Fig. 6

Matching key PPR residues with target sequences for RARE1 and CRR28. Relevant key residues in PPR positions 3, 6 and 1’ were selected from the total alignments of 35 RARE 1 (A) and 64 CRR28 (B) orthologues in angiosperms to obtain weblogo conservation plots at http://weblogo.berkeley.edu/logo.cgi [76]. Target sequences are aligned with the terminal S-type PPR (which contributes position 1’ to the preceding L-type PPR) juxtaposed with nucleotide -4 in front of the C-to-U editing site (underlined). Ambiguities are indicated where represented at least twice in the corresponding targets. Green shading indicates perfect matching of positions 6 and 1’ in P- and S-type repeats with corresponding nucleotides according to the proposed core binding code (T + N:A, N + N:C, T + D:G, N + D:U). Blue matching indicates distinction of pyrimidines vs. purines in position 6 only and grey shading indicates mismatches. Allowing for replacement of threonine by serine matches RARE1 PPR S4 (S + D) with G in its target and CRR28 (S + N) with A in its targets, but also mismatches RARE1 P4 (S + N) with U