Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in <i>Arabidopsis</i> Chloroplasts

Okuda, K; Chateigner-Boutin, Anne Laure; Nakamura, Takahiro; Delannoy, Étienne; Sugita, Mamoru; Myouga, Fumiyoshi; Motohashi, Reiko; Shinozaki, Kazuo; Small, Ian; Shikanai, Toshiharu

doi:10.1105/tpc.108.064667

Cited by 212 publications

(294 citation statements)

References 53 publications

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“…Fisk et al (1999) first reported a maize PPR gene, (for CHLOROPLAST RNA PROCESSING1), which was implicated by genetic analysis in processing and translation of plastid pet transcripts. Similar effects on plastid transcripts were subsequently observed in other mutants from Arabidopsis (Hashimoto et al, 2003;Meierhoff et al, 2003;Yamazaki et al, 2004;ChateignerBoutin et al, 2008ChateignerBoutin et al, , 2011Chi et al, 2008;Okuda et al, 2009Okuda et al, , 2010Yu et al, 2009;Johnson et al, 2010), rice (Kazama and Toriyama, 2003;Komori et al, 2004;Gothandam et al, 2005), and maize (Williams and Barkan, 2003;Schmitz-Linneweber et al, 2006;Pfalz et al, 2009;Prikryl et al, 2011). Additional evidence for a role of PPR proteins in regulating organelle gene expression has also come from positional cloning of several cytoplasmic male sterility (CMS) restorer genes from petunia (Petunia hybrida; Bentolila et al, 2002) and radish (Raphanus sativus; Brown et al, 2003;Desloire et al, 2003;Koizuka et al, 2003).…”

mentioning

confidence: 67%

“…Attempts to identify the in vivo RNA ligands have only been made for a few PPR proteins (Schmitz-Linneweber and Small, 2008;Okuda et al, 2009Okuda et al, , 2010Pfalz et al, 2009;Yu et al, 2009;Johnson et al, 2010;Chateigner-Boutin et al, 2011;Prikryl et al, 2011). Many of the postulated activities of PPR proteins still lack direct biochemical proof and thus leave open the possibility that their roles are more indirect than suspected and may require additional, unidentified factors.…”

Section: Ysa Encodes a Ppr Protein Essential For Chloroplast Biogenesmentioning

confidence: 99%

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Disruption of a Rice Pentatricopeptide Repeat Protein Causes a Seedling-Specific Albino Phenotype and Its Utilization to Enhance Seed Purity in Hybrid Rice Production

Hu²,

Wu³

et al. 2012

Plant Physiology

150

112

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The pentatricopeptide repeat (PPR) gene family represents one of the largest gene families in higher plants. Accumulating data suggest that PPR proteins play a central and broad role in modulating the expression of organellar genes in plants. Here we report a rice (Oryza sativa) mutant named young seedling albino (ysa) derived from the rice thermo/photoperiod-sensitive genic male-sterile line Pei'ai64S, which is a leading male-sterile line for commercial two-line hybrid rice production. The ysa mutant develops albino leaves before the three-leaf stage, but the mutant gradually turns green and recovers to normal green at the sixleaf stage. Further investigation showed that the change in leaf color in ysa mutant is associated with changes in chlorophyll content and chloroplast development. Map-based cloning revealed that YSA encodes a PPR protein with 16 tandem PPR motifs. YSA is highly expressed in young leaves and stems, and its expression level is regulated by light. We showed that the ysa mutation has no apparent negative effects on several important agronomic traits, such as fertility, stigma extrusion rate, selfed seed-setting rate, hybrid seed-setting rate, and yield heterosis under normal growth conditions. We further demonstrated that ysa can be used as an early marker for efficient identification and elimination of false hybrids in commercial hybrid rice production, resulting in yield increases by up to approximately 537 kg ha 21 .

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mentioning

confidence: 67%

Section: Ysa Encodes a Ppr Protein Essential For Chloroplast Biogenesmentioning

confidence: 99%

Disruption of a Rice Pentatricopeptide Repeat Protein Causes a Seedling-Specific Albino Phenotype and Its Utilization to Enhance Seed Purity in Hybrid Rice Production

Hu²,

Wu³

et al. 2012

Plant Physiology

150

112

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“…Contrary to this theoretical consideration, the two plastid RNA editing trans-factors CRR22 and CRR28 are still fully functional without their C-terminal DYW domain [8]. The DYW domain in MEF1 may be more important, since already the mutation of a single nucleotide in the EMS-line mef1-2 completely abolishes editing at two of the three target sites, rps4-956 and nad7-963, and results in a strong reduction at nad2-1160 [11].…”

Section: The Dyw Domain Is Necessary For Efficient Function Of Mef1mentioning

confidence: 81%

“…Concerning the cis-elements around the editing sites, a region between 20 nts upstream and only 3 nts downstream appears to be sufficient to identify a C-nucleotide target [3][4][5]. For the RNA editing in plastids several trans-factors have already been identified during the last few years [6][7][8][9][10], while the first trans-factors acting in mitochondria have been identified only recently [11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

RNA editing competence of trans‐factor MEF1 is modulated by ecotype‐specific differences but requires the DYW domain

Zehrmann¹,

Verbitskiy²,

Härtel³

et al. 2010

FEBS Letters

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a b s t r a c t RNA editing in plant mitochondria posttranscriptionally changes multiple cytidines to uridines. The RNA editing trans-factor MEF1 was identified via ecotype-specific editing polymorphisms in Arabidopsis thaliana. Complementation assays reveal that none of the three amino acid changes between Columbia (Col) and C24 individually alters RNA editing. Only one combination of these polymorphisms lowers editing at two of the three target sites, suggesting additive effects of the involved SNPs. Functional importance of the C-terminal DYW domain was analysed with DYW-truncated and extended constructs. These do not recover RNA editing in protoplasts and regain only low levels in stable transformants. In MEF1, the DYW domain is thus required for full competence in RNA editing and its C-terminus has to be accessible.

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“…However, the enzyme catalyzing the editing reaction, presumably by deamination, is still unknown, although suspicion has fallen on the DYW domain present in some PPR proteins because it contains residues similar to the conserved cytidine deaminase motif (15). The elusiveness of the enzyme responsible for plant RNA editing (16)(17)(18) suggests that some important components of the editing machinery are still to be identified.…”

mentioning

confidence: 99%

An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize

Sun

Germain

Giloteaux

et al. 2013

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

133

185

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Plant RNA editing modifies cytidines (C) to uridines (U) at specific sites in the transcripts of both mitochondria and plastids. Specific targeting of particular Cs is achieved by pentatricopeptide proteins that recognize cis elements upstream of the C that is edited. Members of the RNA-editing factor interacting protein (RIP) family in Arabidopsis have recently been shown to be essential components of the plant editosome. We have identified a gene that contains a pair of truncated RIP domains (RIP-RIP). Unlike any previously described RIP family member, the encoded protein carries an RNA recognition motif (RRM) at its C terminus and has therefore been named Organelle RRM protein 1 (ORRM1). ORRM1 is an essential plastid editing factor; in Arabidopsis and maize mutants, RNA editing is impaired at particular sites, with an almost complete loss of editing for 12 sites in Arabidopsis and 9 sites in maize. Transfection of Arabidopsis orrm1 mutant protoplasts with constructs encoding a region encompassing the RIP-RIP domain or a region spanning the RRM domain of ORRM1 demonstrated that the RRM domain is sufficient for the editing function of ORRM1 in vitro. According to a yeast two-hybrid assay, ORRM1 interacts selectively with pentatricopeptide transfactors via its RIP-RIP domain. Phylogenetic analysis reveals that the RRM in ORRM1 clusters with a clade of RRM proteins that are targeted to organelles. Taken together, these results suggest that other members of the ORRM family may likewise function in RNA editing.

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Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts

Cited by 212 publications

References 53 publications

Disruption of a Rice Pentatricopeptide Repeat Protein Causes a Seedling-Specific Albino Phenotype and Its Utilization to Enhance Seed Purity in Hybrid Rice Production

Disruption of a Rice Pentatricopeptide Repeat Protein Causes a Seedling-Specific Albino Phenotype and Its Utilization to Enhance Seed Purity in Hybrid Rice Production

RNA editing competence of trans‐factor MEF1 is modulated by ecotype‐specific differences but requires the DYW domain

An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize

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