Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

Abstract

BackgroundThe mitochondrial genome of higher plants is unusually dynamic, with recombination and nonhomologous end-joining (NHEJ) activities producing variability in size and organization. Plant mitochondrial DNA also generally displays much lower nucleotide substitution rates than mammalian or yeast systems. Arabidopsis displays these features and expedites characterization of the mitochondrial recombination surveillance gene MSH1 (MutS 1 homolog), lending itself to detailed study of de novo mitochondrial genome activity. In the present study, we investigated the underlying basis for unusual plant features as they contribute to rapid mitochondrial genome evolution.ResultsWe obtained evidence of double-strand break (DSB) repair, including NHEJ, sequence deletions and mitochondrial asymmetric recombination activity in Arabidopsis wild-type and msh1 mutants on the basis of data generated by Illumina deep sequencing and confirmed by DNA gel blot analysis. On a larger scale, with mitochondrial comparisons across 72 Arabidopsis ecotypes, similar evidence of DSB repair activity differentiated ecotypes. Forty-seven repeat pairs were active in DNA exchange in the msh1 mutant. Recombination sites showed asymmetrical DNA exchange within lengths of 50- to 556-bp sharing sequence identity as low as 85%. De novo asymmetrical recombination involved heteroduplex formation, gene conversion and mismatch repair activities. Substoichiometric shifting by asymmetrical exchange created the appearance of rapid sequence gain and loss in association with particular repeat classes.ConclusionsExtensive mitochondrial genomic variation within a single plant species derives largely from DSB activity and its repair. Observed gene conversion and mismatch repair activity contribute to the low nucleotide substitution rates seen in these genomes. On a phenotypic level, these patterns of rearrangement likely contribute to the reproductive versatility of higher plants.

Cell-to-cell movement of mitochondria in plants

“…Still, the rearranged region integrated into the chimeric mitochondrial genomes by homologous recombination preserving either the CMS or fertile mtDNA structure. Thus, nonhomologous end joining, the driving force behind mtDNA rearrangement during evolution, is not involved in the formation of mosaic mtDNAs (31,32). The rearranged mitochondrial genomes were stable for at least three seed generations.…”

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

“…This variation at the level of entire chromosomes is in striking contrast to the overall pattern of structural conservation in the set of shared chromosomes. The lack of inversions and rearrangements is highly unusual for angiosperm mitochondrial genomes, which are often structurally dynamic even within species (27)(28)(29)(30). This difference is likely caused by a reduced rate of intragenomic recombination between small repeats in S. noctiflora mtDNA (22).…”

“…As in this study, the identification of multichromosomal structures in angiosperms has been based almost exclusively on mapping/ sequencing (21-23), but, in some other cases, sequence data have been supplemented with electrophoretic separation of chromosomes and electron microscopy-based observations (11,12,14,15,17,18,20,45,46). To date, the only direct characterization of chromosomal structure in an angiosperm multichromosomal mitochondrial genome was performed in Silene vulgaris (26)(27)(28)(29)(30). In this case, a Southern blot analysis of the smallest (∼5 kb) mitochondrial chromosome confirmed the existence of the predicted circular molecules but found that most of the DNA was present in multimeric forms that varied in susceptibility to exonuclease digestion, indicating diversity in molecular size and structure.…”

“…Angiosperm mitochondrial genomes are characterized by a number of unusual properties, including their large and variable sizes (ranging from ∼200 kb to over 10 Mb), low gene densities, extensive posttranscriptional modifications, and propensity to capture foreign DNA sequences (24,25). They generally exhibit very low rates of nucleotide substitution, but their structures are highly dynamic, varying extensively among and even within species as a result of frequent rearrangements and gain/loss of intergenic sequences (26)(27)(28)(29)(30). 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).…”

The Chloroplast Triggers Developmental Reprogramming When MUTS HOMOLOG1 Is Suppressed in Plants

“…Disruption of MSH1 enhances recombination at 47 pairs of repeated sequences in the mitochondrial genome of Arabidopsis (Arabidopsis thaliana; Shedge et al, 2007;Arrieta-Montiel et al, 2009;Davila et al, 2011) and gives rise to cytoplasmic male sterility in tomato (Solanum lycopersicum ) and tobacco (Nicotiana tabacum; Sandhu et al, 2007). Within the chloroplast, disruption of MSH1 results in low-frequency DNA rearrangements mediated by recombination, together with altered redox properties of the cell and variegation of the plant .…”