Molecular nature of the hyl1 suppressor mutation. (A) Schematic representation of the domain structure of Arabidopsis DCL1 (AtDCL1) and the dcl1-13 mutation in the helicase domain that caused the suppression of the hyl1 mutant phenotype. DCL1 has two nuclear localization signals (NLSs), an ATPase/DExH-box RNA helicase domain, a domain known as DUF238 (domain of unknown function), a PAZ domain, two RNase III domains, and two double-stranded RNA-binding domains (dsRBDs). Between motifs II and III of the helicase domain, the G at position 1183 in the coding sequence was substituted to A in hyl1 suppressor plants, resulting in the amino acid substitution of Glu-395 with Lys (E395K). The transitions of P415S in sin1-1 (dcl1-7) and I431K in sin1-2 were closely located. (B) Alignment of amino acid sequences between motifs II and III in the helicase domains of Arabidopsis DCLs and other Dicer homologs of human, Drosophila, C. elegans, and S. pombe. Sequences that were predicted to form α-helices using the jpred3 program (Cuff et al. 1998) are shown. Arabidopsis DCL1 (AtDCL1; accession no. NP_171612) was aligned with Arabidopsis DCL2 (AtDCL2; NP_566199), DCL3 (AtDCL3; NP_189978), DCL4 (AtDCL4; NP_197532), Homo sapiens Dicer (HsDicer; NP_803187), Drosophila Dcr-2 (DmDcr-2; NP_523778), C. elegans Dcr-1 (CeDcr-1; NP_498761), and S. pombe Dicer (SpDicer; Q09884). Sequences were aligned with the positions of conserved P, Y, and M (letter columns marked with asterisks), which were highly conserved among these proteins. Numbers indicate the positions of the first amino acids. The arrow indicates the position of the hyl1 suppressor mutation in AtDCL1. (C) Homology model of the first RecA-like domain of the AtDCL1 helicase domain (residues 239–433) according to the structure of yeast initiation factor 4A (PDB ID code 1qva). This was constructed using the 3D-JIGSAW program (Bates et al. 2001). The α-helices, β-strands, and turns are indicated with pink, yellow, and blue colors, respectively. Residues E395, P415, and I431 are highlighted.
