Fig 1. PpPPR_56 alignment and binding to the nad3 and nad4 target sites.

(A) Alignment of PpPPR_56 and its RNA targets nad3 and nad4. The key amino acids at positions 5 and last of each PPR motif are indicated. The editing sites C are underlined. The aligned nucleotides are shaded in gray to indicate matches to RNA recognition code, as proposed by Barkan et al. [12]. (B) REMSA was performed using recombinant 56ΔDYW-wt protein and 50 pM of ³²P-labeled RNAs (nad3 and nad4). 56ΔDYW-wt concentrations ranging from 0 to 100 nM are shown above each lane. B and U indicate the bound and unbound probe, respectively. (C) Binding was quantitated from the comparison between the bound (B) and the unbound (U) probes. Each reaction was performed in triplicates. Error bars indicate ± standard deviation (SD).