Mitochondrial DNA repair in an Arabidopsis thaliana uracil N-glycosylase mutant

Authors: Wynn, Emily; PURFEERST, EMMA - University Of Nebraska; CHRISTENSEN, ALAN - University Of Nebraska

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2020
Publication Date: 2/18/2020
Citation: Wynn, E.L., Purfeerst, E., Christensen, A.C. 2020. Mitochondrial DNA repair in an Arabidopsis thaliana uracil N-glycosylase mutant. Plants. 9(2):261. https://doi.org/10.3390/plants9020261.
DOI: https://doi.org/10.3390/plants9020261

Interpretive Summary: Mitochondria are the powerhouse of the cell. They break down food and convert it into energy for the rest of the cell. Mitochondria also have their own DNA, which can be damaged as a side effect of their powerhouse activities. There are mechanisms within a cell to repair this damaged mitochondrial DNA. In plant cells, we know these repair mechanisms can be very accurate because mitochondrial genes mutate slowly. However, many of the DNA repair mechanisms found in other genomes are not found in plant mitochondria. Our hypothesis is that double-strand break repair is a generalized form of DNA repair in plant mitochondrial genomes that can repair the damage usually repaired by the missing repair mechanisms. To test this hypothesis, we used the model organism Arabidopsis thaliana and knocked out the only other known DNA repair pathway in plant mitochondria, base excision repair. We expected that double-strand break repair would be able to repair the DNA damage usually repaired by base excision repair. In these experimental plants, we showed that there was not an increase in mitochondrial mutations, indicating that there is a backup system of repair. To show that double-strand break repair is the backup system, we tested several genes known to be involved in double-strand break repair and showed that they are upregulated to compensate for the loss of base excision repair. Double-strand break repair requires a template; another piece of DNA is required to accurately repair the damaged DNA. In plant meristems, which are like stem cells in plants, the mitochondria fuse together to form a giant mitochondrion. This is an opportunity to bring mitochondrial DNA together for accurate double-strand break repair. We showed that as plant cells get older and further away from the meristem, they accumulate more DNA mutations. This is further evidence that double-strand break repair is the backup system of DNA repair, because the further away a cell is from the meristem, the less likely it is to have a template available to do accurate double-strand break repair.

Technical Abstract: Substitution rates in plant mitochondrial genes are extremely low, indicating strong selective pressure as well as efficient repair. Plant mitochondria possess base excision repair pathways; however, many repair pathways such as nucleotide excision repair and mismatch repair appear to be absent. In the absence of these pathways, many DNA lesions must be repaired by a different mechanism. To test the hypothesis that double-strand break repair (DSBR) is that mechanism, we maintained independent self-crossing lineages of plants deficient in uracil-N-glycosylase (UNG) for 11 generations to determine the repair outcomes when that pathway is missing. Surprisingly, no single nucleotide polymorphisms (SNPs) were fixed in any line in generation 11. The pattern of heteroplasmic SNPs was also unaltered through 11 generations. When the rate of cytosine deamination was increased by mitochondrial expression of the cytosine deaminase APOBEC3G, there was an increase in heteroplasmic SNPs but only in mature leaves. Clearly, DNA maintenance in reproductive meristem mitochondria is very effective in the absence of UNG while mitochondrial genomes in differentiated tissue are maintained through a different mechanism or not at all. Several genes involved in DSBR are upregulated in the absence of UNG, indicating that double-strand break repair is a general system of repair in plant mitochondria. It is important to note that the developmental stage of tissues is critically important for these types of experiments.