Emerging links between iron-sulfur clusters and 5-methylcytosine base excision repair in plants

Abstract

Iron-sulfur (Fe-S) clusters are ancient cofactors present in all kingdoms of life. Both the Fe-S cluster assembly machineries and target apoproteins are distributed across different subcellular compartments. The essential function of Fe-S clusters in nuclear enzymes is particularly difficult to study. The base excision repair (BER) pathway guards the integrity of DNA; enzymes from the DEMETER family of DNA glycosylases in plants are Fe-S cluster-dependent and extend the BER repertowere to excision of 5-methylcytosine (5mC). Recent studies in plants genetically link the majority of proteins from the cytosolic Fe-S cluster biogenesis (CIA) pathway with 5mC BER and DNA repair. This link can now be further explored. First, it opens new possibilities for understanding how Fe-S clusters participate in 5mC BER and related processes. I describe DNA-mediated charge transfer, an Fe-S cluster-based mechanism for locating base lesions with high efficiency, which is used by bacterial DNA glycosylases encoding Fe-S cluster binding domains that are also conserved in the DEMETER family. Second, because detailed analysis of the mutant phenotype of CIA proteins relating to 5mC BER revealed that they formed two groups, we may also gain new insights into both the composition of the Fe-S assembly pathway and the biological contexts of Fe-S proteins.

Redox status of the plant cell determines epigenetic modifications under abiotic stress conditions and during developmental processes

“…The CIA pathway engages several scaffold and carrier proteins [57] . Demeter and ROS1 are 5-methylcytosine DNA glycosylases that play a role in fertilization [58] . This Fe-S cluster assembled DNA demethylase is activated during fertilization, following an oxidative burst in the central cell, leaving evidence that conditions similar to oxidative stress are required for demethylase activity.…”

Active DNA demethylation in plants: 20 years of discovery and beyond

“…ROS1 directly interacts with MET18, a component of the cytosolic iron‐sulfur assembly (CIA) complex; this observation is consistent with the finding that mutants of the CIA pathway exhibit elevated DNA methylation levels at thousands of genomic loci that overlap with those of ros1 or ros1 dml2 dml3 mutants (Duan et al, 2015). The redox state of the iron‐sulfur cluster motif is thought to serve as a mechanism to detect the substrate nucleotide and regulate the binding affinity of the glycosylase with DNA (Buzas, 2016). The conserved C‐terminal domain (aa 1250–1381 in ROS1) contains a permutated CXXC motif and an RNA recognition motif (RRM) fold, which were uniquely identified in DMLs, although this domain is more variable than the DNA glycosylase domain.…”

Active DNA Demethylation in Plants

“…On other hand, point mutations at each cysteine residue of the [4Fe-4S] cluster motif of DME resulted in abrogation of DNA glycosylase activity, suggesting that this motif is also necessary for catalytic activity and/or protein stability [28]. It has been proposed that the oxidation state of the [4Fe-4S] cluster mediates binding and dissociation of DML proteins from DNA [31].…”