RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs.
Journal: 2000/January - Proceedings of the National Academy of Sciences of the United States of America
ISSN: 0027-8424
PUBMED: 10611383
Abstract:
On the basis of the sequence of the mitochondrial genome in the flowering plant Arabidopsis thaliana, RNA editing events were systematically investigated in the respective RNA population. A total of 456 C to U, but no U to C, conversions were identified exclusively in mRNAs, 441 in ORFs, 8 in introns, and 7 in leader and trailer sequences. No RNA editing was seen in any of the rRNAs or in several tRNAs investigated for potential mismatch corrections. RNA editing affects individual coding regions with frequencies varying between 0 and 18.9% of the codons. The predominance of RNA editing events in the first two codon positions is not related to translational decoding, because it is not correlated with codon usage. As a general effect, RNA editing increases the hydrophobicity of the coded mitochondrial proteins. Concerning the selection of RNA editing sites, little significant nucleotide preference is observed in their vicinity in comparison to unedited C residues. This sequence bias is, per se, not sufficient to specify individual C nucleotides in the total RNA population in Arabidopsis mitochondria.
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Proc Natl Acad Sci U S A 96(26): 15324-15329

RNA editing in <em>Arabidopsis</em> mitochondria effects 441 C to U changes in ORFs

Universität Ulm, Allgemeine Botanik, Albert-Einstein-Allee 11, 89069 Ulm, Germany
To whom reprint requests should be addressed. E-mail: ed.mlu-inu.eigoloib@ekcinnerb.lexa.
Edited by C. S. Levins III, North Carolina State University, Raleigh, NC, and approved October 1, 1999
Edited by C. S. Levins III, North Carolina State University, Raleigh, NC, and approved October 1, 1999
Received 1999 Jul 7

Abstract

On the basis of the sequence of the mitochondrial genome in the flowering plant Arabidopsis thaliana, RNA editing events were systematically investigated in the respective RNA population. A total of 456 C to U, but no U to C, conversions were identified exclusively in mRNAs, 441 in ORFs, 8 in introns, and 7 in leader and trailer sequences. No RNA editing was seen in any of the rRNAs or in several tRNAs investigated for potential mismatch corrections. RNA editing affects individual coding regions with frequencies varying between 0 and 18.9% of the codons. The predominance of RNA editing events in the first two codon positions is not related to translational decoding, because it is not correlated with codon usage. As a general effect, RNA editing increases the hydrophobicity of the coded mitochondrial proteins. Concerning the selection of RNA editing sites, little significant nucleotide preference is observed in their vicinity in comparison to unedited C residues. This sequence bias is, per se, not sufficient to specify individual C nucleotides in the total RNA population in Arabidopsis mitochondria.

Abstract

In plants, RNA editing has been identified as C to U as well as U to C conversions in both mitochondria and chloroplasts (14). In chloroplasts between 4 and 25 RNA editing events occur in the total transcribed coding complexity of 110 kilobase (kb), whereas in mitochondria several hundred such changes are estimated to alter the coding text of the RNA population.

Arabidopsis thaliana has evolved into one of the model plant species (5) and is presently the focus of a worldwide genome sequencing project (6). The mitochondrial genome of this plant was the first of the three genomes in the nucleus, the mitochondria and the chloroplasts, respectively, to be fully sequenced (7). This complete higher-plant mitochondrial genome sequence now allows an ordered global analysis of gene expression in Arabidopsis mitochondria. A comprehensive analysis—for practical purposes a cDNA investigation—is required for an overall view of the complexity of RNA editing in this organelle.

To handle the required large numbers of cDNA clones, we have initiated model development of the technology required for the rapidly advancing postgenome-sequencing era. The total Arabidopsis mitochondrial transcript complexity was therefore cloned in a large cDNA library, and the clones were sorted and spotted on high-density filters by using robot technologies (810). Sequence and genome-correspondence analysis of the cDNA population has identified functions coded in this genome (11).

In this plant mitochondrial genome with a total length of about 367 kb, only 30 kb are accounted for by known protein coding genes, which specify mostly subunits of respiratory chain complexes (7). Our cDNA sequence analysis covering all of the identified Arabidopsis mitochondrial mRNA and rRNA coding regions reveals the extent of RNA editing modifications in these organelles and their effect on the coded information. The analysis of the total complexity of RNA editing sites may give clues to the experimental investigation and eventual understanding of the specificity determining an individual RNA editing site.

The orf110c and orf240a are included here.

This represents the ≈40% of the cDNA clones with multiple inserts, one of which usually is an rRNA sequence.

About 8 kb of these ORFs are not detectably transcribed when analyzed by Northern blots (not shown).

The intronic ORF matR is not included here but is included with the identified orfs.

This number includes only the cis-splicing introns.

Data for individual mRNA species previously analyzed have been integrated. These include editing sites for nad2 and rps4 (13), nad4L and orf25 (22), nad5 exons d and e (23), cob, rpl5, and Yrps14 (24), orfX (25), and for ccb6n1 and matR (accession nos. X978254 and {"type":"entrez-nucleotide","attrs":{"text":"X98300","term_id":"1419615"}}X98300, respectively). Cytochrome c biogenesis genes (ccb genes) are shown with new gene names; ccb2 is ccb206 (ccmB in Escherichia coli), ccb3 is ccb256 (ccmC in E. coli), ccb6n1 is ccb382, ccb6n2 is ccb203 and ccb6c is ccb452 (ccmF in E. coli, two genes corresponding to the N-terminal part and one gene corresponding to the C-terminal part, respectively).

Codons are grouped according to the identity of the amino acid encoded and the number of occurrences. Highlighted in bold are the 13 codons edited more frequently than the statistical average. The novel orf110c is included with the identified genes.

The frequency of edited nucleotides is particularly higher in the second codon position and lower in the third.

Acknowledgments

We thank Dr. Volker Knoop for his advice, Dr. Jörg Kudla and Drs. Kanji Ohyama and Katsuyuki Yamato for their support, and Dr. Géraldine Bonnard for suggesting the nomenclature for the cytochrome c biogenesis (ccb) genes. We are grateful to the anonymous reviewers for constructive suggestions to improve the presentation. This work was supported by a grant from the Bundesministerium für Bildung, Wissenschaft und Technologie.

Acknowledgments

Abbreviation

kbkilobase
Abbreviation

Footnotes

This paper was submitted directly (Track II) to the PNAS office.

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (editing site positions as annotations to {"type":"entrez-nucleotide","attrs":{"text":"Y08501","term_id":"49256807"}}Y08501 and {"type":"entrez-nucleotide","attrs":{"text":"Y08502","term_id":"49256807"}}Y08502).

Footnotes

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