title: Evolution and conservation of JmjC domain proteins in the green lineage.
abstract: Histone modification regulates plant development events by epigenetically silencing or activating gene expression, and histone methylation is regulated by histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). The JmjC domain proteins, an important KDM family, erase methyl marks (CH3-) from histones and play key roles in maintaining homeostasis of histone methylation in vivo. Here, we analyzed 169 JmjC domain proteins from whole genomes of plants ranging from green alga to higher plants together with 36 from two animals (fruit fly and human). The plant JmjC domain proteins were divided into seven groups. Group-I KDM4/JHDM3 and Group-V JMJD6 were found in all the plant species and the other groups were detected mainly in vascular or seed plants. Group-I KDM4/JHDM3 was potentially associated with demethylation of H3K9me2/3, H3K27me2/3, and H3K36me1/2/3, Group-II KDM5A with H3K4me1/2/3, Group-III KDM5B with H3K4me1/2/3 and H3K9me1/2/3, Group-V JMJD6 with H3R2, H4R3, and hydroxylation of H4, and Group-VII KDM3/JHDM2 with H3K9me1/2/3. Group-IV/Group-VI JmjC domain-only A/B proteins were involved in hydroxylation and demethylation of unknown substrate sites. The binding sites for the cofactors Fe(II) and α-ketoglutarate in the JmjC domains also were analyzed. In the α-ketoglutarate binding sites, Thr/Phe/Ser and Lys were conserved and in the Fe(II) binding sites, two His and Glu/Asp were conserved. The results show that JmjC domain proteins are a conserved family in which domain organization and cofactor binding sites have been modified in some species. Our results provide insights into KDM evolution and lay a foundation for functional characterization of KDMs.
authors.affiliation: College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China. yonghuang@hunau.edu.cn.|Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China. yonghuang@hunau.edu.cn.
authors.forename: Yong
authors.initials: Y
authors.lastname: Huang
authors.affiliation: College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China.|Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China.
authors.forename: Donghong
authors.initials: D
authors.lastname: Chen
authors.affiliation: Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, 410128, Changsha, China.
authors.forename: Chunlin
authors.initials: C
authors.lastname: Liu
authors.affiliation: College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China.|Institut de Biologie Moléculaire Des Plantes Du CNRS, Université de Strasbourg, 12 Rue Du Général Zimmer, 67084, Strasbourg Cedex, France.
authors.forename: Wenhui
authors.initials: W
authors.lastname: Shen
authors.affiliation: College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China. yingruan@hotmail.com.|Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China. yingruan@hotmail.com.|Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, 410128, Changsha, China. yingruan@hotmail.com.
authors.forename: Ying
authors.initials: Y
authors.lastname: Ruan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D005075:Biological Evolution; D017124:Conserved Sequence / Q000235:genetics; D004330:Drosophila / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D056466:Histone Demethylases / Q000235:genetics; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics; D006657:Histones / Q000235:genetics; D006801:Humans; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics*; D007656:Ketoglutaric Acids / Q000378:metabolism; D008745:Methylation; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics*; D013379:Substrate Specificity / Q000235:genetics
chemical_list: D006657:Histones; D007656:Ketoglutaric Acids; D010940:Plant Proteins; D056466:Histone Demethylases; D056484:Jumonji Domain-Containing Histone Demethylases; D011495:Histone-Lysine N-Methyltransferase
keywords: Domain organization; Evolution; Histone lysine demethylases; JmjC domain; Phylogenetic analysis