File S1 - Genomic Survey, Gene Expression Analysis and Structural Modeling Suggest Diverse Roles of DNA Methyltransferases in Legumes

The following supporting information is available in the online version of this article: Table S1. Details of known methyltransferases of Arabidopsis and rice. Table S2. List of primers used in this study. Table S3. Details of methyltransferases identified in three legumes and grapevine. Table S4. Nuclear localization signal predicted in chickpea and soybean methyltransferases. Table S5. Summary of homology modeling statistics of representative members of soybean and chickpea methyltransferases. Figure S1. Multiple sequence alignment of all the classes of MTases identified in legumes. Multiple sequence alignments were generated using JalView to highlight the conserved domains (line on top of alignments) and residues (black rectangular boxes) in MET (A), CMT (B), DRM (C) and DNMT2 (D). Figure S2. Three-dimensional (3D) structures of soybean and chickpea CMT proteins constructed by homology modeling. Ribbon representation of GmCMT2 and CaCMT2 protein structures with bound H3(1–15)K9me2 peptide. The BAH, methyltransferase, and Chr domains are colored in red, cyan, and blue, respectively, with bound S-adenosylhomocysteine (SAH) molecule (orange) and H3(1–15)K9me2 peptide (yellow, bound to Chr domain) shown in a space filling representation. The K9me2 is accommodated within an aromatic cage formed by Tyr400, Phe370 and Trp397in GmCMT2 and by Tyr415, Trp431 and Tyr434 in CaCMT2 (Inset). Intermolecular hydrogen bonds between H3K9me2 peptide and Chr domain are designated by dashed lines (Inset). Figure S3. Structural features of plant METs. (A) The RFD domain pluged into the DNA-binding pocket. The RFD domain (magenta) is positioned in the DNA-binding pocket (cyan) of MET and stabilized by several hydrogen bonds (inset; yellow dashed lines) or non-bonded interactions (inset; interacting residues shown as sticks) with the catalytic domain. PCQ region of the catalytic domain is highlighted in red color. (B) Comparison of the TRD subdomain of MET with CMT. Comparison of the TRD subdomains of MET (purple) and CMT (cyan) by superimposing their structures. The regulatory region of TRD subdomain in CMTs is occupied by two antiparallel sheets (arrow), whereas only loop is present in MET indicative of different regulatory mechanisms in these MTases. Chromodomain is shown in red color. Figure S4. Structural features of plant DRMs. (A) Ribbon representation of the structure of CMT with bound SAH to motif I (magenta) and motif X (red). Bound SAH molecule shown in a space filling representation. (B) The UBA domains (UBA1 and UBA2) are colored in cyan and green. (C) Comparison of UBA1 (cyan), UBA2 (green) and UBA3 (magenta) structures with conserved MGF/MGY shown as sticks.