Dataset Information

Differences in editing at homologous sites in messenger RNAs from angiosperm mitochondria.

ABSTRACT: Recent work has shown that amino acid sequence comparisons can be used to infer sites of C-to-U RNA editing in plant mitochondrial mRNAs (1). In order to test such predictions further and to search for conserved mRNA structural motifs that might provide insight into the mechanism of recognition of editing sites, the complete sequences of the cytochrome c oxidase subunit II (COXII) mRNAs of wheat, maize and pea were determined by reverse transcriptase sequencing. The results affirm the high reliability of editing predictions based on amino acid sequence alignments, and prompt us to make the further inference that COXI (cytochrome oxidase subunit I) mRNA is extensively edited in dicotyledonous plants but not in monocotyledons. In plant COXII mRNAs, additional non-predicted editing occurs such that the resulting derived amino acid sequences are more similar to those of non-plants than is indicated by the respective plant COXII DNA sequences. A number of homologous sites show differences in editing among species, and certain positions show partial editing within a species. Despite some deviation from expected nucleotide frequencies in the vicinity of editing sites, no extensive conserved primary or secondary structural motifs are apparent. The relevance of these data to the mechanism of RNA editing in plant mitochondria is discussed.

SUBMITTER: Covello PS

PROVIDER: S-EPMC332141 | biostudies-other | 1990 Sep

REPOSITORIES: biostudies-other

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Differences in editing at homologous sites in messenger RNAs from angiosperm mitochondria.

Covello P S PS Gray M W MW

Nucleic acids research 19900901 17

Recent work has shown that amino acid sequence comparisons can be used to infer sites of C-to-U RNA editing in plant mitochondrial mRNAs (1). In order to test such predictions further and to search for conserved mRNA structural motifs that might provide insight into the mechanism of recognition of editing sites, the complete sequences of the cytochrome c oxidase subunit II (COXII) mRNAs of wheat, maize and pea were determined by reverse transcriptase sequencing. The results affirm the high relia ...[more]

PMID: 1698279

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Project description:Species within the angiosperm genus Silene contain the largest mitochondrial genomes ever identified. The enormity of these genomes (up to 11 Mb in size) appears to be the result of increased non-coding DNA, which represents >99 % of the genome content. These genomes are also fragmented into dozens of circular-mapping chromosomes, some of which contain no identifiable genes, raising questions about if and how these 'empty' chromosomes are maintained by selection. To assess the possibility that they contain novel and unannotated functional elements, we have performed RNA-seq to analyze the mitochondrial transcriptome of Silene noctiflora.We identified regions of high transcript abundance in almost every chromosome in the mitochondrial genome including those that lack any annotated genes. In some cases, these transcribed regions exhibited higher expression levels than some core mitochondrial protein-coding genes. We also identified RNA editing sites throughout the genome, including 97 sites that were outside of protein-coding gene sequences and found in pseudogenes, introns, UTRs, and transcribed intergenic regions. Unlike in protein-coding sequences, however, most of these RNA editing sites were only edited at intermediate frequencies. Finally, analysis of mitochondrial small RNAs indicated that most were likely degradation products from longer transcripts, but we did identify candidates for functional small RNAs that mapped to intergenic regions and were not associated with longer RNA transcripts.Our findings demonstrate transcriptional activity in many localized regions within the extensive intergenic sequence content in the S. noctiflora mitochondrial genome, supporting the possibility that the genome contains previously unidentified functional elements. However, transcription by itself is not proof of functional importance, and we discuss evidence that some of the observed transcription and post-transcriptional modifications are non-adaptive. Therefore, further investigations are required to determine whether any of the identified transcribed regions have played a functional role in the proliferation and maintenance of the enormous non-coding regions in Silene mitochondrial genomes.

Dataset Information

Differences in editing at homologous sites in messenger RNAs from angiosperm mitochondria.

Publications

Differences in editing at homologous sites in messenger RNAs from angiosperm mitochondria.

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