RNA editing in the cytochrome b locus of the higher plant Oenothera berteriana includes a U-to-C transition (original) (raw)
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Between DNA and protein - RNA editing in plant mitochondria
Physiologia Plantarum, 1991
Higher plants contain the largest mitochondrial genomes found so far. Several factors contribute to this expansion in size, notably integrated plastid and nuclear sequences; numerous repeats, some of which are active in recombination and sequence rearrangements; introns of more than 3400 nucleotides and several genes unique to plant mitochondrial DNA. Genes are transcribed into mono-and polycistronic mRNAs and translated by the standard genetic code. However. mRNAs are altered from the DNA encoded sequence by RNA editing with mostly cytidine to uridine and occasionally uridine to cytidine transitions. Edited mRNAs specify different polypeptides than those predicted by open reading frames in the DNA. Partially edited mRNA molecules raise the question of which proteins are actually synthesized. RNA editing of mitochondrial transcripts appears to occur in all higher piants and may date back to the common ancestors of modem plants.
Assays for Investigating RNA Editing in Plant Mitochondria
Methods, 1998
In plant organelles transcripts are modified posttranscriptionally by RNA editing. This modification process changes almost every protein-coding RNA at specific cytidine and uridine positions. Therefore, mitochondrially encoded protein sequences differ from the genomically fixed information and show, after editing, a higher conservation. To investigate this unusual processing step in plant mitochondria, several assays have been developed. However, compared with the progress made in other RNA editing fields, knowledge about the factors involved in plant mitochondrial editing is limited. One reason for this is the lack of a reliable in vitro system for mitochondria. To reveal the biochemical nature of the RNA editing reaction in plant mitochondria, we developed an in vitro system by which we were able to show that cytidine is specifically modified to uridine by a deamination or transamination process. Here we describe the development of a pea in vitro system and discuss assays to follow the editing process.
Nucleic Acids Research, 1992
A number of cytosines are altered to be recognized as uridines in transcripts of the NADH-dehydrogenase subunit 3 (nad3) gene in the mitochondria of the higher plant Petunia hybrida. Here we show that the extent of editing for three of the edit sites, all of which change the encoded amino acid, varies between different Petunia lines. Genetic analysis indicates that a single nuclear gene is responsible for this variation. Interestingly, according to RNA blot hybridization analysis, RNA editing extent and transcript abundance are correlated. This observation is consistent with the hypothesis that RNA editing is a post-transcriptional event.
RNA editing in plant mitochondria and chloroplasts
Plant Molecular Biology, 1996
In the mitochondria and chloroplasts of flowering plants (angiosperms), transcripts of proteincoding genes are altered after synthesis so that their final primary nucleotide sequence differs from that of the corresponding DNA sequence. This posttranscriptional mRNA editing consists almost exclusively of C-to-U substitutions. Editing occurs predominantly within coding regions, mostly at isolated C residues, and usually at first or second positions of codons, thereby almost always changing the amino acid from that specified by the unedited codon. Editing may also create initiation and termination codons. The net effect of C-to-U RNA editing in plants is to make proteins encoded by plant organelles more similar in sequence to their nonpiant homologs. In a few cases, a strong argument can be made that specific C-to-U editing events are essential for the production of functional plant mitochondrial proteins. Although the phenomenon of RNA editing in plants is now well documented, fundamental questions remain to be answered: What determines the specificity of editing? What is the biochemical mechanism (deamination, base exchange, or nucleotide replacement)? How did the system evolve? RNA editing in plants, as in other organisms, challenges our traditional notions of genetic information transfer.-Gray, M. W.; Covello, P. S. RNA editing in plant mitochondria and chloroplasts. FASEB
RNA editing in wheat mitochondria proceeds by a deamination mechanism
FEBS Letters, 1995
Most if not all mitochondrial messenger RNAs from seed plants undergo a post-transcriptional modification (RNA editing) involving the conversion of some cytidine residues to uridine. Using a molecular hybridization approach, an in vitro RNA editing system, able to faithfully reproduce the in vivo observed C to U changes of subunit 9 (atp9) of wheat mitochondrial ATP synthase mRNA, has been described [Araya et al. (1992) Proc. Natl. Acad. Sci. USA 89, 1040-1044]. In this work we extend these studies to better understand the biochemical mechanism of this process. RNA editing was analysed by P1 nuclease digestion of the reaction product followed by thin layer chromatography. Experiments performed with unedited [3H]RNA labelled on the base and with unedited [32p]RNA labelled at the a-phosphate of cytidine residues, indicate that plant mitochondrial RNA editing operates through a deamination mechanism.
RNA editing in plant mitochondria, cytoplasmic male sterility and plant breeding
Electronic Journal of Biotechnology, 1998
RNA editing in plant mitochondria is a post-transcriptional process involving the partial change of C residues into U. These C to U changes lead to the synthesis of proteins with an amino acid sequence different to that predicted from the gene. Proteins produced from edited mRNAs are more similar to those from organisms where this process is absent. This biochemical process involves cytidine deamination. The cytoplasmic male sterility (CMS) phenotype generated by the incompatibility between the nuclear and the mitochondrial genomes is an important agronomical trait which prevents inbreeding and favors hybrid production. The hypothesis that RNA editing leads to functional proteins has been proposed. This hypothesis was tested by constructing transgenic plants expressing a mitochondrial protein translated fom unedited mRNA. The transgenic "unedited" protein was addressed to the mitochondria leading to the appearance of mitochondrial dysfunction and generating the male sterile phenotype in transgenic tobacco plants. Male sterile plants were also obtained by expressing specifically a bacterial ribonuclease in the anthers. The economical benefits of artificially engineered male-sterile plants or carrying the (native) spontaneous CMS phenotype, implies the restoration to obtain fertile hybrids that will be used in agriculture. Restoration to fertility of transgenic plants was obtained either by crossing male-sterile plants carrying the "unedited" mRNA with plants carrying the same RNA, but in the antisense orientation or, in the case of plants expresing the ribonuclease, by crossing male-sterile plants with plants expressing an inhibitor specific of this enzyme.
Curr Genetics, 1996
Transcripts of most plant mitochondrial protein-coding genes exhibit C-to-U RNA editing events. In Petunia, two co-transcribed genes, nad3 and rps12, exhibit transcripts which are not fully edited at all potential editing sites. We investigated the nad3/rps12 transcript population in four different genotypes. In one pair of genotypes, the nuclear genome is identical but the nad3/rps12 genes are in different transcriptional contexts. Both the nad3/ rps12 genes and the plant mitochondrial genomes are identical in a second pair of genotypes, but the nuclear background is derived from two different Petunia species. We found that the overall extent of editing varied greatly between genotypes and is affected by nuclear genotype but not by the global transcriptional context. Local sequence context around a particular site does affect editing frequency. In all genotypes, certain sites exhibit high editing frequency, but these sites do not share obvious primary sequence characteristics. In all genotypes examined, editing sites which do not affect the encoded amino acid are less frequently edited than sites which alter codons to non-synonymous forms. All these data indicate that an unidentified property of the sequences immediately surrounding a cytosine affect its selection as a target in the editing process.
RNA Editing and Its Molecular Mechanism in Plant Organelles
Genes, 2016
RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria and chloroplasts. In some plant taxa, "reverse" U-to-C editing also occurs. However, to date, no instance of RNA editing has yet been reported in green algae and the complex thalloid liverworts. RNA editing may have evolved in early land plants 450 million years ago. However, in some plant species, including the liverwort, Marchantia polymorpha, editing may have been lost during evolution. Most RNA editing events can restore the evolutionarily conserved amino acid residues in mRNAs or create translation start and stop codons. Therefore, RNA editing is an essential process to maintain genetic information at the RNA level. Individual RNA editing sites are recognized by plant-specific pentatricopeptide repeat (PPR) proteins that are encoded in the nuclear genome. These PPR proteins are characterized by repeat elements that bind specifically to RNA sequences upstream of target editing sites. In flowering plants, non-PPR proteins also participate in multiple RNA editing events as auxiliary factors. C-to-U editing can be explained by cytidine deamination. The proteins discovered to date are important factors for RNA editing but a bona fide RNA editing enzyme has yet to be identified.
cis Recognition Elements in Plant Mitochondrion RNA Editing
Molecular and Cellular Biology, 2001
RNA editing in higher plant mitochondria modifies mRNA sequences by means of C-to-U conversions at highly specific sites. To determine the cis elements involved in recognition of an editing site in plant mitochondria, deletion and site-directed mutation constructs containing the cognate cox II mitochondrial gene were introduced into purified mitochondria by electroporation. The RNA editing status was analyzed for precursor and spliced transcripts from the test construct. We found that only a restricted number of nucleotides in the vicinity of the target C residue were necessary for recognition by the editing machinery and that the nearest neighbor 3 residues were crucial for the editing process. We provide evidence that two functionally distinguishable sequences can be defined: the 16-nucleotide 5 region, which can be replaced with the same region from another editing site, and a 6-nucleotide 3 region specific to the editing site. The latter region may play a role in positioning the actual editing residue.
A hypothesis on the identification of the editing enzyme in plant organelles
FEBS Letters, 2007
RNA editing in plant organelles is an enigmatic process leading to conversion of cytidines into uridines. Editing specificity is determined by proteins; both those known so far are pentatricopeptide repeat (PPR) proteins. The enzyme catalysing RNA editing in plants is still totally unknown. We propose that the DYW domain found in many higher plant PPR proteins is the missing catalytic domain. This hypothesis is based on two compelling observations: (i) the DYW domain contains invariant residues that match the active site of cytidine deaminases; (ii) the phylogenetic distribution of the DYW domain is strictly correlated with RNA editing.