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A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

Figure 2

Alignments between PPR Proteins and Cognate Binding Sites.

(A) Statistically optimal alignments between amino acids at positions 6 (blue) and 1′ (red) in PPR10's PPR motifs and its RNA ligands (italics). PPR10's in vivo footprints are shown at top; the box marks the minimal binding site defined in vitro. Dark green shading indicates experimentally validated matches (Figure 5). Light green shading indicates significant correlation between position 6 and the purine/pyrimidine class of the matched nucleotide (Table S3). Magenta shading indicates significant anti-correlation between position 6 and the purine/pyrimidine class of the matched nucleotide (Table S3). Compensatory changes in orthologous protein/RNA pairs are indicated with a star. The PPR motifs are ordered from N to C terminus in the protein, and nucleotides are ordered from 5′ to 3′ in the RNA. The same schemes apply to panels (C) and (D). (B) Structural model illustrating physical plausibility of the cooperation between amino acids at positions 6 and 1′ in nucleotide specification. The model of the PPR10-atpH RNA complex was produced using distance geometry methods as previously described [10]. RNA bases were constrained to be within 3 Å of residues 6 and 1′ of helices A and A′ of adjacent motifs. Each PPR motif consists of one “A” and one “B” helix, as marked. (C) Alignments between amino acids at positions 6 and 1′ in PPR motifs of HCF152 and CRP1 and their RNA ligands. The psbH-petB sequence is HCF152's in vivo footprint [17], within which HCF152 binds in vitro [16]. The petB-petD sequence is a CRP1-dependent in vivo footprint [16]. The psaC sequence maps within the 70-nt region that most strongly coimmunoprecipitates with CRP1 [19]. (D) Alignments between amino acids at positions 6 and 1′ in PPR motifs of the RNA editing factors OTP82, CRR22 and CRR4 and their RNA targets [14], [29]. Minimal binding sites determined in vitro are boxed. The edited C (magenta) is the last nucleotide in each case. The type of PPR motif, either P, L or S, is indicated above. Only matches involving P or S motifs are shaded, as L motifs cannot be accommodated within the code developed here.

Figure 2

doi: https://doi.org/10.1371/journal.pgen.1002910.g002