title: AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in Arabidopsis.
abstract: DNA methylation is a primary epigenetic modification regulating gene expression and chromatin structure in many eukaryotes. Plants have a unique DNA demethylation system in that 5-methylcytosine (5mC) is directly removed by DNA demethylases, such as DME/ROS1 family proteins, but little is known about the downstream events. During 5mC excision, DME produces 3'-phosphor-α, β-unsaturated aldehyde and 3'-phosphate by successive β- and δ-eliminations, respectively. The kinetic studies revealed that these 3'-blocking lesions persist for a significant amount of time and at least two different enzyme activities are required to immediately process them. We demonstrate that Arabidopsis AP endonucleases APE1L, APE2 and ARP have distinct functions to process such harmful lesions to allow nucleotide extension. DME expression is toxic to E. coli due to excessive 5mC excision, but expression of APE1L or ARP significantly reduces DME-induced cytotoxicity. Finally, we propose a model of base excision repair and DNA demethylation pathway unique to plants.
authors.affiliation: Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
authors.forename: Jiyoon
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
authors.forename: Hosung
authors.initials: H
authors.lastname: Jang
authors.affiliation: Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
authors.forename: Hosub
authors.initials: H
authors.lastname: Shin
authors.affiliation: Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
authors.forename: Woo Lee
authors.initials: WL
authors.lastname: Choi
authors.affiliation: Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
authors.forename: Young Geun
authors.initials: YG
authors.lastname: Mok
authors.affiliation: Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea huhjh@snu.ac.kr.
authors.forename: Jin Hoe
authors.initials: JH
authors.lastname: Huh
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism*; D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics; D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D045647:DNA Glycosylases / Q000378:metabolism; D004260:DNA Repair; D018744:DNA, Plant / Q000096:biosynthesis / Q000378:metabolism*; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D004720:Endonucleases / Q000145:classification / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D009699:N-Glycosyl Hydrolases / Q000378:metabolism; D009687:Nuclear Proteins / Q000378:metabolism; D010744:Phosphoric Monoester Hydrolases / Q000145:classification / Q000378:metabolism; D015534:Trans-Activators / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D009687:Nuclear Proteins; C471271:ROS1 protein, Arabidopsis; D015534:Trans-Activators; D044503:5-Methylcytosine; C540281:Ape1L protein, Arabidopsis; C540282:Ape2 protein, Arabidopsis; C540283:Arp protein, Arabidopsis; D004720:Endonucleases; D010744:Phosphoric Monoester Hydrolases; C463261:DEMETER protein, Arabidopsis; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase