A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [RNA-seq]

Methylation of cytosine to 5-methylcytosine (5mC) is a prevalent DNA modification found in many organisms. Sequential oxidation of 5mC by TET dioxygenases results in a cascade of additional epigenetic marks and promotes DNA demethylation in mammals. However, the enzymatic activity and the function of TET homologs present in lower eukaryotes remains largely unexplored. In our study of TET homologs in the green alga Chlamydomonas reinhardtii (C. reinhardtii), we have found a 5mC-modifying enzyme (CMD1) that catalyzes conjugation of a glyceryl moiety onto the methyl group of 5mC through a carbon-carbon bond, resulting in two novel stereoisomeric nucleotide products. The catalytic activity of CMD1 requires Fe(II) and the integrity of its His-x-Asp (HxD) binding motif, which is conserved in Fe-dependent oxygenases. However, unlike all previous described TET enzymes which utilize 2-oxoglutarate (2-OG) as a co-substrate, CMD1 utilizes L-ascorbic acid (vitamin C, VC) as an essential co-substrate. VC itself is the source of the glyceryl moiety that modifies 5mC, with concurrent formation of glyoxylic acid and CO2. The VC-derived DNA modification is present in the genome of C. reinhardtii and its level decreases significantly in a CMD1 mutant strain. The fitness of CMD1 mutant cells to high light exposure is reduced, mainly due to deficient expression of the critical non-photochemical quenching (NPQ) effector gene LHCSR3, which is hypermethylated in the mutant cells. Our study thus reveals a new eukaryotic DNA base modification, and its involvement in a functionally conserved but mechanistically divergent DNA demethylation pathway for the epigenetic regulation of photosynthesis. Overall design: Test the change of gene expression in CMD1 mutant cells