Identification and characterization of the RNA binding surface of the pentatricopeptide repeat protein

Kobayashi, Kenzo; Kawabata, Masuyo; Hisano, K.; Kazama, Tomohiko; Matsuoka, Ken; Sugita, Mamoru; Nakamura, Takahiro

doi:10.1093/nar/gkr1084

Cited by 51 publications

(62 citation statements)

References 42 publications

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“…Perhaps the C-terminal PPR repeats are involved in interaction with RNA cis-elements, whereas the N-terminal repeats mediate interaction with RIP1. Supporting this model is the recent finding that two PPR motifs are sufficient to bind to an RNA target in vitro (55).…”

Section: Discussionmentioning

confidence: 86%

RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing

Bentolila¹,

Heller²,

Sun³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

214

266

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Transcripts of plant organelle genes are modified by cytidine-touridine (C-to-U) RNA editing, often changing the encoded amino acid predicted from the DNA sequence. Members of the PLS subclass of the pentatricopeptide repeat (PPR) motif-containing family are site-specific recognition factors for either chloroplast or mitochondrial C targets of editing. However, other than PPR proteins and the cis-elements on the organelle transcripts, no other components of the editing machinery in either organelle have previously been identified. The Arabidopsis chloroplast PPR protein Required for AccD RNA Editing 1 (RARE1) specifies editing of a C in the accD transcript. RARE1 was detected in a complex of >200 kDa. We immunoprecipitated epitope-tagged RARE1, and tandem MS/MS analysis identified a protein of unknown function lacking PPR motifs; we named it RNA-editing factor interacting protein 1 (RIP1). Yeast two-hybrid analysis confirmed RIP1 interaction with RARE1, and RIP1-GFP fusions were found in both chloroplasts and mitochondria. Editing assays for all 34 known Arabidopsis chloroplast targets in a rip1 mutant revealed altered efficiency of 14 editing events. In mitochondria, 266 editing events were found to have reduced efficiency, with major loss of editing at 108 C targets. Virusinduced gene silencing of RIP1 confirmed the altered editing efficiency. Transient introduction of a WT RIP1 allele into rip1 improved the defective RNA editing. The presence of RIP1 in a protein complex along with chloroplast editing factor RARE1 indicates that RIP1 is an important component of the RNA editing apparatus that acts on many chloroplast and mitochondrial C targets.nucleoid | RNA editosome | dual targeting P osttranscriptional C-to-U RNA editing occurs in plastid and plant mitochondrial transcripts. In a typical vascular plant, ∼30 C targets in chloroplasts and over 500 C targets in mitochondria are targeted for editing (1, 2). The majority of the editing events results in encoding of a different amino acid than the one predicted from the genomic sequence. The editing-encoded amino acid is usually more conserved relative to residues present in homologous proteins in other organisms than the genomically encoded amino acid. Because there is presently no known case in which useful genetic variation results from partial editing of a transcript population, the current concept is that editing is a correction mechanism for thymidine-to-cytidine (T-to-C) mutations that have arisen in plant organelle genomes (1,3,4).Little is known about the molecular apparatus that is responsible for recognizing the correct C target for editing and converting it to U, although plant mitochondrial RNA editing was discovered over 20 y ago (5-7). cis-Elements for recognition of editing sites have been identified proximal and 5′ to the nucleotide to be modified (8-10). As few as 22 nt in sequence surrounding the C target is sufficient to specify RNA editing (9). In 2005, a pentatricopeptide repeat (PPR) motif-containing protein termed CRR4 was discovered to ...

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Section: Discussionmentioning

confidence: 86%

RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing

Bentolila¹,

Heller²,

Sun³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

214

266

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“…Proteins with arrays of PPRs that are all approximately 35 amino acids long are designated as "P class" proteins. The second type of PPR proteins are designated as "PLS class," 54 residue 34 is also defined as ii according to Kobayashi et al, 54 while the numbering scheme used by Fujii et al 53 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, 84 and a typical PLS class PPr protein, Arabidopsis Crr22.…”

Section: The Modes Of Rna-recognition By Ppr Proteinsmentioning

confidence: 99%

“…53 A detailed study by Kobayashi et al used truncations of the Arabidopsis HCF152 protein, consisting of two adjacent PPRs, to perform extensive mutagenesis to identify amino acids that are important for the affinity or specificity of RNA-binding by these proteins. 54 This study identified residues 1, 4, 8, 12, and 34 as the most important for maintaining high-affinity RNA-binding. The close overlap between the positions identified by co-variation analysis 53 and mutagenesis 54 suggested that these residues play a key role in the recognition of RNA.…”

mentioning

confidence: 90%

“…54 This study identified residues 1, 4, 8, 12, and 34 as the most important for maintaining high-affinity RNA-binding. The close overlap between the positions identified by co-variation analysis 53 and mutagenesis 54 suggested that these residues play a key role in the recognition of RNA. 55 Barkan et al recently used computational analysis of correlations between specific PPR residues and RNA bases within their binding sites to elucidate the code for RNA recognition by PPR proteins.…”

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confidence: 90%

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Pentatricopeptide repeats

Filipovska

Rackham

2013

RNA Biology

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“…91 Based on the accumulated information on trans-factors (PLS members) and their corresponding RNA editing sites, a statistical study was performed to elucidate the principal components of the PPR code; the study was also based on the research that had focused on the amino acid residues involved in RNA recognition in PPRs. 70,92 In summary, a strong correlation was observed between the combination of positions 6 and 1 on the following PPR (position 1') and the corresponding RNA base (Fig.…”

mentioning

confidence: 99%