Analysis of the nucleotide context of Arabidopsis thaliana mitochondrial mRNA editing sites

• Published in: Biophysics (Oxford) Vol. 51; no. S1; pp. 1 - 6
• Main Authors: Vishnevsky, O. V., Titov, I. I., Konstantinov, Yu. M.
• Format: Journal Article
• Language: English
• Published: Moscow Springer Nature B.V 01.02.2006
• Subjects: Amino acids; Arabidopsis thaliana; Biophysics; Mitochondria; Plant biology; Ribonucleic acid; RNA
• ISSN: 0006-3509; 1555-6654
• DOI: 10.1134/S0006350906070013

C [arrow right] T deamination is among the most widespread types of mitochondrial mRNA editing in higher plants. In the majority of cases, the first and second codon positions are edited, which leads to "correction" of the codon, substitution in amino acid sequence, and synthesis of a fully functional protein. Numerous experimental works have demonstrated that the 5'-and 3'-flanks of the editing site are important for precise and efficient editing. However, no significant motifs have been detected in the flanking regions, and the editing mechanism is still unknown. We analyzed the editing sites of Arabidopsis thaliana mitochondrial mRNA using region-specific degenerate oligonucleotide motifs and trinucleotide weight matrices. In addition, we compared the mRNA folding energies in the regions of editing sites. Significant oligonucleotide patterns were discovered in the region [-50; 50] relative to the editing site. Jackknife assessment suggested that such signals could play an important role in the functioning of editing sites. However, the detected characteristics alone were insufficient for efficient recognition of editing sites in A. thaliana mitochondrial mRNA.[PUBLICATION ABSTRACT]