A DYW Domain–Containing Pentatricopeptide Repeat Protein Is Required for RNA Editing at Multiple Sites in Mitochondria of <i>Arabidopsis thaliana</i>

Zehrmann, Anja; Verbitskiy, Daniil; Merwe, Johannes A. van der; Brennicke, Axel; Takenaka, Mizuki

doi:10.1105/tpc.108.064535

Cited by 162 publications

(164 citation statements)

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“…Experiments with transgenic plastids and in vitro RNA editing assays using organelle extracts delimited the primary region recognized by putative trans-factors to the 20 or so nucleotides immediately upstream of the editing site, with, in most cases, the most important recognition elements situated from 25 to 215 with respect to the edited C (reviewed in Shikanai, 2006). Binding to this region was confirmed for CRR4, the first editing factor to be genetically identified (Okuda et al, 2006), and it has been assumed that the other PPR proteins identified as editing factors function in a similar way (Okuda et al, 2007(Okuda et al, , 2009ChateignerBoutin et al, 2008;Cai et al, 2009;Kim et al, 2009;Robbins et al, 2009;Yu et al, 2009;Zehrmann et al, 2009;Zhou et al, 2009). However, no proof of specific binding has been shown for any of these subsequent editing factors, including the six new ones identified in the screen described here.…”

Section: Discussionmentioning

confidence: 86%

“…Unlike the majority of the previously characterized editing mutants (Okuda et al, 2006(Okuda et al, , 2007(Okuda et al, , 2009Chateigner-Boutin et al, 2008;Kim et al, 2009;Yu et al, 2009;Zhou et al, 2009), which were identified via visible growth or fluorescence phenotypes, these mutants were identified directly via a screen for unedited RNAs. It is striking that of the eight mutants discovered in this way, including RARE1 (Robbins et al, 2009) and MEF1 (Zehrmann et al, 2009), none have growth or The curve shows a typical trace of chlorophyll fluorescence in the wild type and a mutant totally impaired in NDH activity (crr21) (Okuda et al, 2007) compared with traces from otp85 and two independent otp84 mutants (otp84-1 and otp84-2). Leaves were exposed to actinic light (AL) (50 mmol of photons m À2 s À1 ) for 5 min.…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, in plastids, the majority of editing factors are required for a single site, with a maximum of three in the cases of CRR22 (Okuda et al, 2009) and OTP84. The first mitochondrial editing factors to be found, OGR1 and MEF-1, are required for at least seven and three editing sites in rice (Oryza sativa) and Arabidopsis mitochondria, respectively (Kim et al, 2009;Zehrmann et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

“…Investigation of Arabidopsis mutants with such phenotypes has identified a number of nuclear genes suspected to encode RNAediting specificity factors (Kotera et al, 2005;Okuda et al, 2007Okuda et al, , 2009Chateigner-Boutin et al, 2008;Cai et al, 2009;Kim et al, 2009;Robbins et al, 2009;Yu et al, 2009;Zehrmann et al, 2009;Zhou et al, 2009). In each case, loss of one of these factors leads to a specific loss of editing of one or at most a few sites.…”

Section: Introductionmentioning

confidence: 99%

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A Study of New Arabidopsis Chloroplast RNA Editing Mutants Reveals General Features of Editing Factors and Their Target Sites

et al. 2009

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RNA editing in higher plant organelles results in the conversion of specific cytidine residues to uridine residues in RNA. The recognition of a specific target C site by the editing machinery involves trans-acting factors that bind to the RNA upstream of the C to be edited. In the last few years, analysis of mutants affected in chloroplast biogenesis has identified several pentatricopeptide repeat (PPR) proteins from the PLS subfamily that are essential for the editing of particular RNA transcripts. We selected other genes from the same subfamily and used a reverse genetics approach to identify six new chloroplast editing factors in Arabidopsis thaliana (OTP80, OTP81, OTP82, OTP84, OTP85, and OTP86). These six factors account for nine editing sites not previously assigned to an editing factor and, together with the nine PPR editing proteins previously described, explain more than half of the 34 editing events in Arabidopsis chloroplasts. OTP80, OTP81, OTP85, and OTP86 target only one editing site each, OTP82 two sites, and OTP84 three sites in different transcripts. An analysis of the target sites requiring the five editing factors involved in editing of multiple sites (CRR22, CRR28, CLB19, OTP82, and OTP84) suggests that editing factors can generally distinguish pyrimidines from purines and, at some positions, must be able to recognize specific bases.

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Section: Discussionmentioning

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Study of New Arabidopsis Chloroplast RNA Editing Mutants Reveals General Features of Editing Factors and Their Target Sites

et al. 2009

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“…The PLS subfamily, which is specific to the plant kingdom, can be further separated into smaller subclasses based on two C-terminal motifs, the E and DYW motifs (14). All of the well-characterized organelle editing factors that are required for editing at specific sites are members of the PLS subfamily of PPR proteins (11,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29).…”

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confidence: 99%

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.

201

253

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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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The Cross-Talk Between Genomes

Budar

Mireau

2017

Annual Plant Reviews, Volume 50

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A DYW Domain–Containing Pentatricopeptide Repeat Protein Is Required for RNA Editing at Multiple Sites in Mitochondria of Arabidopsis thaliana

Cited by 162 publications

References 41 publications

A Study of New Arabidopsis Chloroplast RNA Editing Mutants Reveals General Features of Editing Factors and Their Target Sites

A Study of New Arabidopsis Chloroplast RNA Editing Mutants Reveals General Features of Editing Factors and Their Target Sites

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

The Cross-Talk Between Genomes

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