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Tetrapyrrole Biosynthetic Enzyme Protoporphyrinogen IX Oxidase 1 Is Required for Plastid RNA Editing

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Tetrapyrrole Biosynthetic Enzyme Protoporphyrinogen IX Oxidase 1 Is Required for Plastid RNA Editing Tetrapyrrole biosynthetic enzyme protoporphyrinogen IX oxidase 1 is required for plastid RNA editing Fan Zhanga,b, Weijiang Tanga, Boris Hedtkec, Linlin Zhonga,b, Lin Liua, Lianwei Penga, Congming Lua,d, Bernhard Grimmc, and Rongcheng Lina,d,1 aKey Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; bUniversity of Chinese Academy of Sciences, Beijing 100049, China; cDepartment of Plant Physiology, Institute of Biology, Humboldt University of Berlin, D-10099 Berlin, Germany; and dNational Center for Plant Gene Research, Beijing 100093, China Edited by Joanne Chory, The Salk Institute for Biological Studies and Howard Hughes Medical Institute, La Jolla, CA, and approved December 19, 2013 (received for review September 3, 2013) RNA editing is a posttranscriptional process that covalently alters Tetrapyrrole biosynthesis is a universal metabolic process, the sequence of RNA molecules and plays important biological occurring in all kingdoms of life. In plants, tetrapyrroles play roles in both animals and land plants. In flowering plants, RNA critical roles in various biological processes, including photo- editing converts specific cytidine residues to uridine in both plastid synthesis and respiration. They serve as cofactors for essential and mitochondrial transcripts. Previous studies identified penta- proteins involved in a wide variety of crucial cellular functions tricopeptide repeat (PPR) motif-containing proteins as site-specific (16, 17). Tetrapyrrolic metabolites, such as Mg protoporphyrin recognition factors for cytidine targets in RNA sequences. How- and heme, have also been suggested to act as signaling molecules ever, the regulatory mechanism underlying RNA editing was largely that coordinate organellar functions within the cell (18, 19). The unknown. Here, we report that protoporphyrinogen IX oxidase 1 tetrapyrrole biosynthesis pathway in plants consists of two major (PPO1), an enzyme that catalyzes protoporphyrinogen IX into pro- branches, the Mg and Fe branch, and is thought to take place toporphyrin IX in the tetrapyrrole biosynthetic pathway, plays an almost exclusively within the plastid (16, 17). Over 20 enzymes unexpected role in editing multiple sites of plastid RNA transcripts, directly involved in tetrapyrrole biosynthesis have been identi- most of which encode subunits of the NADH dehydrogenase-like fied, some of which have been functionally characterized by complex (NDH), in the reference plant Arabidopsis thaliana.We biochemical and genetic approaches (reviews in refs. 16 and 20). identified multiple organellar RNA editing factors (MORFs), includ- It was hitherto unclear whether these enzymes have biological functions that extend beyond their well-established roles as cat- ing MORF2, MORF8, and MORF9, that interact with PPO1. We alysts in the tetrapyrrole pathway. found that two conserved motifs within the 22-aa region at the In this study, we show that disruption of protoporphyrinogen IX N terminus of PPO1 are essential for its interaction with MORFs, its oxidase 1 (PPO1), which encodes the last enzyme in the common RNA editing function, and subsequently, its effect on NDH activity. pathway to chlorophyll and heme biosynthesis (21), causes RNA However, transgenic plants lacking key domains for the tetrapyr- editing defects in 18 of 34 known plastid RNA targets, especially role biosynthetic activity of PPO1 exhibit normal RNA editing. Fur- those encoded by NADH dehydrogenase-like complex (ndh)genes. thermore, MORF2 and MORF9 interact with three PPRs or related PPO1 interacts with plastid-localized MORF proteins, which in PLANT BIOLOGY ndhB ndhD proteins required for editing of and sites. These results turn, additionally interact with two PPR proteins, CHLOROR- reveal that the tetrapyrrole biosynthetic enzyme PPO1 is required ESPIRATORY REDUCTION 28 (CRR28) and ORGANELLE for plastid RNA editing, acting as a regulator that promotes the TRANSCRIPT PROCESSING 82 (OTP82), and a DYW domain- stability of MORF proteins through physical interaction. containing protein, DYW1. We found that the interaction with MORFs is critical for the RNA editing function of PPO1. Our metabolism | organelle | editosome study not only elucidates a role for PPO1 that does not involve tetrapyrrole biosynthesis but also, identifies a distinct regulator NA editing, the process of covalently altering the sequence of plastid RNA editing in higher plants. Rof an RNA molecule, generates protein diversity in eukar- yotes (1, 2). Generally, in land plants, RNA editing highly spe- Significance cifically converts cytidine to uridine nucleotides in transcripts of both plastid and mitochondrial genes (3); 34 cytidine residues in Both posttranscriptional RNA editing and tetrapyrrole metab- plastids and more than 500 residues in mitochondria have been olism are important processes in land plants and animals. A reported to be editing target sites in Arabidopsis thaliana (4, 5). direct link between these two distinct programs had hitherto A series of studies identified members of the PLS subfamily of not been established. This study reveals an unexpected pentatricopeptide repeat (PPR) motif-containing proteins as the function for protoporphyrinogen IX oxidase 1 from model site-specific recognition factors for cytidine targets (6). These spe- plant Arabidopsis thaliana in regulating plastid RNA editing cific PPR trans-acting proteins recognize cis elements within a re- through interacting with and modulating the stability of mul- gion of ∼30 nt within the sites to be edited (1, 6–11). Although the tiple organellar RNA editing factors. In addition to furthering DYW domains of some PPR factors contain several conserved our knowledge of the composition of the plant organellar editing residueswithacytidinedeaminasemotif(12),theenzymethat apparatus, this research provides insight into both the con- executes the editing reaction is elusive. Two recent reports docu- served and divergent roles of enzymes in the tetrapyrrole mented that members of multiple organellar RNA editing fac- metabolism during evolution. tors (MORFs)/RNA editing factor interacting proteins (RIPs) Author contributions: F.Z. and R.L. designed research; F.Z., W.T., B.H., and L.Z. performed widely affect RNA editing sites in both mitochondria and plas- research; L.L. and C.L. contributed new reagents/analytic tools; F.Z., B.H., L.P., B.G., and tids (13, 14). Organelle RNA recognition motif protein 1, which R.L. analyzed data; and F.Z. and R.L. wrote the paper. contains two truncated RIP domains, is also essential for plastid The authors declare no conflict of interest. RNA editing (15). These studies reveal additional components This article is a PNAS Direct Submission. of the plant organellar editing apparatus. However, the mecha- 1To whom correspondence should be addressed. E-mail: [email protected]. nism by which these proteins edit RNA and the complete com- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. position of the editing machinery remain largely unknown. 1073/pnas.1316183111/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1316183111 PNAS | February 4, 2014 | vol. 111 | no. 5 | 2023–2028 Downloaded by guest on September 24, 2021 Results light harvesting complex of PSI, and light harvesting complex Disruption of PPO1 Severely Impairs Seedling Growth, Chlorophyll of PSII. The content of some representative subunits of these Synthesis, and NDH Complex Accumulation. The PPO enzymes are complexes was drastically decreased in the ppo1 alleles (Fig. S2A), encoded by PPO1 (At4g01690) and PPO2 (At5g14220) in the indicating that loss of PPO1 widely affects stability of the thy- A. thaliana genome. PPO1 is induced by light and ubiquitously lakoid proteins. Most strikingly, NdhH and NdhK, two subunits expressed in plant tissues, whereas PPO2 transcripts are barely of the chloroplast NDH, were absent in ppo1 (Fig. 1H). The detectable (Fig. S1 A and B). To determine the biological absence of the NDH complex is unlikely caused by changes in function of PPO1 in Arabidopsis, we obtained and analyzed two transcriptional control, because the transcript level of ndhH, independent T-DNA mutant alleles (Fig. 1A). Homozygosity for ndhK, ndhB,andndhD was not affected by the PPO1 mutations either the ppo1-1 or ppo1-2 null mutation resulted in etiolated (Fig. S2B). Moreover, it is also unlikely the result of secondary cotyledons and eventually, seedling lethality (Fig. 1 B and C). effects of seedling lethality, because the NDH complex is pres- To test how the tetrapyrrole biosynthetic pathway was affected ent, even in etioplasts. by the ppo1 mutation, several key intermediates in this pathway were determined by HPLCy. Protoporphyrin IX was drastically Loss of PPO1 Affects Multiple Editing Sites in Plastids. Previous increased in ppo1-1 compared with the WT, consistent with the studies revealed that 16 of 34 known editing sites in plastids occur loss of PPO1 function in the mutant (Fig. 1D). Importantly, the in transcripts encoding multiple subunits of the NDH complex (8). steady state levels of Mg protoporphyrin and chlorophyll were We tested whether the RNA editing status in these sites was al- decreased in ppo1-1 (Fig. 1 E and F). However, the heme level tered in ppo1 mutants. Interestingly, except for the ndhB-746 site, was not influenced by the PPO1 mutation (Fig. 1G). These results the editing efficiencies of all sites in ndhB, ndhD, ndhF,andndhG indicate that PPO1 dominantly affects the Mg branch
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