Family Proteins Are Required for RNA Editing in Mitochondria and Plastids of Plants
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Correction PLANT BIOLOGY Correction for “Multiple organellar RNA editing factor issue 13, March 27, 2012, of Proc Natl Acad Sci USA (109: (MORF) family proteins are required for RNA editing in 5104–5109; first published March 12, 2012; 10.1073/pnas. mitochondria and plastids of plants,” by Mizuki Takenaka, 1202452109). Anja Zehrmann, Daniil Verbitskiy, Matthias Kugelmann, The authors note that Fig. 2 appeared incorrectly. The cor- Barbara Härtel, and Axel Brennicke, which appeared in rected Fig. 2 and its legend appear below. Fig. 2. The MORF family of proteins contains nine genes and a potential pseudogene in A. thaliana.(A) The cladogram of similarities between the MORF proteins shows that the plastid editing factors MORF2 and MORF9 are rather distant from each other and more similar to the mitochondrial proteins MORF3 and MORF1, respectively. Predictions (marked mt or cp) and experi- mental data obtained by GFP-fusion protein localization (only MORF2) or proteomics MS data (marked with an asterisk) for the respective organellar locations are indicated. The MORF8 protein encoded by At3g15000 has been found in mitochondria in three independent assays. Proteins investigated here for their function are boxed. The conserved ∼100-amino acids domain is shaded; the other sequences show much less conservation (SI Appendix, Fig. S2). The potential pseudogene (At1g53260) contains only the C-terminal part of this conserved region. (B) Exon structures of the MORF3, MORF4 and MORF6 genes are similar to the MORF1 locus and contribute similar frag- ments but differ in their C-terminal extensions. MORF3 is a mitochondrial editing factor involved at more than 40 sites. Locations of the T-DNA in- sertions in mutants morf3-1, morf4-1, and morf6-1 are shown. LB denotes the location of the left border of the T-DNA. (C) Numbers of editing sites affected by T-DNA insertions in the respective MORF genes. In mutants morf4-1 and morf6-1, only one noncoding site each shows somewhat reduced editing. www.pnas.org/cgi/doi/10.1073/pnas.1208592109 10606 | PNAS | June 26, 2012 | vol. 109 | no. 26 www.pnas.org Downloaded by guest on October 1, 2021 Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants Mizuki Takenaka1, Anja Zehrmann, Daniil Verbitskiy, Matthias Kugelmann, Barbara Härtel, and Axel Brennicke Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Edited by Larry Simpson, University of California, Los Angeles, CA, and accepted by the Editorial Board February 21, 2012 (received for review August 26, 2011) RNA editing in plastids and mitochondria of flowering plants Results changes hundreds of selected cytidines to uridines, mostly in Mutation of MORF1 Affects Numerous Editing Sites in Plant Mitochon- coding regions of mRNAs. Specific sequences around the editing dria. Our forward genetic screen of an ethylmethanesulfonate sites are presumably recognized by up to 200 pentatricopeptide (EMS)-mutated population of Arabidopsis thaliana ecotype Co- repeat (PPR) proteins. The here identified family of multiple lumbia (Col) plants with a multiplexed single-nucleotide extension organellar RNA editing factor (MORF) proteins provides additional protocol yielded a number of mutant plants that have lost detectable components of the RNA editing machinery in both plant organ- editing at specific sites (18). The mutations were mapped and the elles. Two MORF proteins are required for editing in plastids; at nuclear encoded genes identified several of the site-specific trans least two are essential for editing in mitochondria. The loss of factors of the PPR family (19). One of the mutants, however, shows a MORF protein abolishes or lowers editing at multiple sites, many reduced RNA editing at more than 40 mitochondrial sites, very of which are addressed individually by PPR proteins. In plastids, different from PPR proteins, which affect only one or several such both MORF proteins are required for complete editing at almost all sites (Fig. 1A and SI Appendix,TableS1). The effect of the mutation sites, suggesting a heterodimeric complex. In yeast two-hybrid and is specific to RNA editing defects; other RNA-processing steps and pull-down assays, MORF proteins can connect to form hetero- and RNA stability are not affected (SI Appendix,Fig.S1). Genomic homodimers. Furthermore, MORF proteins interact selectively with mapping in a cross of wild-type ecotype Landsberg erecta (Ler) PPR proteins, establishing a more complex editosome in plant plants and the mutant ecotype Col plant narrowed the locus to a organelles than previously thought. region where no PPR protein is encoded. Sequence analysis re- vealed an EMS-typical mutation inanunassignedreadingframe, n all flowering plants, RNA editing alters more than 400 cytidines At4g20020 (Fig. 1B). To confirm this identification, protoplasts from Ito uridines in the mRNAs of mitochondria and converts 30–40 the mutant plant were transfected with the wild-type gene. In these cytidines in plastids (1, 2). In Lycopodiaceae, more than a thousand assays, editing at the target sites was increased but not fully restored. nucleotide identities in mitochondria and several hundred in In mutant plants stably transformedwiththeintactColgeneunder plastids are changed (3). This process was recognized about 20 y control of the 35S promoter, RNA editing was fully recovered at all ago (4–6), but only in recent years have the first determinants in- affected sites (Fig. 1C). The complementation of the editing defects volved in the recognition of specific editing sites been identified (7). at the target sites confirms that indeed the right locus has been In target RNAs, the crucial sequence parameters that determine identified. This gene was named MORF1 because it encodes a mul- a nucleotide to be edited were identified by transgenic, in vivo, tiple organellar RNA editing factor. Homozygous mutant plants in vitro, and in organello assays to be similarly structured in the two with a T-DNA insertion in the MORF1 gene are not viable (morf1-2; organelles (8–10). These cis targets, located mostly 5–20 nucleo- Fig. 1 D and E). This finding suggests that the EMS mutant (morf1- tides 5′ of the target cytidine, are postulated to be recognized by 1)isa“soft” mutation, which only partially disables the function of specific trans-acting proteins of the 450 members strong penta- the encoded MORF1 protein. Therefore, presumably further, es- tricopeptide repeat (PPR) protein family (11–13). sential editing sites are also targeted by the MORF1 protein, and/or Roughly 30 individual PPR proteins have been assigned to one those RNA editing sites that are still partially processed in the EMS morf1-1 or several targets by connecting a dysfunctional gene with the mutant are vitally required. The residual level of editing in fi loss of RNA editing at specific sites (14, 15). These proteins, this EMS mutant is suf cient for the viability of the plant. which are essential for processing of single or very few RNA MORF3, Another Member of the MORF Family, Is Required for Different editing sites, belong to a subgroup within the PPR family char- RNA Editing Sites in Mitochondria. MORF1 acterized by their patterns of repeats and C-terminal extensions. The gene belongs to a small family of nine genes and one potential pseudogene (Fig. 2A Some are extended by only an extension (E) domain; others and SI Appendix,Fig.S2). Of the encoded proteins, four are pre- contain an additional conserved region terminating with the dicted by Predotar to be targeted to plastids (MORF2, At1g53260, name-giving amino acids DYW. This subgroup can supply up to MORF8, and MORF9). In three different proteome analyses, 200 proteins for editing at specific sites, providing an explanation however, fragments of MORF8 were identified in mitochondrial of how the numerous RNA editing sites in flowering plant mi- fi extracts, thus correcting the theoretical prediction. In one of these tochondria and plastids can be speci cally addressed (12, 13). investigations, the MORF8 protein as well as MORF3 were found For the enzymatic reaction of converting a cytidine to a uridine, a deaminating activity is required. Because a separate enzyme has not been identified so far, it was proposed that possibly one Author contributions: M.T., A.Z., D.V., and A.B. designed research; M.T., A.Z., D.V., M.K., of the additional C-terminal domains directly contributes the and B.H. performed research; M.T. contributed new reagents/analytic tools; M.T., A.Z., enzymatic activity, in cis when present and in trans through and D.V. analyzed data; and M.T. and A.B. wrote the paper. heterodimer formation (16, 17). We now find that an entirely The authors declare no conflict of interest. unexpected class of proteins constitutes an additional, essential This article is a PNAS Direct Submission. L.S. is a guest editor invited by the Editorial Board. component of the plant organellar editosome and is required for 1To whom correspondence should be addressed. E-mail: [email protected]. processing of almost all editing sites in plastids and of at least This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. many sites in mitochondria. 1073/pnas.1202452109/-/DCSupplemental. 5104–5109 | PNAS | March 27, 2012 | vol. 109 | no. 13 www.pnas.org/cgi/doi/10.1073/pnas.1202452109 Fig. 2. The MORF family of proteins contains nine genes and a potential pseudogene in A. thaliana.(A) The cladogram of similarities between the Fig. 1. The MORF1 protein is required for RNA editing at multiple sites. (A) MORF proteins shows that the plastid editing factors MORF2 and MORF9 are Sample sequences of the more than 40 editing sites affected in morf1-1 EMS rather distant from each other and more similar to the mitochondrial proteins mutant plants. The first five sites show editing reduced to different degrees.