stretch of incompletely edited sequence at the junction of mature and unedited sequences. The characteristics of the junctions suggest editing of sites multiple times and that editing within each junction does not proceed precisely 3' to 5'. Analyses of gRNAs and corresponding junction sequences predict a series of progressively more stable, but incompletely base-paired, interactions in the junction region. The predicted interactions suggest that the gRNA is progressively realigned with the mRNA being edited. We suggest that gRNA interactions with the mRNA result in regions of lower thermodynamic stability that are selected for editing, thus driving toward the most stable structure, the complete gRNA/mRNA duplex.

Adenosine Triphosphatases↗

PubMed1990

RNA editing of ATPase subunit 9 transcripts in Oenothera mitochondria.

The mRNA for subunit 9 of the ATPase (atp9) in the higher plant Oenothera is edited in four nucleotide positions. Three events alter genomic serine and proline codons to triplets specifying leucine. A UGA termination codon is introduced into the reading frame by modification of a CGA arginine codon. This modification shortens the polypeptide by four amino acids. Direct sequencing of PCR amplified cDNA from the total mitochondrial mRNA population gives no indication of partially edited transcripts suggesting a rapid and efficient modification of atp9 transcripts in Oenothera mitochondria.

Amino Acid Sequence↗

PubMed1991

RNA editing in ATPase subunit 6 mRNAs in Oenothera mitochondria. A new termination codon shortens the reading frame by 35 amino acids.

The open reading frame encoding ATPase subunit 6 in Oenothera mitochondria is edited at 21 positions in all cDNA clones investigated. Only one of these events is silent, all others improve similarity between the homologous polypeptides of other species. The introduction of a new UAA termination codon shortens the polypeptide by 35 amino acids to a carboxy terminus conserved in other species. In one of the cDNA clones, an additional editing event was observed resulting in a premature UAA termination codon in the amino terminal region.

Adenosine Triphosphatases↗

PubMed1990

Apolipoprotein B messenger RNA editing is developmentally regulated in pig small intestine: nucleotide comparison of apolipoprotein B editing regions in five species.

Apolipoprotein B (apo B) mRNA undergoes a posttranscriptional tissue-specific editing reaction which changes codon 2153 from glutamine (CAA) in apoB-100 mRNA to an in-frame stop codon (UAA) in apoB-48 mRNA. Small intestinal apo B mRNA was found to be predominantly (greater than 90%) unedited in fetal (40-day gestational age) piglets but greater than 95% edited in neonatal, suckling and adult animals. By contrast, both fetal, neonatal and adult pig liver contained greater than 99% unedited, apo B-100 mRNA. The nucleotide sequence spanning the edited region in apo B mRNA was found to be highly conserved. We speculate that the regulation of apo B mRNA editing may be developmentally modulated in pig small intestine.

Aging↗

PubMed1990

Sequence analysis of the phosphoprotein (P) genes of human parainfluenza type 4A and 4B viruses and RNA editing at transcript of the P genes: the number of G residues added is imprecise.

We cloned and sequenced the cDNAs against genomic RNAs and mRNAs for phosphoproteins (Ps) of human parainfluenza virus types 4A (PIV-4A) and 4B (PIV-4B). The PIV-4A and -4B P genes were 1535 nucleotides including poly(A) tract and were found to have two small open reading frames, neither of which was apparently large enough to encode the P protein. A cluster of G residues was found in genomic RNA and the number of G residues was 6 in both PIV-4A and -4B. However, the number of G residues at the corresponding site in the mRNAs to the genomic RNA was not constant. Three different mRNA cDNA clones were obtained; the first type of mRNA encodes a larger (P) protein of 399 amino acids, the second type encodes V protein of 229 or 230 amino acids, and the third type encodes the smallest protein (156 amino acids). Comparisons on the nucleotide and the amino acid sequences P and V proteins between these two subtypes revealed extensive homologies. However, these homology degrees are lower than that of NP protein. The C-terminal regions of the P and V proteins of PIV-4s could be aligned with all other Paramyxoviruses, PIV-2, mumps virus (MuV), simian virus 5 (SV 5), Newcastle disease virus (NDV), measles virus (MV), canine distemper virus (CDV), Sendai virus (SV), and PIV-3. On the other hand, the P-V common (N-terminal) regions showed no homology with MV, CDV, SV, and PIV-3. Seven phylogenetic trees of Paramyxoviruses were constructed from the entire and partial regions of P and V proteins.

Amino Acid Sequence↗

PubMed1997

RNA editing in kinetoplastid parasites: what to do with U.

The editing of the mitochondrial RNAs of kinetoplastid protozoa is a bizarre form of transcript maturation that involves insertion and deletion of uridylate residues. Editing leads to the formation of translational initiation and termination codons, the correction of gene-encoded reading frame shifts and the creation of complete reading frames in mRNAs. It is therefore an essential step in mitochondrial gene expression.

Animals↗

PubMed1989

Apolipoprotein B48 RNA editing in chimeric apolipoprotein EB mRNA.

Apolipoprotein (apo) B occurs in two forms, apoB100 (512 kDa) and apoB48 (240 kDa); both are derived from the same gene. A novel mechanism involving editing of the apoB mRNA causes the formation of apoB48; the first base of codon 2153 is changed from cytosine to uracil, converting a glutamine codon to a premature stop codon. To identify the apoB mRNA sequence elements recognized by the apoB mRNA editing mechanism, two apoB cDNA fragments (354 and 63 base pairs) with codon 2153 near their centers were inserted into a high expression vector of another secreted apolipoprotein, apoE. The resulting vectors, pHEB-354 and -63, were transfected into Chinese hamster ovary cells, HepG2 cells, and apoB48-producing CaCo-2 cells. The secreted chimeric apolipoproteins (apoEB354 and apoEB63) were analyzed for premature truncation, and the mRNA was analyzed for the presence of an edited base. The pHEB-354 construct produced a truncated protein only in CaCo-2 cells, whereas pHEB-63 produced no truncated protein in any of the three cell types. The mRNA was converted to cDNA and amplified by the polymerase chain reaction technique. Differential hybridization of the polymerase chain reaction products with CAA (Gln) and TAA (Stop) specific probes detected an edited base only in cDNA from CaCo-2 cells transfected with pHEB-354, in agreement with the protein analysis. We conclude that the nucleotide sequence of the apoB cDNA insert in pHEB-354 contains sufficient information to be edited in CaCo-2 cells. In these cells, a cryptic polyadenylation site was activated in the edited pHEB-354 mRNA. As a result, CaCo-2 cells transfected with pHEB-354 produced a short, edited pHEB-354 mRNA and a long, unedited pHEB-354 mRNA. Chinese hamster ovary cells transfected with pHEB-354 or CaCo-2 cells transfected with pHEB-63 produced only a full length transcript. Amplification of the pHEB-354 cDNA using 3'-primers upstream and downstream of the poly(A) addition site and hybridization with the TAA probe confirmed these results. This unusual mRNA editing apparently occurs before polyadenylation, probably in the nucleus.

Adenocarcinoma↗

PubMed1994

Cloning of complementary DNAs encoding the amphibian bombesin-like peptides Phe8 and Leu8 phyllolitorin from Phyllomedusa sauvagei: potential role of U to C RNA editing in generating neuropeptide diversity.

The bombesin-like peptides were originally characterized in frog skin, then later found to have a wide distribution and range of actions in mammals. The bombesin-like peptides have classically been divided into three subfamilies, the bombesin subfamily, of which gastrin-releasing peptide (GRP) is the mammalian form; the ranatensin subfamily, of which neuromedin-B (NMB) is the mammalian form; and the phyllolitorin subfamily, which to date has only been characterized in amphibians. As a first step in characterizing mammalian phyllolitorin-like peptides, we have cloned complementary DNAs (cDNAs) encoding Leu8 and Phe8 phyllolitorin from Phyllomedusa sauvagei. Sequence analysis revealed that the amphibian phyllolitorin messenger RNA (mRNA) encodes a precursor of 90 amino acids containing a signal peptide sequence, an amino-terminal extension peptide, the phyllolitorin peptide of nine amino acids, and a carboxy-terminal extension peptide. Northern blot, reverse transcriptase-polymerase chain reaction (PCR), and in situ hybridization analysis showed that the mRNA was present at highest levels in skin, at lower levels in brain, and at lowest levels in gut. Phylogenetic analysis of bombesin-like peptide prohormone sequences showed that the phyllolitorin prohormones are much more closely related to the bombesin and ranatensin prohormones than to the GRP and NMB prohormones. This analysis suggests that the bombesin-like peptides should be reclassified into the GRP subfamily, the NMB subfamily, and the skin peptide subfamily. Surprisingly, the cDNAs encoding Phe8 and Leu8 phyllolitorins were identical except for a single T to C difference in the codon coding for the Phe or Leu residue of phyllolitorin.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1992

RNA editing in tobacco chloroplasts leads to the formation of a translatable psbL mRNA by a C to U substitution within the initiation codon.

The psbL gene which codes for a 38 amino acid peptide of photosystem II, together with the photosynthetic genes psbE and psbF, is contained in a conserved position of many species of higher plant plastomes. The alignment of the psbL nucleotide sequences from ten species shows strong conservation, which is indicative of a functional gene. The tobacco and spinach psbL genes have, however, an ACG codon instead of the initiator ATG codon observed in the homologous position of the other eight species. Evidence is presented that in tobacco chloroplasts a translatable psbL mRNA containing an AUG initiator codon is formed by a C to U editing of the ACG codon. This observation, following the previously reported editing of an rpl2 gene in maize chloroplasts, underlines a more widespread occurrence of this type of posttranscriptional mRNA modification and demonstrates its presence in a dicotyledon plant.

Base Sequence↗

PubMed2003

Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex.

The Trypanosoma brucei editosome catalyzes the maturation of mitochondrial mRNAs through the insertion and deletion of uridylates and contains at least 16 stably associated proteins. We examined physical and functional associations among these proteins using three different approaches: purification of complexes via tagged editing ligases TbREL1 and TbREL2, comprehensive yeast two-hybrid analysis, and coimmunoprecipitation of recombinant proteins. A purified TbREL1 subcomplex catalyzed precleaved deletion editing in vitro, while a purified TbREL2 subcomplex catalyzed precleaved insertion editing in vitro. The TbREL1 subcomplex contained three to four proteins, including a putative exonuclease, and appeared to be coordinated by the zinc finger protein TbMP63. The TbREL2 subcomplex had a different composition, contained the TbMP57 terminal uridylyl transferase, and appeared to be coordinated by the TbMP81 zinc finger protein. This study provides insight into the molecular architecture of the editosome and supports the existence of separate subcomplexes for deletion and insertion editing.

Animals↗

PubMed1990

Apolipoprotein B messenger RNA editing in the rat liver. Modulation by fasting and refeeding a high carbohydrate diet.

Apolipoprotein B (apoB) mRNA is modified by a posttranscriptional editing reaction in which a single base (C to U) change in apoB100 mRNA modifies a glutamine (CAA) to a translational stop codon (UAA), producing apoB48 mRNA in mammalian intestine. Rat liver normally contains both edited and unedited apoB mRNAs and previous work (Davidson, N. O., Powell, L. M., Wallis, S. C., and Scott, J. (1988) J. Biol. Chem. 263, 13482-13485) has demonstrated that the introduction of a translational stop codon can be modulated by thyroid hormone. In the current study, hepatic lipogenesis was modulated in vivo by fasting and refeeding a high carbohydrate diet, a maneuver which produced a 30-fold increase in hepatic triglyceride content. In this setting, hepatic apoB100 synthesis became undetectable in animals subjected to 48 h fasting and subsequently refed a high carbohydrate diet for either 24 or 48 h. This change was accountable for by an increase in the proportion of edited apoB mRNA, as determined by primer extension analysis, from 37% UAA in fasted animals to 79 and 91% UAA at 24 and 48 h of refeeding, respectively. The effect of this regimen on the expression of other hepatic apolipoprotein genes was less dramatic. ApoA-I and apoA-IV gene expression was modulated over a 2-fold range, in contrast to the (6-14-fold) pretranslational changes induced by thyroid hormone administration. ApoCIII mRNA abundance was unaltered in the setting of either fasting and refeeding or thyroid hormone administration, while apoE gene expression demonstrated a pretranslational increase following prolonged fasting. Taken together the data provide evidence that apoB mRNA editing is modulated by alterations in hepatic lipogenesis which additionally produce effects on the expression of other hepatic apolipoprotein genes suggesting that they are not coordinately regulated in vivo.

Animals↗

PubMed1992

Apolipoprotein B messenger RNA editing in rat liver: developmental and hormonal modulation is divergent from apolipoprotein A-IV gene expression despite increased hepatic lipogenesis.

Rat hepatic apolipoprotein B (apoB) mRNA editing is regulated developmentally as well as by hormonal and nutritional modulation of hepatic lipogenesis, changes previously associated with coordinate modulation of hepatic apoA-IV gene expression. We have examined the effects of dexamethasone administration on apoB mRNA editing and the expression of other apolipoprotein genes in both neonatal and adult rats. Administration of dexamethasone increased hepatic triglyceride content in neonatal rats and increased hepatic but not intestinal apoA-IV mRNA abundance. However, neither the developmental profile nor the extent of hepatic apoB mRNA editing was changed after hormone administration. Dexamethasone produced a dose-dependent increase in adult hepatic triglyceride content and a coordinate fourfold increase in hepatic but not intestinal apoA-IV mRNA abundance, and hepatic and serum apoA-IV protein concentrations. Immunocytochemical localization revealed apoA-IV to be expressed in hepatocytes around the central vein while dexamethasone treatment produced a dose-dependent appearance of fat-filled hepatocytes throughout the lobule that were immunoreactive for apoA-IV. Despite these changes in hepatic triglyceride accumulation there was no change in the extent of hepatic apoB mRNA editing at any dose of dexamethasone. The data suggest that hormonal and metabolic modulation of hepatic apoB mRNA editing may be independent of factors that modulate apoA-IV gene expression despite alterations in hepatic triglyceride content.

Animals↗

PubMed1992

Two nucleotides next to the anticodon of cytoplasmic rat tRNA(Asp) are likely generated by RNA editing.

The nucleotide sequences of major cytoplasmic tRNA(Asp) from rat liver and rat ascites hepatoma comprise a U32 and C33 next to the anticodon as was confirmed by different procedures. Additionally we identified a tRNA(Asp) with C32 and U33 in a minor proportion. We have shown earlier that the tRNA(Asp) gene is part of a cluster of tRNA genes which is amplified at least ten times in the rat nuclear genome. Six independent isolated clones display identical sequences in the coding region of the tRNA(Asp) gene which differ from tRNA(Asp) in having C32 and T33. Using a combination of single-strand conformation polymorphism (SSCP) analyses and direct sequencing of polymerase chain reaction (PCR) products we have now demonstrated that no variant allele of the tRNA(Asp) gene with T32 and C33 exists in the rat genome. Together with the RNA sequencing data these findings strongly indicate that major rat tRNA(Asp) is generated by post-transcriptional pyrimidine transitions at positions 32 and 33 and that the minor tRNA(Asp) is its unedited precursor.

Animals↗

PubMed1996

Loss of RNA editing of rps1 sequences in Oenothera mitochondria.

We have analysed a region downstream from the atp9 gene in Oenothera mitochondrial DNA which contains an open reading frame of 224 codons. This open reading frame, designated orf224, is co-transcribed with the atp9 gene. In wheat mitochondria, a homologous reading frame (orf174) has been described which is considerably shorter at the N-terminus compared to the putative Oenothera gene. The deduced polypeptides from both species show high similarity to the N-terminal third of ribosomal protein S1 of bacteria. Transcripts of orf174 are edited in wheat mitochondria whereas the similarly conserved cytidine positions in orf224 mRNAs of Oenothera are silent. On the other hand, atp9 sequences, which are located upstream on the same co-transcript, are fully edited. Because of this, we conclude that editing sites are selected independently for mRNA sections. Our results suggest that orf224 represents a transcribed pseudogene in Oenothera. The active gene for a functional ribosomal protein S1 for mitochondria is therefore expected to be present in the nucleus. A nuclear localization for this gene is likewise suggested for Arabidopsis due to the fact that rps1 sequences are absent from the mitochondrial genome.

Amino Acid Sequence↗

PubMed1989

RNA editing at a splicing site of NADH dehydrogenase subunit IV gene transcript in wheat mitochondria.

Comparison between the sequence of the gene coding for the wheat mitochondrial NADH dehydrogenase subunit IV (nad4) and the cDNA sequence obtained by reverse transcription, using total wheat mtRNA as template, has shown the presence of a uridine residue, not encoded by the genomic sequence, at the exon2-exon3 junction of the spliced transcript. This U creates a non-encoded CUG leucine codon which is essential for maintaining the reading frame, as shown by the conservation of the amino acid sequence of the NAD4 protein in various species. The addition of a U or the specific post-transcriptional conversion of a C to a U could explain this phenomenon.

Amino Acid Sequence↗

PubMed2006

Correction: genetic algorithm learning as a robust approach to RNA editing site site prediction.

After the publication of [1], we were alerted to an error in our data. The error was an one-off miscalculation in the extraction of position information for our set of true negatives. Our data set should have used randomly selected non-edited cytosines (C) as true negatives, but the data generation phase resulted in a set of nucleotides that were each one nucleotide downstream of known, unedited cytosines. The consequences of this error are reflected in changes to our results, although the general conclusions presented in our original publication remain largely unchanged.

Published Erratum↗

PubMed1996

The rps4-gene is encoded upstream of the nad2-gene in Arabidopsis mitochondria.

In Arabidopsis mitochondria the nad2-gene consists of five exons (a-e) which are separated by three cis-splicing introns and one trans-splicing intron. Sequence analysis of the region upstream of exons a and b reveals an open reading frame encoding ribosomal protein S4 (rps4). In the second nad2 coding region (exons c-e) a pseudo tRNA(Tyr) sequence and a fragment of the plastid psbA gene are located upstream of the trans-spliced exon c. Primer extension analysis identifies RNA 5'-termini within the pseudo-tRNA(Tyr) confirming this sequence to be non-functional. Northern blot analysis suggests the rps4-gene to be cotranscribed with at least the first part of the nad2-gene. The rps4 and nad2 coding sequences as well as the first cis-intron and the trans-intron sequences of the nad2 gene are altered by RNA editing. RNA editing in the open reading frames improves in most instances conservation of the specified amino acids.

Amino Acid Sequence↗

PubMed2005

Small regulatory RNAs in mammals.

Mammalian cells harbor numerous small non-protein-coding RNAs, including small nucleolar RNAs (snoRNAs), microRNAs (miRNAs), short interfering RNAs (siRNAs) and small double-stranded RNAs, which regulate gene expression at many levels including chromatin architecture, RNA editing, RNA stability, translation, and quite possibly transcription and splicing. These RNAs are processed by multistep pathways from the introns and exons of longer primary transcripts, including protein-coding transcripts. Most show distinctive temporal- and tissue-specific expression patterns in different tissues, including embryonal stem cells and the brain, and some are imprinted. Small RNAs control a wide range of developmental and physiological pathways in animals, including hematopoietic differentiation, adipocyte differentiation and insulin secretion in mammals, and have been shown to be perturbed in cancer and other diseases. The extent of transcription of non-coding sequences and the abundance of small RNAs suggests the existence of an extensive regulatory network on the basis of RNA signaling which may underpin the development and much of the phenotypic variation in mammals and other complex organisms and which may have different genetic signatures from sequences encoding proteins.

Animals↗