CMS
Davila JI, Arrieta-Montiel MP, Wamboldt Y, Cao J, Hagmann J, Shedge V, Xu Y-Z, Weigel D & Mackenzie SA 2011 Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis. BMC Biol 9:64.
- extensive 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
- the majority of the structural polymorphisms found can be attributed to DSB repair activity by either nonhomologous end-joining (NHEJ) or intermediate-sized repeat-mediated recombination
- the extensive mitochondrial DNA polymorphism among lines within a species was not surprising
- nearly all of the variation observed could be accounted for by DSB repair activity or nucleotide substitutions
- strand invasion occurs throughout the genome, a likely consequence of random DSBs, but is prevented by MSH1 from producing successful DNA exchange in stretches of sequence homology under about 556 bp
- in the absence of MSH1, strand invasion proceeds at smaller lengths of homology to a lower limit of approximately 50 bp
- in the wild-type line, mitochondrial DNA exchange at intermediate repeats does occur, but at very low levels
- MSH1 encodes a carboxy-terminal GIY-YIG endonuclease domain, although direct participation in double-strand cleavage to abort DNA exchange has not yet been formally tested
- MSH1 presumably permits repair of a DSB at stretches of homology greater than 550 bp following heteroduplex formation, assuming a break-induced replication model
- in the msh1 mutant, heteroduplex formation occurs within the intermediate repeat stretches of homology
- the observation of heteroduplex-mediated mismatch repair in this study provides important evidence relevant to the low mitochondrial nucleotide substitution rates reported in plants
- this mismatch repair activity is independent of MSH1
- nucleotide divergence within intermediate repeat intervals, estimated across 72 Arabidopsis ecotypes at 5.5 per 10,000 bp, approximates the average for the genome as a whole, which is 5 per 10,000 bp
- in regions of the genome where high-frequency reciprocal DNA exchange occurs, within large (more than 1,000 bp) repeats, levels of polymorphism were 66 times lower, averaging 7.5 per Mbp for the 6.5-kb repeat across 72 ecotypes
- the low-frequency exchanges observed at intermediate repeats in the wild-type line may be sufficient to confer the low nucleotide substitution rate observed generally in the Arabidopsis mitochondrial genome
- in animal lineages, nucleotide substitution rates in the mitochondrial genome are much higher, with the notable exception of corals and their relatives
- the corals appear to be the only known animal lineage encoding a mitochondrial Msh1, with similarities in structure to MSH1 in plants
