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1. A RanBP2-type zinc finger protein functions in intron splicing in Arabidopsis mitochondria and is involved in the biogenesis of respiratory complex I

   https://doi.org/10.1093/nar/gkab066  

   Bentolila, Stéphane ; Gipson, Andrew B ; Kehl, Alexander J ; Hamm, Lauren N ; Hayes, Michael L ; Mulligan, R Michael ; Hanson, Maureen R ( February 2021 , Nucleic Acids Research)

   Abstract The RanBP2 zinc finger (Znf) domain is a prevalent domain that mediates protein interaction and RNA binding. In Arabidopsis, a clade of four RanBP2 Znf-containing proteins, named the Organelle Zinc (OZ) finger family, are known or predicted to be targeted to either the mitochondria or the plastids. Previously we reported that OZ1 is absolutely required for the editing of 14 sites in chloroplasts. We now have investigated the function of OZ2, whose null mutation is embryo lethal. We rescued the null mutant by expressing wild-type OZ2 under the control of the seed-specific ABSCISIC ACID-INSENSITIVE3 (ABI3) promoter. Rescued mutant plants exhibit severely delayed development and a distinctive morphological phenotype. Genetic and biochemical analyses demonstrated that OZ2 promotes the splicing of transcripts of several mitochondrial nad genes and rps3. The splicing defect of nad transcripts results in the destabilization of complex I, which in turn affects the respiratory ability of oz2 mutants, turning on the alternative respiratory pathway, and impacting the plant development. Protein-protein interaction assays demonstrated binding of OZ2 to several known mitochondrial splicing factors targeting the same splicing events. These findings extend the known functional repertoire of the RanBP2 zinc finger domain in nuclear splicing to include plant organelle splicing. 

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2. The dicot homolog of maize PPR103 carries a C-terminal DYW domain and may have a role in C-to-U editing of some chloroplast RNA transcripts

   https://doi.org/10.1007/s11103-024-01424-1  

   McCray, Tyra N. ; Azim, Mohammad F. ; Burch-Smith, Tessa M. ( March 2024 , Plant Molecular Biology)

   In plants, cytidine-to-uridine (C-to-U) editing is a crucial step in processing mitochondria- and chloroplast-encoded transcripts. This editing requires nuclear-encoded proteins including members of the pentatricopeptide (PPR) family, especially PLS-type proteins carrying the DYW domain.IPI1/emb175/PPR103is a nuclear gene encoding a PLS-type PPR protein essential for survival inArabidopsis thalianaand maize. Arabidopsis IPI1 was identified as likely interacting with ISE2, a chloroplast-localized RNA helicase associated with C-to-U RNA editing in Arabidopsis and maize. Notably, while the Arabidopsis andNicotianaIPI1 orthologs possess complete DYW motifs at their C-termini, the maize homolog, ZmPPR103, lacks this triplet of residues which are essential for editing. In this study we examined the function of IPI1 in chloroplast RNA processing inN. benthamianato gain insight into the importance of the DYW domain to the function of the EMB175/PPR103/ IPI1 proteins. Structural predictions suggest that evolutionary loss of residues identified as critical for catalyzing C-to-U editing in other members of this class of proteins, were likely to lead to reduced or absent editing activity in theNicotianaand Arabidopsis IPI1 orthologs. Virus-induced gene silencing ofNbIPI1led to defects in chloroplast ribosomal RNA processing and changes to stability ofrpl16transcripts, revealing conserved function with its maize ortholog.NbIPI1-silenced plants also had defective C-to-U RNA editing in several chloroplast transcripts, a contrast from the finding that maize PPR103 had no role in editing. The results indicate that in addition to its role in transcript stability, NbIPI1 may contribute to C-to-U editing inN. benthamianachloroplasts.

    

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3. Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

   https://doi.org/10.1111/nph.16297  

   Gerke, Philipp ; Szövényi, Péter ; Neubauer, Anna ; Lenz, Henning ; Gutmann, Bernard ; McDowell, Rose ; Small, Ian ; Schallenberg‐Rüdinger, Mareike ; Knoop, Volker ( December 2019 , New Phytologist)

   Hornworts are crucial to understand the phylogeny of early land plants. The emergence of ‘reverse’ U‐to‐C RNA editing accompanying the widespread C‐to‐U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort–tracheophyte clade. C‐to‐U RNA editing is well understood after identification of many editing factors in models likeArabidopsis thalianaandPhyscomitrella patens, but there is no plant model yet to investigate U‐to‐C RNA editing. The hornwortAnthoceros agrestisis now emerging as such a model system.

   We report on the assembly and analyses of theA. agrestischloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors.

   Both organelles inA. agrestisfeature high amounts of RNA editing, with altogether > 1100 sites of C‐to‐U and 1300 sites of U‐to‐C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains.

   We observe significant variants of the ‘classic’ DYW domain, in the meantime confirmed as the cytidine deaminase for C‐to‐U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U‐to‐C editing targets according to the PPR‐RNA binding code.

    

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4. Nodule‐specific PLAT domain proteins are expanded in the Medicago lineage and required for nodulation

   https://doi.org/10.1111/nph.15697  

   Trujillo, Diana I. ; Silverstein, Kevin A. T. ; Young, Nevin D. ( February 2019 , New Phytologist)

   Symbiotic nitrogen fixation in legumes is mediated by an interplay of signaling processes between plant hosts and rhizobial symbionts. In legumes, several secreted protein families have undergone expansions and play key roles in nodulation. Thus, identifying lineage‐specific expansions (LSEs) of nodulation‐associated genes can be a strategy to discover candidate gene families.

   Using bioinformatic tools, we identified 13LSEs of nodulation‐related secreted protein families, each unique to eitherGlycine,ArachisorMedicagolineages. In theMedicagolineage, nodule‐specific Polycystin‐1, Lipoxygenase, Alpha Toxin (PLAT) domain proteins (NPDs) expanded to five members. We examinedNPDfunction usingCRISPR/Cas9 multiplex genome editing to createMedicago truncatulaNPDknockout lines, targeting one to fiveNPDgenes.

   Mutant lines with differing combinations ofNPDgene inactivations had progressively smaller nodules, earlier onset of nodule senescence, or ineffective nodules compared to the wild‐type control. Double‐ and triple‐knockout lines showed dissimilar nodulation phenotypes but coincided in upregulation of aDHHC‐type zinc finger and an aspartyl protease gene, possible candidates for the observed disturbance of proper nodule function.

   By postulating that gene family expansions can be used to detect candidate genes, we identified a family of nodule‐specificPLATdomain proteins and confirmed that they play a role in successful nodule formation.

    

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5. CFM1, a member of the CRM‐domain protein family, functions in chloroplast group II intron splicing in Setaria viridis

   https://doi.org/10.1111/tpj.15060  

   Feiz, Leila ; Asakura, Yukari ; Mao, Linyong ; Strickler, Susan R. ; Fei, Zhangjun ; Rojas, Margarita ; Barkan, Alice ; Stern, David B. ( December 2020 , The Plant Journal)

   The chloroplast RNA splicing and ribosome maturation (CRM) domain is a RNA‐binding domain found in a plant‐specific protein family whose characterized members play essential roles in splicing group I and group II introns in mitochondria and chloroplasts. Together, these proteins are required for splicing of the majority of the approximately 20 chloroplast introns in land plants. Here, we provide evidence fromSetaria viridisand maize that an uncharacterized member of this family, CRM Family Member1 (CFM1), promotes the splicing of most of the introns that had not previously been shown to require a CRM domain protein. ASetariamutant expressing mutated CFM1 was strongly disrupted in the splicing of three chloroplast tRNAs:trnI,trnVandtrnA. Analyses by RNA gel blot and polysome association suggest that the tRNA deficiencies lead to compromised chloroplast protein synthesis and the observed whole‐plant chlorotic phenotypes. Co‐immunoprecipitation data demonstrate that the maize CFM1 ortholog is bound to introns whose splicing is disrupted in thecfm1mutant. With these results, CRM domain proteins have been shown to promote the splicing of all but two of the introns found in angiosperm chloroplast genomes.

    

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