RNA editing sites in plant mitochondria can share <i>cis</i>‐elements

Merwe, Johannes A. van der; Takenaka, Mizuki; Neuwirt, Julia; Verbitskiy, Daniil; Brennicke, Axel

doi:10.1016/j.febslet.2005.12.011

Cited by 44 publications

(23 citation statements)

References 17 publications

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“…Target Sequences at the RNA-editing Sites-For several editing sites in mitochondria and plastids, in vitro and in organello investigations have identified the cis-elements in the RNA context to occupy the region between 20 or 25 nucleotides upstream (5Ј) and 1 or 3 nucleotides downstream (3Ј) of the edited C (5,6,8,10,11,(43)(44)(45)(46). Therefore, for the sites affected in the mef18 to mef22 mutants, a similar extent of the recognition sequences may be expected.…”

Section: Refs T-dna Insertion Lines T-dna Locationmentioning

confidence: 99%

Reverse Genetic Screening Identifies Five E-class PPR Proteins Involved in RNA Editing in Mitochondria of Arabidopsis thaliana

Takenaka

Verbitskiy

Zehrmann

et al. 2010

Journal of Biological Chemistry

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RNA editing in flowering plant mitochondria post-transcriptionally alters several hundred nucleotides from C to U, mostly in mRNAs. Several factors required for specific RNA-editing events in plant mitochondria and plastids have been identified, all of them PPR proteins of the PLS subclass with a C-terminal E-domain and about half also with an additional DYW domain. Based on this information, we here probe the connection between E-PPR proteins and RNA editing in plant mitochondria. We initiated a reverse genetics screen of T-DNA insertion lines in Arabidopsis thaliana and investigated 58 of the 150 E-PPRcoding genes for a function in RNA editing. Six genes were identified to be involved in mitochondrial RNA editing at specific sites. Homozygous mutants of the five genes MEF18-MEF22 display no gross disturbance in their growth or development patterns, suggesting that the editing sites affected are not crucial at least in the greenhouse. These results show that a considerable percentage of the E-PPR proteins are involved in the functional processing of site-specific RNA editing in plant mitochondria.RNA editing in mitochondria of flowering plants changes 400 -500 selected cytosines to uridines mostly in coding regions of mRNAs and some tRNAs (1-3). In non-flowering plants such as Isoetes species, the number of edited nucleotides is estimated to be more than 1,500 (4), raising the question of how the to-be-edited nucleotides are distinguished from other unaltered moieties.Specific sequence contexts in the pre-mRNA yield the first part of an answer; such cis-elements are required to identify a bona fide editing site as in vivo, in organelle, and in vitro analyses of several mitochondrial RNA-editing sites have shown (5-11). The second part of the answer seems to be provided by the identification of nuclear encoded specificity factors in Arabidopsis thaliana such as MEF1, MEF9, and MEF11 (mitochondrial-editing factor (MEF)2 ), which are required intact for correct editing of specific different sites (12)(13)(14)(15).The present theory is that the cis-elements in the mitochondrial RNA molecules are individually recognized by RNA-binding proteins, which may be these MEF proteins. This model makes several predictions, which need to be tested to correct or substantiate this connection. First, the nuclear-encoded MEF proteins must show an evolutionary diversity and a variation sufficient to recognize and target the more than 400 editing sites in plant mitochondria in, for example, A. thaliana. Secondly, the MEF proteins must be able to bind RNA and do so selectively to specific RNA sequences, the identified cis-elements. Specific RNA binding has been experimentally verified for one of the proteins required for a plastid RNA-editing event, the CRR4 protein (16) in addition to similar proteins involved in other RNA maturation steps (see Refs. 17, 18; for reviews, see Refs. 19,20).In this study, we addressed the first question and initiated an analysis to test if other proteins similar to MEF1, MEF9, and MEF11 are involved i...

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Section: Refs T-dna Insertion Lines T-dna Locationmentioning

confidence: 99%

Reverse Genetic Screening Identifies Five E-class PPR Proteins Involved in RNA Editing in Mitochondria of Arabidopsis thaliana

Takenaka

Verbitskiy

Zehrmann

et al. 2010

Journal of Biological Chemistry

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“…The size and extent of this region is in the range of the specific cis-regions delineated by in vitro assays for several plastid editing sites (Chaudhuri and Maliga, 1996;Hirose and Sugiura, 2001;Miyamoto et al, 2002;Sasaki et al, 2006). Recognition of mitochondrial editing sites seems to occur through similar cis-element motifs that in the last few years have been characterized by in organello and in vitro analyses of several such sites (Farré et al, 2001;Neuwirt et al, 2005;van der Merwe et al, 2006;Takenaka et al, 2008).…”

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confidence: 99%

MEF9, an E-Subclass Pentatricopeptide Repeat Protein, Is Required for an RNA Editing Event in the nad7 Transcript in Mitochondria of Arabidopsis

Takenaka

2009

Plant Physiol.

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RNA editing in plants alters specific nucleotides from C to U in mRNAs in plastids and in mitochondria. I here characterize the nuclear gene MITOCHONDRIAL EDITING FACTOR9 (MEF9) that is required for RNA editing of the site nad7-200 in the nad7 mitochondrial mRNA in Arabidopsis (Arabidopsis thaliana). The MEF9 protein belongs to the E subfamily of pentatricopeptide repeat proteins and unlike the three previously identified mitochondrial editing factors MEF1 and MEF11 in Arabidopsis and OGR1 in rice (Oryza sativa) does not contain a DYW C-terminal domain. In addition, the E domain is incomplete, but seems to be functionally required, since one of the two independent EMS mutants encodes a MEF9 protein truncated by a stop codon at the beginning of the E domain. In both mutant plants premature stop codons in MEF9 inactivate RNA editing at site nad7-200. The homozygous mutant plants are viable and develop rather normally. The lack of RNA editing at site nad7-200 thus seems to be tolerated although this editing event is conserved in most plant species or the genomic sequence already codes for a T at this position, resulting in a generally conserved amino acid codon.

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“…Substrate RNAs containing vector sequences at the 5 0 -and 3 0 -ends of the mitochondrial insert sequences were synthesized from the T7 RNA polymerase promoter in the linearized template DNA. The bordering bacterial sequences were used for specific amplification of the substrate RNAs by RT-PCR after the in vitro assay [9,10]. The 32 P-labelled RNA templates for the gel shift assays were obtained by direct incorporation of labelled ATP into the RNA during run-off transcription from the DNA template.…”

Section: Rna Substratesmentioning

confidence: 99%

In vitro RNA editing in plant mitochondria does not require added energy

et al. 2007

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RNA editing in flowering plant mitochondria is investigated by in vitro assays. These cauliflower mitochondrial lysates require added NTP or dNTP. We have now resolved the reason for this requirement to be the inhibition of the RNA binding activity of the glutamate dehydrogenases (GDH). Both GDH1 and GDH2 were identified in RNA-protein cross-links. The inhibition of in vitro RNA editing by GDH is confirmed by the ability of the GDH-specific herbicide phosphinothricin to substitute for NTP. NADH and NADPH, but not NAD or NADP, can also replace NTP, suggesting that the NAD(P)Hbinding-pocket configuration of the GDH contacts the RNA. RNA editing in plant mitochondria is thus intrinsically independent of added energy in the form of NTP.

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RNA editing sites in plant mitochondria can share cis‐elements

Cited by 44 publications

References 17 publications

Reverse Genetic Screening Identifies Five E-class PPR Proteins Involved in RNA Editing in Mitochondria of Arabidopsis thaliana

Reverse Genetic Screening Identifies Five E-class PPR Proteins Involved in RNA Editing in Mitochondria of Arabidopsis thaliana

MEF9, an E-Subclass Pentatricopeptide Repeat Protein, Is Required for an RNA Editing Event in the nad7 Transcript in Mitochondria of Arabidopsis

In vitro RNA editing in plant mitochondria does not require added energy

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