Conserved Sequence Motifs in Cellular RdRPs

Multiple sequence alignment of a representative subset of cRdRPs. Amino acid sequences of 30 cRdRPs from fungi from the groups of Ascomycota (Schizosaccharomyces pombe, Spo; Neurospora crassa, Ncr; and Gibberella zeae, Gze) and Basidiomycota (Cryptococcus neoformans, Cne), slime molds (Dictyostelium discoideum, Ddi), dicot plants (Arabidopsis thaliana, Ath; Solanum tuberosum, Stu; and Nicotiana tabacum, Ntu), monocot plants (Oryza sativa, Osa), protozoa (Entamoeba histolytica, Ehi), and nematodes (Caenorhabditis elegans, Cel) were aligned using standard settings of ClustalW algorithm. Local alignment was improved by manual editing. N. crassa QDE-1 protein sequence is shown on the top. N. crassa contains two additional non-allelic cRdRP genes��SAD-1 (essential for meiotic silencing by unpaired DNA ) and RdRP-3��that likely function in distinct cellular pathways. Invariant residues are shaded in black; other residues with 80% or more conservation are shaded in grey. Conserved sequence motifs comprising invariant residues are outlined: motif 1, red; motif 2, orange; motif 3, dark yellow; motif 4, purple; motif 5, violet; motif 6, light pink; and motif 7, blue. QDE-1 secondary structure elements are shown on top, coloured according to domain definition (slab, blue; catalytic, deep purple; neck, pink; and head, red). The identified double-psi ��-barrels DPBB1 and DPBB2 are outlined by deep purple boxes. The flap sub-domain and the potential ��bridge helices�� are also represented by boxes, coloured light purple and grey, respectively. (914 KB DOC)