Multiple sequence rearrangements accompanying the duplication of a tRNAPro gene in wheat mitochondrial DNA

Abstract

In the course of isolating tRNA genes from wheat mtDNA, we have found the same tRNA(Pro) gene in two different Hind III restriction fragments, H-P1 (0.7 kbp) and H-P2 (1.7 kbp). Sequences immediately flanking these duplicate genes are closely related, although not identical; sequence comparisons suggest that multiple rearrangements have occurred in the vicinity of the H-P2 tRNA(Pro) gene, relative to the H-P1 version. The chimeric nature of H-P2 is emphasized by the presence of sequences that are also found upstream of the wheat mitochondrial 26S rRNA gene, as well as sequences derived from chloroplast DNA. Comparison of H-P2 with H-P1 plus upstream sequences provides some insight into possible molecular events that might have generated H-P2. In particular, such comparisons suggest a model in which the homologous sequences in H-P2 are seen to be derived from H-P1 plus upstream sequences as a result of an intragenomic, site-specific rearrangement event, followed by amplification of the product, its fixation in the mitochondrial genome, and subsequent sequence divergence (single base changes as well as insertions/deletions of up to 50 nucleotides). The results reported here implicate particular primary sequence motifs in certain of the rearrangements that characterize H-P2.

The potato mitochondrial initiator methionine tRNA gene and its flanking regions: an illustration of the diversity of mitochondrial genome rearrangements among plant species

“…These observations may also reflect different evolution 'tempos' of the mt sequences, leading to considerable variation in the degree of homology exhibited by the flanking regions of a given mt gene among plant species [ 14]. Finally, the presence, in these extensively rearranged mt genome regions containing the tRNAf ~et gene, of short sequences (the 't-elements' in wheat, the tRNA 'pseudogene' in potato, a not yet precisely identified sequence in soybean [3]) which are repeated in several other regions of the mt DNA strengthens the hypothesis that such repeats are involved as recognition elements in the plant mt DNA recombination mechanism(s) [7].…”

Nucleotide sequence of a tRNA pseudogene from wheat mitochondrial DNA

“…It should be noted that in this structure is present the T G C A A G A sequence (marked by solid line) very similar to the motif accompanying tRNA Pr° gene in wheat mitochondrial D N A found by Joyce et al [ 1 ]. …”

Sequence and organization of a 7.2 kb region of wheat mitochondrial DNA containing the large subunit (26S) rRNA gene

“…1). As summarized in Fig 2, this fragment (P7.2) contains (i)a large subunit (26S) rRNA gene, rrn26; (ii)a tandem array of two identical direct repeats of 70 bp; and(iii) a tRNA-like element (t4) of a type previously described in wheat mtDNA [10,12]. P7.2 contains nine open reading frames (ORFs) of 100 or more codons; six of these ORFs occur within rrn26 and three are found within the largest variable domain (V2 [6]) of the 26S rRNA sequence (two in the sense strand, one in the antisense strand).…”

“…1) is intriguing in the context of a possible role in the regulation of 26S rRNA gene expression. The 70 bp elements represent a class of short repeats in wheat mtDNA, with homologues of portions of this sequence or its complement found within rrn26 (in a region designated V2 [6], a highly variable and expanded domain in the mature rRNA [9]); upstream of had3 [8] and a tRNA l'r° gene [ 12]; and downstream ofrpsl3 [ 1]. We note, however, that no known member of this repeat family, other than those upstream of the 26S rRNA gene, includes a copy of the putative rrn26 promoter motif(see, e.g., Fig.…”

“…Short direct tandem repeats at il and i3 are marked by single underlines. Note that the alignment through il follows that in [ 12], although il could be considered to be part of h2. [8]).…”