Cytosine methylation of rice mitochondrial DNA from grain and leaf tissues

Mitochondrial DNA and the largest nuclear-mitochondrial DNA in Arabidopsis can be separated by their methylation levels

Methylation of cytosines in plant mitochondrial DNA (mtDNA) has been a controversial issue. Results supporting mtDNA methylation may have been subject to contamination due to the presence of nuclear sequences originating from the mitochondrial genome called nuclear mitochondrial insertions (NUMT). In Arabidopsis (Arabidopsis thaliana) Columbia 0 (Col-0), the largest NUMT, located on Chromosome 2, is nearly twice the size of the entire mitochondrial genome and exhibits a sequence almost identical to the mitochondrial genome, albeit with shuffling and repeats. In the presence of such high similarity, it is challenging to eliminate interference when determining mtDNA methylation levels. Here, we applied a methyl-CpG-binding domain (MBD) protein-based affinity assay to separate total DNA, applied next-generation sequencing to the pre- and postseparation DNA samples, and examined the single nucleotide polymorphism (SNP) sites between NUMT and mtDNA. The results revealed successful separation of methylated and non-methylated DNA within the total DNA, with simultaneous separation achieved between NUMT DNA and mtDNA. These results suggest that our method can achieve separation based on the differential methylation levels of the whole lengths of NUMT and mtDNAs. The bisulfite sequencing results for the postseparation DNA samples suggest that mtDNA exhibits not only a lack of CpG methylation but also an absence of CHH and CHG methylation. In contrast, the NUMT shows high levels of methylation across all 3 contexts, at least in the Col-0 accession.

DEMETHYLATION REGULATOR 1 regulates DNA demethylation of the nuclear and mitochondrial genomes

Active DNA demethylation effectively modulates gene expression during plant development and in response to stress. However, little is known about the upstream regulatory factors that regulate DNA demethylation. We determined that the demethylation regulator 1 (demr1) mutant exhibits a distinct DNA methylation profile at selected loci queried by methylation-sensitive polymerase chain reaction and globally based on whole-genome bisulfite sequencing. Notably, the transcript levels of the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1) were lower in the demr1 mutant. We established that DEMR1 directly binds to the ROS1 promoter in vivo and in vitro, and the methylation level in the DNA methylation monitoring sequence of ROS1 promoter decreased by 60% in the demr1 mutant. About 40% of the hyper-differentially methylated regions (DMRs) in the demr1 mutant were shared with the ros1-4 mutant. Genetic analysis indicated that DEMR1 acts upstream of ROS1 to positively regulate abscisic acid (ABA) signaling during seed germination and seedling establishment stages. Surprisingly, the loss of DEMR1 function also caused a rise in methylation levels of the mitochondrial genome, impaired mitochondrial structure and an early flowering phenotype. Together, our results show that DEMR1 is a novel regulator of DNA demethylation of both the nuclear and mitochondrial genomes in response to ABA and plant development in Arabidopsis.

An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update

Besides the nuclear genome, plants possess two small extra chromosomal genomes in mitochondria and chloroplast, respectively, which contribute a small fraction of the organelles’ proteome. Both mitochondrial and chloroplast DNA have originated endosymbiotically and most of their prokaryotic genes were either lost or transferred to the nuclear genome through endosymbiotic gene transfer during the course of evolution. Due to their immobile nature, plant nuclear and organellar genomes face continuous threat from diverse exogenous agents as well as some reactive by-products or intermediates released from various endogenous metabolic pathways. These factors eventually affect the overall plant growth and development and finally productivity. The detailed mechanism of DNA damage response and repair following accumulation of various forms of DNA lesions, including single and double-strand breaks (SSBs and DSBs) have been well documented for the nuclear genome and now it has been extended to the organelles also. Recently, it has been shown that both mitochondria and chloroplast possess a counterpart of most of the nuclear DNA damage repair pathways and share remarkable similarities with different damage repair proteins present in the nucleus. Among various repair pathways, homologous recombination (HR) is crucial for the repair as well as the evolution of organellar genomes. Along with the repair pathways, various other factors, such as the MSH1 and WHIRLY family proteins, WHY1, WHY2, and WHY3 are also known to be involved in maintaining low mutation rates and structural integrity of mitochondrial and chloroplast genome. SOG1, the central regulator in DNA damage response in plants, has also been found to mediate endoreduplication and cell-cycle progression through chloroplast to nucleus retrograde signaling in response to chloroplast genome instability. Various proteins associated with the maintenance of genome stability are targeted to both nuclear and organellar compartments, establishing communication between organelles as well as organelles and nucleus. Therefore, understanding the mechanism of DNA damage repair and inter compartmental crosstalk mechanism in various sub-cellular organelles following induction of DNA damage and identification of key components of such signaling cascades may eventually be translated into strategies for crop improvement under abiotic and genotoxic stress conditions. This review mainly highlights the current understanding as well as the importance of different aspects of organelle genome maintenance mechanisms in higher plants.