The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA)

Abstract

We determined the complete nucleotide sequence of the mitochondrial genome of an angiosperm, sugar beet (Beta vulgaris cv TK81-O). The 368 799 bp genome contains 29 protein, five rRNA and 25 tRNA genes, most of which are also shared by the mitochondrial genome of Arabidopsis thaliana, the only other completely sequenced angiosperm mitochondrial genome. However, four genes identified here (namely rps13, trnF-GAA, ccb577 and trnC2-GCA) are missing in Arabidopsis mitochondria. In addition, four genes found in Arabidopsis (ccb228, rpl2, rpl16 and trnY2-GUA) are entirely absent in sugar beet or present only in severely truncated form. Introns, duplicated sequences, additional reading frames and inserted foreign sequences (chloroplast, nuclear and plasmid DNA sequences) contribute significantly to the overall size of the sugar beet mitochondrial genome. Nevertheless, 55.6% of the genome has no obvious features of information. We identified a novel tRNA(Cys) gene (trnC2-GCA) which shows no sequence homology with any tRNA(Cys) genes reported so far in higher plants. Intriguingly, this tRNA gene is actually transcribed into a mature tRNA, whereas the native tRNA(Cys) gene (trnC1-GCA) is most likely a pseudogene.

Figure 1

Gene map of the sugar beet mitochondrial genome. Protein, rRNA and tRNA coding genes and ORFs longer than 100 amino acids are indicated by gray boxes. cis-splicing introns are shown by thin lines. Orientations are clockwise for the genes shown outside the circle and counterclockwise for the genes shown inside the circle. Abbreviations for the three classes of tRNA genes are: na, native (genuine); cp, chloroplast-like; un, origin unknown. Three-copy repeated sequences which are active in recombination are indicated by bold lines. Map coordinate 0 has been arbitrarily assigned to the first nucleotide of the nad9 ORF (top of the figure) and numbering proceeds clockwise.

Figure 2

Cloverleaf structure deduced from the trnC1-GCA and trnC2-GCA gene sequences in sugar beet mitochondria. A mutation (T54→G54) in trnC1-GCA is indicated by an arrow.

Figure 3

Northern blot analysis to detect and determine the relative sizes of RNA transcripts of the two sugar beet tRNA^Cys genes. Hybridization probes were trnC2-GCA-, trnC1-GCA-, trnN-GUU- and trnY1-GUA-specific sequences whose positions are given in Figure 1. The sizes of the transcripts are shown in kilobases.