Pentatricopeptide repeats: modular blocks for building RNA-binding proteins

Abstract

Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism across the eukaryotic domain. Recent computational and structural studies have provided new insights into how they recognize RNA, and show that the recognition is sequence-specific and modular. The modular code for RNA-binding by PPR proteins holds great promise for the engineering of new tools to target RNA and identifying RNAs bound by natural PPR proteins.

Keywords: RNA-binding; RNA-protein interactions; pentatricopeptide repeat; repeat proteins; synthetic biology.

Figure 1. Pentatricopeptide repeats. (A) A sequence logo illustrating the characteristic amino acid composition of PPR sequences. The logo was derived from 14,466 PPRs found in the PROSITE PPR entry (PDOC51375) using WebLogo. These sequences are derived from the following taxonomic groups: 86% plants, 5.7% fungi, 4.3% animals, 1.8% algae, 1% trypanosomes and 1.2% others. Amino acids are color-coded according to the physiochemical properties of their side chains: small (A, G) in black, nucleophilic (C, S, T) in blue, hydrophobic (I, L, V, M, P) in green, aromatic (F, W, Y) in red, acidic (D, E) in purple, amides (Q, N) in pink and basic (H, K, R) in orange. Regions of α-helical structure are shown below. Amino acids are numbered based on the Pfam model, which functions as a minimal unit. Residue 34 is also defined as ii according to Kobayashi et al., while the numbering scheme used by Fujii et al. is shifted to the N terminus by two amino acids such that amino acids 1, 4 and 34 in the Pfam model are annotated as 3, 6 and 1, respectively. (B) Schematic structures of a typical P class PPR protein, human PTCD3 and a typical PLS class PPR protein, Arabidopsis CRR22. PPRs, mitochondrial targeting sequence (MTS), chloroplast targeting peptide (CTP) and the E/E+/DYW domain, often associated with editing PPR proteins, are highlighted. (C) The recognition code of PPRs for RNA bases. Only representative predictions by Yagi et al. are shown; for a full list, refer to the original research paper.

Figure 2. Structures of PPR-containing proteins. (A) Crystal structure of two tandem PPRs within the human POLRMT protein (PDB accession code 3SPA). The N-terminal PPR is colored in gray and the C-terminal PPR is colored in green. Residues 4 and 34 of each PPR are highlighted in red. The active site residues predicted to be in close proximity to the phosphate groups in incoming nucleoside triphosphates are highlighted in blue. (B) Crystal structure of five-and-a-half tandem PPRs within the Arabidopsis thaliana PRORP1 protein (PDB accession code 4G24). PPRs are colored in alternating gray and green. Residues 4 and 34 of each PPR are highlighted in red and active site residues of the metallonuclease domain are shown in blue.