RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs - PubMed (original) (raw)

RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs

P Giegé et al. Proc Natl Acad Sci U S A. 1999.

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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Figures

Figure 1

Figure 1

Bar graphs show the overall biochemical nature of amino acids (aa) specified by the 425 edited codons before and after the alteration by RNA editing. RNA editing thus tends to increase the hydrophobicity of the encoded mitochondrial proteins.

Figure 2

Figure 2

Secondary structure model of domains V and VI from two Arabidopsis mitochondrial group II introns. (A) The nad5a/b intron; (B) the nad7b/c intron. Thin black arrows indicate the splice sites. Gray arrows show nucleotides modified by RNA editing. Stars designate nucleotides predicted to be edited to stabilize intron structure but never actually seen altered in unspliced precursor RNAs.

Figure 3

Figure 3

Distribution of nucleotide identities around editing sites. Histograms show the relatively overrepresented bases around editing sites (position 0) in A, and around 30 randomly selected not edited Cs in B. Meaningful asymmetries could be only those not introduced by the general base composition and the third codon position bias as discussed in the text and as apparent in B. Positions not differing greatly from the overall base composition are not indicated.

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