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TitleMolecular basis of the plant ROS1-mediated active DNA demethylation.
Journal, issue, pagesNat Plants, Vol. 9, Issue 2, Page 271-279, Year 2023
Publish dateJan 9, 2023
AuthorsXuan Du / Zhenlin Yang / Guohui Xie / Changshi Wang / Laixing Zhang / Kaige Yan / Maojun Yang / Sisi Li / Jian-Kang Zhu / Jiamu Du /
PubMed AbstractActive DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly ...Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly excise 5-methyl-cytosine (5mC), representing an efficient DNA demethylation pathway distinct from that of animals. Here, we report the cryo-electron microscopy structures of an Arabidopsis ROS1 catalytic fragment in complex with substrate DNA, mismatch DNA and reaction intermediate, respectively. The substrate 5mC is flipped-out from the DNA duplex and subsequently recognized by the ROS1 base-binding pocket through hydrophobic and hydrogen-bonding interactions towards the 5-methyl group and Watson-Crick edge respectively, while the different protonation states of the bases determine the substrate preference for 5mC over T:G mismatch. Together with the structure of the reaction intermediate complex, our structural and biochemical studies revealed the molecular basis for substrate specificity, as well as the reaction mechanism underlying 5mC demethylation by the ROS1/DME family of plant-specific DNA demethylases.
External linksNat Plants / PubMed:36624257
MethodsEM (single particle)
Resolution3.1 - 3.9 Å
Structure data

33832

7yho

EMDB-33832, PDB-7yho:
CryoEM structure of Arabidopsis ROS1 in complex with TG mismatch dsDNA at 3.3 Angstroms resolution
Method: EM (single particle) / Resolution: 3.3 Å

33835

7yhp

EMDB-33835, PDB-7yhp:
CryoEM structure of Arabidopsis ROS1 in complex with 5mC-dsDNA at 3.1 Angstroms resolution
Method: EM (single particle) / Resolution: 3.1 Å

33836

7yhq

EMDB-33836, PDB-7yhq:
CryoEM structure of Arabidopsis ROS1 in complex with a covalent-linked reaction intermediate at 3.9 Angstroms resolution
Method: EM (single particle) / Resolution: 3.9 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

Source
  • homo sapiens (human)
  • arabidopsis thaliana (thale cress)
KeywordsDNA BINDING PROTEIN/DNA / ROS1 / DNA glycosylase / DNA demethylation / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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