Molecular basis for the methylation specificity of ATXR5 for histone H3

Abstract

In plants, the histone H3.1 lysine 27 (H3K27) mono-methyltransferases ARABIDOPSIS TRITHORAX RELATED PROTEIN 5 and 6 (ATXR5/6) regulate heterochromatic DNA replication and genome stability. Our initial studies showed that ATXR5/6 discriminate between histone H3 variants and preferentially methylate K27 on H3.1. In this study, we report three regulatory mechanisms contributing to the specificity of ATXR5/6. First, we show that ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Second, we demonstrate that post-transcriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. Third, we show that ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Finally, we demonstrate that deletion or mutation of the PHD domain reduces the catalytic efficiency (kcat/Km of AdoMet) of ATXR5 up to 58-fold, highlighting the multifunctional nature of ATXR5 PHD domain. Overall, our results suggest that several molecular determinants regulate ATXR5/6 methyltransferase activity and epigenetic inheritance of H3.1 K27me1 mark in plants.

Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis

“…8a ), which recognizes the unmodified H3K4 (ref. 52 ). We modeled the AIPP2 and PAIPP2-PHD fingers using the ATXR5 PHD finger, as a template to analyze the interactions with unmodified H3K4 (Fig.…”

Computational characterization of substrate and product specificities, and functionality of S‐adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize

“…All the analyzed plant ATXR5 and ATXR6 proteins may catalyse H3K27 monomethylation, since they contain two Tyr residues in the substrate binding pocket (Figure A). This prediction is consistent with rcATXR5, atATXR5 and atATXR6, which were characterized as H3K27 monomethyltransferases through biochemical, structural and/or functional studies …”

“…The SET domain of ATXR5 and ATXR6 is distinct from other classes of HKMTs . The ternary structure (complex with histone H3.1 peptide and SAM) of the Arabidopsis ATXR5 homolog, from the plant Ricinus communis (rcATXR5), shows that SET domain and nSET (absent in other SET domain HKMTs) are involved in the selective recognition of the H3.1 peptide and H3K27 monomethylation . Although ATXR5 and ATXR6 catalyse monomethylation of H3K27, they do not incorporate into PRC2 complexes, and they exhibit no evolutionary or phylogenetic relationship with E(Z) …”

Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex inArabidopsis

“…Moreover, both AIPP2 and PAIPP2 PHD fingers share approximately 35% sequence identity with the PHD finger of Glycine max ATXR5 (PDB ID: 5VAB) ( Supplementary Fig. 8a), which recognizes the unmodified H3K4 52 . We modelled the AIPP2 and PAIPP2 PHD fingers using the ATXR5 PHD finger as a template to analyze the interactions with unmodified H3K4 ( Fig.…”