A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts

Kotera, Emi; Tasaka, Masao; Shikanai, Toshiharu

doi:10.1038/nature03229

Cited by 490 publications

(477 citation statements)

References 29 publications

Supporting

Mentioning

459

Contrasting

Unclassified

Order By: Relevance

“…In tobacco, editing of ndhD C2 is affected by overexpression of an ndhF transgene, and sequences 5Ј to both C targets exhibit some similarity, suggesting that the two sites may share the same or related transfactors. The Arabidopsis ndhF C290 and ndhD C2 editing sites also exhibit 5Ј sequence similarity, but no effect on ndhF C290 editing in the ndhD C2 editing-deficient mutant was detected (16). Several hypotheses can be created to explain these apparently contradictory findings.…”

Section: Discussionmentioning

confidence: 99%

“…A study of an Arabidopsis editing mutant has shown that the lack of a single trans-factor, CRR4, can prevent editing of the ATndhD C2 target (16) and that CRR4 specifically binds to an RNA fragment containing ndhD C2 (17). In tobacco, editing of ndhD C2 is affected by overexpression of an ndhF transgene, and sequences 5Ј to both C targets exhibit some similarity, suggesting that the two sites may share the same or related transfactors.…”

Section: Discussionmentioning

confidence: 99%

“…Two nuclear-encoded protein factors have been identified that are believed to be responsible for sequence recognition of editing sites in the ndhD transcript of Arabidopsis: CRR4, which is critical for ATndhD C2 editing, and CRR21, which is required for ATndhD C383 editing (16,17). Both of these proteins are members of the pentatricopeptide repeat class of proteins, which consists of Ͼ450 members in Arabidopsis that are largely targeted to chloroplasts and/or mitochondria (18).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Cross-competition in Editing of Chloroplast RNA Transcripts in Vitro Implicates Sharing of Trans-factors between Different C Targets

Heller

Hayes

Hanson

2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

C 3 U plant organellar RNA editing is required for the translation of evolutionarily conserved and functional proteins. 28 different C targets of RNA editing have been identified in maize chloroplasts, and hundreds of Cs are edited in mitochondria. Mutant analysis in Arabidopsis has indicated that absence of a single site-specific recognition protein can result in loss of editing of a single C target, raising the possibility that each C target requires a recognition protein. Here we show that transcripts encompassing two editing sites, ZMrpoB C467 and ZMrps14 C80, can compete editing activity from each other in vitro despite limited sequence similarity. The signal causing competition overlaps a 5 -cis element required for editing efficiency. A single five-nucleotide mutation spanning the region from ؊20 to ؊16 relative to the edited C of rpoB C467 is sufficient to eliminate its substrate editing as well as its ability to compete editing activity from rps14 C80 substrates. A corresponding mutation in an rps14 C80 competitor likewise eliminated its ability to compete editing activity from rpoB C467 substrates. Taken together, our results indicate that the RNA sequences mediating both editing efficiency and cross-competition are highly similar and that a common protein is involved in their editing. Sharing of trans-factors can facilitate editing of the large number of different C targets in plant organelles so that a different protein factor would not be required for every editing site.Post-transcriptional modification of plant organellar mRNAs by RNA editing is required for maintenance of functional protein sequences (1-3) and also for the introduction of translation initiation codons in particular transcripts (4, 5). Typically, chloroplast genomes of higher land plants have on the order of 30 -40 editing sites, whereas mitochondria generally have greater than 400 (6 -12). To date, 28 cytidine-to-uridine editing sites have been identified in 15 chloroplast transcripts in maize (12, 13), all of which alter the encoded amino acid, except one site in the 5Ј-untranslated region of ndhG.It is currently believed that the plant organellar RNA editing machinery consists of two distinct components: the ciselement, which uniquely identifies a given editing site by its sequence and structure within the transcript itself, and the trans-acting factors, which are likely to be proteins that recognize the cis-element and catalyze the editing reaction (14). The sequences surrounding all editing sites in a given organism do not show obvious similarity to each other either by direct sequence alignment or by secondary structure prediction. However, transplastomic tobacco that overexpress a fragment of maize rpoB or tobacco ndhF transcripts spanning the rpoB C467 or ndhF C290 editing sites, respectively, showed reduced editing at the cognate tobacco sites, as well as at additional sites (15), indicating that at least some ciselements are related. These three editing sites therefore form a "cluster" affected by overexpression of transc...

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Cross-competition in Editing of Chloroplast RNA Transcripts in Vitro Implicates Sharing of Trans-factors between Different C Targets

Heller

Hayes

Hanson

2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…Most of the few that have been characterized play a role in posttranscriptional processes in organelles (reviewed in Nakamura et al, 2004;Andres et al, 2007). PPR proteins have been implicated in RNA editing (Kotera et al, 2005;Okuda et al, 2007), RNA processing (Meierhoff et al, 2003;Hattori et al, 2007), RNA splicing (Schmitz-Linneweber et al, 2006), and translational activation (Schmitz-Linneweber et al, 2005). During a reverse genetics screen of PPR mutants, we identified one with a defect in splicing of nad1 transcripts.…”

Section: Introductionmentioning

confidence: 99%

“…As at least one PPR protein is known to be involved in RNA editing (Kotera et al, 2005), we sequenced cDNAs covering the five exons of nad1 cDNA and both halves of intron 1 from the mutant in case an RNA editing defect was at the root of the RNA splicing defect. Twenty-four C-to-U editing sites have been described in exons 1, 3, and 5 of nad1 mRNA from Arabidopsis (Giegé and Brennicke, 1999).…”

Section: New Rna Editing Sites In Nad1 Intron 1 and Exonmentioning

confidence: 99%

The Pentatricopeptide Repeat GeneOTP43Is Required fortrans-Splicing of the Mitochondrialnad1Intron 1 inArabidopsis thaliana

et al. 2007

View full text Add to dashboard Cite

The mitochondrial NADH:ubiquinone oxidoreductase complex (Complex I) is a large protein complex formed from both nuclearly and mitochondrially encoded subunits. Subunit ND1 is encoded by a mitochondrial gene comprising five exons, and the mature transcript requires four RNA splicing events, two of which involve trans-splicing independently transcribed RNAs. We have identified a nuclear gene (OTP43) absolutely required for trans-splicing of intron 1 (and only intron 1) of Arabidopsis thaliana nad1 transcripts. This gene encodes a previously uncharacterized pentatricopeptide repeat protein.Mutant Arabidopsis plants with a disrupted OTP43 gene do not present detectable mitochondrial Complex I activity and show severe defects in seed development, germination, and to a lesser extent in plant growth. The alternative respiratory pathway involving alternative oxidase is significantly induced in the mutant.

show abstract

Chloroplast Genome

Howe¹

2012

Encyclopedia of Life Sciences

View full text Add to dashboard Cite

Chloroplasts contain a genome that is a relic of the endosymbiont that gave rise to the organelle. These genomes typically contain 100–200 genes and encode proteins important for photosynthesis and other chloroplast functions, although dinoflagellate algae have a greatly reduced and fragmented chloroplast genome. Many nonphotosynthetic taxa retain a remnant chloroplast genome. In some organisms the chloroplast genome may be retained to allow redox‐mediated control of gene expression, whereas in others it may continue to exist because transfer of essential genes to the nucleus is no longer possible. Multiple ribonucleic acid (RNA) polymerases are involved in chloroplast transcription in land plants, and post‐transcriptional processing involving nuclear‐encoded RNA‐binding proteins also plays an important part in the expression of the chloroplast genome. Gene expression may be regulated at a number of levels, and redox poise in the organelle may be particularly important for this. Key Concepts: Chloroplasts originated in the ancestor of plants and red and green algae by endosymbiotic acquisition of a cyanobacterium, and then spread to many other eukaryotic lineages. There are other examples of stable acquisition of a cyanobacterium by a nonphotosynthetic host. Chloroplast genomes are typically 100–200 kbp in size, and include a set of genes for proteins essential to photosynthesis. Other genes present in the ancestral symbiont have been lost or relocated to the nucleus. Many nonphotosynthetic organisms retain remnant chloroplasts, with genomes, reflecting the fact that photosynthesis is not the only biochemical process that takes place in the chloroplast. In many organisms, gene transfer from chloroplast to nucleus can still take place, at an unexpectedly high frequency. Establishment of the chloroplast has resulted in the development of nuclear‐encoded RNA‐binding protein families and, in land plants, additional RNA polymerases that play a central role in chloroplast gene expression. Post‐transcriptional RNA processing plays an important role in chloroplast gene expression. In photosynthetic organisms, chloroplast gene expression is closely linked to the organelle's redox poise. The chloroplast can also influence the expression of nuclear genes.

show abstract

A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts

Cited by 490 publications

References 29 publications

Cross-competition in Editing of Chloroplast RNA Transcripts in Vitro Implicates Sharing of Trans-factors between Different C Targets

Cross-competition in Editing of Chloroplast RNA Transcripts in Vitro Implicates Sharing of Trans-factors between Different C Targets

The Pentatricopeptide Repeat GeneOTP43Is Required fortrans-Splicing of the Mitochondrialnad1Intron 1 inArabidopsis thaliana

Chloroplast Genome

Contact Info

Product

Resources

About