The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants

Abstract

Tobacco is a valuable model system for investigating the origin of mitochondrial DNA (mtDNA) in amphidiploid plants and studying the genetic interaction between mitochondria and chloroplasts in the various functions of the plant cell. As a first step, we have determined the complete mtDNA sequence of Nicotiana tabacum. The mtDNA of N. tabacum can be assumed to be a master circle (MC) of 430,597 bp. Sequence comparison of a large number of clones revealed that there are four classes of boundaries derived from homologous recombination, which leads to a multipartite organization with two MCs and six subgenomic circles. The mtDNA of N. tabacum contains 36 protein-coding genes, three ribosomal RNA genes and 21 tRNA genes. Among the first class, we identified the genes rps1 and psirps14, which had previously been thought to be absent in tobacco mtDNA on the basis of Southern analysis. Tobacco mtDNA was compared with those of Arabidopsis thaliana, Beta vulgaris, Oryza sativa and Brassica napus. Since repeated sequences show no homology to each other among the five angiosperms, it can be supposed that these were independently acquired by each species during the evolution of angiosperms. The gene order and the sequences of intergenic spacers in mtDNA also differ widely among the five angiosperms, indicating multiple reorganizations of genome structure during the evolution of higher plants. Among the conserved genes, the same potential conserved nonanucleotide-motif-type promoter could only be postulated for rrn18-rrn5 in four of the dicotyledonous plants, suggesting that a coding sequence does not necessarily move with the promoter upon reorganization of the mitochondrial genome.

The Pentatricopeptide Repeat GeneOTP43Is Required fortrans-Splicing of the Mitochondrialnad1Intron 1 inArabidopsis thaliana

“…Mitochondrial Complex I is comprised of >40 subunits in Arabidopsis thaliana (Heazlewood et al, 2003). The majority of these are encoded by nuclear genes, and only nine genes have been retained in the land plant mitochondrial genome, namely, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, and nad9 (Sugiyama et al, 2005). With such a plethora of genes involved, one might have expected many mutants with alterations in Complex I activity to have been investigated, but in fact, the literature is very sparse.…”

The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes

“…In most angiosperm mitochondria, there is also a high frequency of recombination between large repeated sequences within the genome, interconverting between a suite of alternative conformations that coexist within an individual (31). As a result, angiosperm mitochondrial genomes typically produce multipartite maps that can be represented either as a single "master circle" or as a set of subgenomes (32,33).…”

Mitochondrial mRNA Polymorphisms in Different Arabidopsis Accessions

“…Mitochondrial genomes in higher plants are extraordinarily large (up to 2.4 Mb), but usually encode less than 60 genes and therefore have large noncoding regions (Unseld et al, 1997;Kubo et al, 2000;Notsu et al, 2002;Handa, 2003;Clifton et al, 2004;Satoh et al, 2004;Ogihara et al, 2005;Sugiyama et al, 2005). This is accompanied by high genome complexity provoked by frequent DNA recombinations and rearrangements (Mackenzie, 2007;Kubo and Newton, 2008).…”