Quantitative trait locus mapping identifies REME2, a PPR-DYW protein required for editing of specific C targets in Arabidopsis mitochondria

RNA Biology

Volumn 10, Issue 9, 2013, Pages 1520-1525

  Bentolila, Stéphane ^a   Babina, Arianne M ^b   Germain, Arnaud ^a   Hanson, Maureen R ^a  

^a Department of Obstetrics Gynecology   (United States)

^b BOSTON COLLEGE   (United States)

Author keywords

Plant mitochondria; QTL mapping; RPS3; RPS4; Virus induced gene silencing

Indexed keywords

AMINO ACID; REQUIRED FOR EFFICIENCY OF MITOCHONDRIAL EDITING2 PROTEIN; RIBOSOME PROTEIN; UNCLASSIFIED DRUG; VEGETABLE PROTEIN; ARABIDOPSIS PROTEIN; BACTERIAL DNA; REME2 PROTEIN, ARABIDOPSIS; RNA BINDING PROTEIN; RPS3 PROTEIN, ARABIDOPSIS; RPS4 PROTEIN, PLANT; T-DNA;

ANGIOSPERM; ARABIDOPSIS THALIANA; ARTICLE; CONTROLLED STUDY; GENE INSERTION; GENE SILENCING; MITOCHONDRION; NONHUMAN; PROTEIN ANALYSIS; QUANTITATIVE TRAIT LOCUS MAPPING; RNA EDITING; SINGLE NUCLEOTIDE POLYMORPHISM; AMINO ACID SEQUENCE; ARABIDOPSIS; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; QUANTITATIVE TRAIT LOCUS; REGULATORY SEQUENCE; SEQUENCE HOMOLOGY;

ARABIDOPSIS; MAGNOLIOPHYTA;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA, BACTERIAL; GENE EXPRESSION REGULATION, PLANT; GENE KNOCKDOWN TECHNIQUES; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID; RIBOSOMAL PROTEINS; RNA EDITING; RNA-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84885122466     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.25297     Document Type: Article

References (24)

1. Bentolila S, Heller WP, Sun T, Babina AM, Friso G, van Wijk KJ, et al. RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proc Natl Acad Sci USA 2012; 109:E1453-61; PMID:22566615; http://dx.doi.org/10.1073/pnas.1121465109
2. Takenaka M, Zehrmann A, Verbitskiy D, Kugelmann M, Härtel B, Brennicke A. Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants. Proc Natl Acad Sci USA 2012; 109:5104-9; PMID:22411807; http://dx.doi.org/10.1073/pnas. 1202452109
3. Gutmann B, Gobert A, Giege P, Marechal-Drouard L, ed. Mitochondrial Genome Evolution and the Emergence of PPR Proteins. Advances in Botanical Research: Academic press; 2012:253-313.
4. Giegé P, Brennicke A. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci USA 1999; 96:15324-9; PMID:10611383; http://dx.doi.org/10.1073/pnas.96.26.15324
5. Bentolila S, Elliott LE, Hanson MR. Genetic architecture of mitochondrial editing in Arabidopsis thaliana. Genetics 2008; 178:1693-708; PMID:17565941; http://dx.doi.org/10.1534/genetics.107.073585
6. Bentolila S, Chateigner-Boutin AL, Hanson MR. Ecotype allelic variation in C-to-U editing extent of a mitochondrial transcript identifies RNA-editing quantitative trait loci in Arabidopsis. Plant Physiol 2005; 139:2006-16; PMID:16286447; http://dx.doi.org/10.1104/pp.105.069013
7. Bentolila S, Knight WE, Hanson MR. Natural variation in Arabidopsis leads to the identification of REME1, a pentatricopeptide repeat-DYW protein controlling the editing of mitochondrial transcripts. Plant Physiol 2010; 154:1966-82; PMID:20974892; http://dx.doi.org/10.1104/pp.110.165969
8. Small I, Peeters N, Legeai F, Lurin C. Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 2004; 4:1581-90; PMID:15174128; http://dx.doi.org/10.1002/pmic.200300776
9. Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000; 300:1005-16; PMID:10891285; http://dx.doi.org/10.1006/jmbi.2000.3903
10. Kim SR, Yang JI, Moon S, Ryu CH, An K, Kim KM, et al. Rice OGR1 encodes a pentatricopeptide repeat-DYW protein and is essential for RNA editing in mitochondria. Plant J 2009; 59:738-49; PMID:19453459; http://dx.doi.org/10.1111/ j.1365-313X.2009.03909.x
11. Zehrmann A, Verbitskiy D, van der Merwe JA, Brennicke A, Takenaka M. A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana. Plant Cell 2009; 21:558-67; PMID:19252080; http://dx.doi.org/10.1105/tpc.108.064535
12. Verbitskiy D, Zehrmann A, van der Merwe JA, Brennicke A, Takenaka M. The PPR protein encoded by the LOVASTATIN INSENSITIVE 1 gene is involved in RNA editing at three sites in mitochondria of Arabidopsis thaliana. Plant J 2010; 61:446-55; PMID:19919573; http://dx.doi.org/10.1111/j.1365-313X.2009.04076.x
13. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, et al. Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008; 2008:420747; PMID:19956698; http://dx.doi.org/10.1155/2008/420747
14. Okuda K, Nakamura T, Sugita M, Shimizu T, Shikanai T. A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing. J Biol Chem 2006; 281:37661-7; PMID:17015439; http://dx.doi.org/10.1074/jbc.M608184200
15. Hammani K, des Francs-Small CC, Takenaka M, Tanz SK, Okuda K, Shikanai T, et al. The pentatricopeptide repeat protein OTP87 is essential for RNA editing of nad7 and atp1 transcripts in Arabidopsis mitochondria. J Biol Chem 2011; 286:21361-71; PMID:21504904; http://dx.doi.org/10.1074/jbc.M111.230516
16. Tasaki E, Hattori M, Sugita M. The moss pentatricopeptide repeat protein with a DYW domain is responsible for RNA editing of mitochondrial ccmFc transcript. Plant J 2010; 62:560-70; PMID:20163555; http://dx.doi.org/10.1111/j. 1365-313X.2010.04175.x
17. Barkan A, Rojas M, Fujii S, Yap A, Chong YS, Bond CS, et al. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet 2012; 8:e1002910; PMID:22916040; http://dx.doi.org/10.1371/ journal.pgen.1002910
18. Yagi Y, Hayashi S, Kobayashi K, Hirayama T, Nakamura T. Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants. PLoS One 2013; 8:e57286; PMID:23472078; http://dx.doi.org/10.1371/journal.pone.0057286
19. Sung TY, Tseng CC, Hsieh MH. The SLO1 PPR protein is required for RNA editing at multiple sites with similar upstream sequences in Arabidopsis mitochondria. Plant J 2010; 63:499-511; PMID:20497377; http://dx.doi.org/10. 1111/j.1365-313X.2010.04258.x
20. Zehrmann A, van der Merwe J, Verbitskiy D, Härtel B, Brennicke A, Takenaka M. The DYW-class PPR protein MEF7 is required for RNA editing at four sites in mitochondria of Arabidopsis thaliana. RNA Biol 2012; 9:155-61; PMID:22258224; http://dx.doi.org/10.4161/rna.18644
21. Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 2011; 477:419-23; PMID:21874022; http://dx.doi.org/10.1038/nature10414
22. Shikanai T. Why do plants edit RNA in plant organelles? In: Bullerwell C, ed. Organelle genetics: evolution of organelle genomes and gene expression. Berlin; Heidelberg: Springer, 2012:381-397.
23. Robbins JC, Heller WP, Hanson MR. A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript. RNA 2009; 15:1142-53; PMID:19395655; http://dx.doi.org/10.1261/rna.1533909
24. Crowe ML, Serizet C, Thareau V, Aubourg S, Rouzé P, Hilson P, et al. CATMA: a complete Arabidopsis GST database. Nucleic Acids Res 2003; 31:156-8; PMID:12519971; http://dx.doi.org/10.1093/nar/gkg071