DOCSLIB.ORG

The Pentatricopeptide Repeat Protein MEF100 Is Required for the Editing of Four Mitochondrial Editing Sites in Arabidopsis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Pentatricopeptide Repeat Protein MEF100 Is Required for the Editing of Four Mitochondrial Editing Sites in Arabidopsis cells Article The Pentatricopeptide Repeat Protein MEF100 Is Required for the Editing of Four Mitochondrial Editing Sites in Arabidopsis Bernard Gutmann †, Michael Millman †, Lilian Vincis Pereira Sanglard , Ian Small and Catherine Colas des Francs-Small * Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; [email protected] (B.G.); [email protected] (M.M.); [email protected] (L.V.P.S.); [email protected] (I.S.) * Correspondence: [email protected]; Tel.: +61-864884409 † Contributed equally. Abstract: In Arabidopsis thaliana there are more than 600 C-to-U RNA editing events in the mitochon- dria and at least 44 in the chloroplasts. Pentatricopeptide repeat (PPR) proteins provide the specificity for these reactions. They recognize RNA sequences in a partially predictable fashion via key amino acids at the fifth and last position in each PPR motif that bind to individual ribonucleotides. A combined approach of RNA-Seq, mutant complementation, electrophoresis of mitochondrial protein complexes and Western blotting allowed us to show that MEF100, a PPR protein identified in a genetic screen for mutants resistant to an inhibitor of γ -glutamylcysteine synthetase, is required for the editing of nad1-493, nad4-403, nad7-698 and ccmFN2-356 sites in Arabidopsis mitochondria. The absence of editing in mef100 leads to a decrease in mitochondrial Complex I activity, which probably Citation: Gutmann, B.; Millman, M.; Vincis Pereira Sanglard, L.; Small, I.; explains the physiological phenotype. Some plants have lost the requirement for MEF100 at one Colas des Francs-Small, C. The or more of these sites through mutations in the mitochondrial genome. We show that loss of the Pentatricopeptide Repeat Protein requirement for MEF100 editing leads to divergence in the MEF100 binding site. MEF100 Is Required for the Editing of Four Mitochondrial Editing Sites in Keywords: plant mitochondria; editing; pentatricopeptide repeat (PPR) proteins Arabidopsis. Cells 2021, 10, 468. https://doi.org/10.3390/cells10020468 Academic Editors: Alexander 1. Introduction E. Kalyuzhny and Inhwan Hwang RNA editing is a post-transcriptional process that alters the nucleotide sequences of RNA molecules such that the information contained in the mature RNA differs from that Received: 31 December 2020 defined in the genome [1]. In the mitochondria and chloroplasts of angiosperms, RNA Accepted: 17 February 2021 editing occurs as singular cytidine (C) to uridine (U) changes by deamination [2]. Editing is Published: 22 February 2021 catalysed by editosomes, multifactor protein-RNA complexes in which RNA recognition is mediated by pentatricopeptide repeat (PPR) proteins [3]. The majority of the PPR proteins Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in involved in editing belong to the PLS subfamily whose PPR array is composed of three published maps and institutional affil- variants of PPR motifs named P, L and S [4]. The PLS proteins usually carry additional PPR- iations. like motifs (E1 and E2) and a cytidine-deaminase-like domain (the DYW domain) at their C-terminus. The zinc-binding DYW domain is required for catalysis of the deamination reaction [5–9]. A PPR-RNA code was developed to describe the observed correlations between amino acids at two key positions of known editing factors and their aligned nucleotides on the transcripts to which they bind [1,10,11]. Subsequently, the amino acids Copyright: © 2021 by the authors. at these positions were shown to bind to the aligned nucleotide via hydrogen bonds [12]. Licensee MDPI, Basel, Switzerland. Although this code can be used to predict the targets of some PPR proteins [7,11,13–16], This article is an open access article distributed under the terms and most PPR proteins required for the editing of mitochondrial sites in Arabidopsis have not conditions of the Creative Commons been identified. The characterisation of new editing factors remains an important step in Attribution (CC BY) license (https:// understanding how PPR proteins recognise their targets and the role of RNA editing in creativecommons.org/licenses/by/ organelle gene expression. 4.0/). Cells 2021, 10, 468. https://doi.org/10.3390/cells10020468 https://www.mdpi.com/journal/cells Cells 2021, 10, 468 2 of 13 In wild-type plants, exposure to buthionine sulfoximine (BSO) inhibits the activity of γ-glutamylcysteine synthetase, severely reducing the plant’s ability to produce the tripeptide glutathione (γ-L-glutamyl-L-cysteinylglycine, GSH) [17]. GSH is involved in multiple biochemical processes, including the detoxification of reactive oxygen species [18] and an inability to produce it results in a specific loss of root meristem activity, stopping root growth [19]. In a screen of Col-0 ecotype plants treated with ethane methyl sulfonate (EMS), 10 bir mutants (for BSO-insensitive roots), including two PPR mutants had almost normal root growth in the presence of BSO [20]. This BSO-insensitive-root phenotype observed in the bir6 mutant [20] was also shared by the Arabidopsis Complex I mutants css1 [21] and otp439 [20,22], suggesting that the phenotype is related to the reduced activity of mitochondrial Complex I. In this paper, we show that the mutant named here as mef100 (for mitochondrial editing factor 100) is unable to effectively edit four mitochondrial sites and has moderately reduced levels of assembled Complex I. 2. Materials and Methods 2.1. Plant Growth and Selection Arabidopsis seeds were surface sterilized in a solution containing 70% (v/v) ethanol and 0.05% Triton X-100 for 5 min, washed in 100% ethanol and then dried in sterile conditions. The seeds were plated (0.5× MS medium), vernalized at 4 ◦C in the dark for at least 24 h and then grown under a long-day photoperiod (16 h light, 100 µmol photons m−2 s−1). Three weeks after plating, they were transferred to the soil. The mef100 mutant plants were obtained from Stanislav Kopriva’s lab at the Depart- ment of Metabolic Biology at the John Innes Centre (United Kingdom). Plants were con- firmed for homozygosity for the point mutation in the coding sequence of the AT3G61170 gene by Sanger sequencing of the PCR product obtained using the primer pair Mef100_859F and Mef100_2211R (Table S1). The mef100 mutants were complemented (see Section 2.2) by floral dip [23] and their seeds were screened for successful transformation on 0.5× MS media containing 25 µg/µL hygromycin. Complementation was confirmed by PCR using primer pair mef100_1865F and pGWB1_C-terminal_R-1 (Table S1). 2.2. Plant Complementation The region of genomic DNA corresponding to the full mef100 gene and 522 nt up- stream of the mef100 start codon was amplified by PCR from Col-0 genomic DNA using mef100_ups_attB_F and mef100-stop_attBR (Table S1), which was cloned into the Gateway donor vector pDONR207 (Thermo Fisher Scientific, Waltham, MA, USA) according to the recommended protocol and used to transform DH5α. The fragment verified by Sanger sequencing was cloned into the pGWB1 binary vector and transferred into plants via Agrobacterium tumefaciens transformation [23]. 2.3. RNA Editing Analyses RNA from young leaves of mef100, Columbia-0 and three complemented mef100 lines was extracted and DNase treated as previously described [24]. Reverse transcription using random primers and SuperScript III (Thermo Fisher Scientific, Waltham, MA, USA) was done according to their recommended protocol. PCR of the cDNA of mef100, Columbia- 0 and complemented lines was done using Taq polymerase (Thermo Fisher Scientific, Waltham, MA, USA) according to their recommended protocol using primers specific to each of the four editing sites. PCR of the nad1-493 site was done using the primer pair nad1-224-F and nad1-861-RV1; nad4-403 using nad4-176-F and nad4-830-RV1; nad7-698 using nad7-382-F and nad7-1004-RV1; ccmFN2-356 using ccmFN2-88-F and ccmFN2-500-RV1 (Table S1). 2.4. Analysis of RNA Editing in RNA-seq Data Crude mitochondrial pellets were isolated from 8-week-old leaves of mef100 and Col-0 as previously described [25]. Mitochondrial RNA was extracted from these crude Cells 2021, 10, 468 3 of 13 mitochondrial fractions using TRIzol (Thermo Fisher Scientific, Waltham, MA, USA). Two µg of RNA were treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) for 1 h at 37 ◦C and tested for DNA contamination as previously described [26]. Three hundred µg of mitochondrial RNA were used for cDNA library preparation using the TruSeq Stranded mRNA Library Prep kit with RIBO zero (Illumina, San Diego, Cal- ifornia). The sequencing run (50 nt, single read) was performed on an Illumina Hi-Seq 2500 platform. RNA editing analyses were carried out as described in [27]. Reads were analysed with the BBMap package (sourceforge.net/projects/bbmap/). Clumpify was used to remove optical duplicates (with parameters dedupe optical dist = 40), BBDuk was used to remove adapters (with parameters ktrim = r k = 23 mink = 11 hdist = 1 tpe tbo ftm = 5) and BBMap was used to map trimmed reads to the organelle genomes (with parameters ambiguous = random). Nucleotide counting to identify the extent of editing was carried out with Pyrimid (https://github.com/ian-small/pyrimid, accessed on 21 January 2021). Nucleotide count data was analysed statistically with a Fisher exact test as implemented in the Python scipy.stats package and the p-values were corrected for multiple testing using statsmodels.stats.multitest.multipletests with the Simes-Hochberg procedure. Odds ratios were calculated after adding a pseudocount of 0.5 to all observations to avoid division by zero. 2.5. Analysis of Complex I and Complex III Crude membrane pellets were prepared from Arabidopsis leaves as previously de- scribed [25] and the complexes separated by BN-PAGE using precast NativePAGETM mini-gels (Thermo Fisher Scientific, Waltham, MA, USA).
Load more

Recommended publications
  • PPR Proteins – Orchestrators of Organelle RNA Metabolism Aleix
    1 PPR proteins – orchestrators of organelle RNA metabolism 2 Aleix Gorchs Rovira and Alison G Smith* 3 Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA UK 4 Correspondence 5 *Corresponding author, 6 e-mail: [email protected] 7 8 Pentatricopeptide repeat (PPR) proteins are important RNA regulators in chloroplasts and mitochondria, 9 aiding in RNA editing, maturation, stabilisation or intron splicing, and in transcription and translation 10 of organellar genes. In this review, we summarise all PPR proteins documented so far in plants and the 11 green alga Chlamydomonas. By further analysis of the known target RNAs from Arabidopsis thaliana 12 PPR proteins, we find that all organellar-encoded complexes are regulated by these proteins, although 13 to differing extents. In particular, the orthologous complexes of NADH dehydrogenase (Complex I) in 14 the mitochondria and NADH dehydrogenase-like (NDH) complex in the chloroplast were the most 15 regulated, with respectively 60 and 28% of all characterised A. thaliana PPR proteins targeting their 16 genes. 17 Abbreviations – CMS, Cytoplasm Male Sterility; PMT, Post-transcriptional modification; T/P/OPR, 18 tetra-, penta-, octo-tricopeptide repeat. 19 20 The need to regulate organelle genetic expression 21 Photosynthesis and respiration, which arose initially in prokaryotic organisms, requires the assembly of 22 many different components to form functional protein complexes (Vermaas 2001) and networks for 23 effective electron transfer (Anraku 1988). After the endosymbiotic events in which a free-living 24 cyanobacterium and an alpha-proteobacterium gave rise respectively to the chloroplasts and 25 mitochondria found in eukaryotic cells, there was migration of essential genes from the “new organelle” 26 to the nucleus.
    [Show full text]
  • TAL Effectors Are Remote Controls for Gene Activation Heidi Scholze and Jens Boch
    Available online at www.sciencedirect.com TAL effectors are remote controls for gene activation Heidi Scholze and Jens Boch TAL (transcription activator-like) effectors constitute a novel typically 34 amino acids (aa) long, but also repeat types of class of DNA-binding proteins with predictable specificity. They 30–42 aa can be found ([2], Figure 2). The last repeat is are employed by Gram-negative plant-pathogenic bacteria of only a half repeat. Repeat-to-repeat variations are limited the genus Xanthomonas which translocate a cocktail of to a few aa positions including two hypervariable residues different effector proteins via a type III secretion system (T3SS) at positions 12 and 13 per repeat. Typically, TALs differ into plant cells where they serve as virulence determinants. in their number of repeats while most contain 15.5–19.5 Inside the plant cell, TALs localize to the nucleus, bind to target repeats [2]. The repeat domain determines the specificity promoters, and induce expression of plant genes. DNA-binding of TALs which is mediated by selective DNA binding specificity of TALs is determined by a central domain of tandem [7,8]. TAL repeats constitute a novel type of DNA- repeats. Each repeat confers recognition of one base pair (bp) binding domain [7] distinct from classical zinc finger, in the DNA. Rearrangement of repeat modules allows design of helix–turn–helix, and leucine zipper motifs. proteins with desired DNA-binding specificities. Here, we summarize how TAL specificity is encoded, first structural data The recent understanding of the DNA-recognition speci- and first data on site-specific TAL nucleases.
    [Show full text]
  • Eukaryotic Genome Annotation
    Comparative Features of Multicellular Eukaryotic Genomes (2017) (First three statistics from www.ensembl.org; other from original papers) C. elegans A. thaliana D. melanogaster M. musculus H. sapiens Species name Nematode Thale Cress Fruit Fly Mouse Human Size (Mb) 103 136 143 3,482 3,555 # Protein-coding genes 20,362 27,655 13,918 22,598 20,338 (25,498 (13,601 original (30,000 (30,000 original est.) original est.) original est.) est.) Transcripts 58,941 55,157 34,749 131,195 200,310 Gene density (#/kb) 1/5 1/4.5 1/8.8 1/83 1/97 LINE/SINE (%) 0.4 0.5 0.7 27.4 33.6 LTR (%) 0.0 4.8 1.5 9.9 8.6 DNA Elements 5.3 5.1 0.7 0.9 3.1 Total repeats 6.5 10.5 3.1 38.6 46.4 Exons % genome size 27 28.8 24.0 per gene 4.0 5.4 4.1 8.4 8.7 average size (bp) 250 506 Introns % genome size 15.6 average size (bp) 168 Arabidopsis Chromosome Structures Sorghum Whole Genome Details Characterizing the Proteome The Protein World • Sequencing has defined o Many, many proteins • How can we use this data to: o Define genes in new genomes o Look for evolutionarily related genes o Follow evolution of genes ▪ Mixing of domains to create new proteins o Uncover important subsets of genes that ▪ That deep phylogenies • Plants vs. animals • Placental vs. non-placental animals • Monocots vs. dicots plants • Common nomenclature needed o Ensure consistency of interpretations InterPro (http://www.ebi.ac.uk/interpro/) Classification of Protein Families • Intergrated documentation resource for protein super families, families, domains and functional sites o Mitchell AL, Attwood TK, Babbitt PC, et al.
    [Show full text]
  • Modern Trends in Plant Genome Editing: an Inclusive Review of the CRISPR/Cas9 Toolbox
    International Journal of Molecular Sciences Review Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox Ali Razzaq 1 , Fozia Saleem 1, Mehak Kanwal 2, Ghulam Mustafa 1, Sumaira Yousaf 2, Hafiz Muhammad Imran Arshad 2, Muhammad Khalid Hameed 3, Muhammad Sarwar Khan 1 and Faiz Ahmad Joyia 1,* 1 Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan 2 Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan 3 School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China * Correspondence: [email protected] Received: 14 June 2019; Accepted: 15 August 2019; Published: 19 August 2019 Abstract: Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing.
    [Show full text]
  • An Overview of Pentatricopeptide Repeat Proteins and Their Applications
    Biochimie 113 (2015) 93e99 Contents lists available at ScienceDirect Biochimie journal homepage: www.elsevier.com/locate/biochi Review An overview of pentatricopeptide repeat proteins and their applications Sam Manna Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia article info abstract Article history: Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which Received 19 February 2015 mediate several aspects of gene expression primarily in organelles but also in the nucleus. These proteins Accepted 3 April 2015 facilitate processing, splicing, editing, stability and translation of RNAs. While major advances in PPR Available online 14 April 2015 research have been achieved with plant PPR proteins, the significance of non-plant PPR proteins is becoming of increasing importance. PPR proteins are classified into different subclasses based on their Keywords: domain architecture, which is often a reflection of their function. This review provides an overview of the Pentatricopeptide repeat protein significant findings regarding the functions, evolution and applications of PPR proteins. Horizontal gene Mitochondria Chloroplast transfer appears to have played a major role in the sporadic phylogenetic distribution of different PPR Horizontal gene transfer subclasses in both eukaryotes and prokaryotes. Additionally, the use of synthetic biology and protein tRNA guanine methyltransferase engineering to create designer PPR proteins to control gene expression in vivo is discussed. This review also highlights some of the aspects of PPR research that require more attention particularly in non-plant organisms. This includes the lack of research into the recently discovered PPR-TGM subclass, which is not only the first PPR subclass absent from plants but present in economically and clinically-relevant pathogens.
    [Show full text]
  • Pentatricopeptide Repeat Protein MID1 Modulates Nad2 Intron 1
    www.nature.com/scientificreports OPEN Pentatricopeptide repeat protein MID1 modulates nad2 intron 1 splicing and Arabidopsis development Peng Zhao1,2,3, Fang Wang1,2,3, Na Li1,2, Dong-Qiao Shi1,2 & Wei-Cai Yang 1,2* As one of the best-studied RNA binding proteins in plant, pentatricopeptide repeats (PPRs) protein are mainly targeted to mitochondria and/or chloroplasts for RNA processing to regulate the biogenesis and function of the organelles, but its molecular mechanism and role in development remain to be further revealed. Here, we identifed a mitochondria-localized P-type small PPR protein, MITOCHONDRION- MEDIATED GROWTH DEFECT 1 (MID1) that is crucial for Arabidopsis development. Mutation in MID1 causes retarded embryo development and stunted plant growth with defects in cell expansion and proliferation. Molecular experiments showed that MID1 is required for the splicing of the nad2 intron 1 in mitochondria. Consistently, mid1 plants display signifcant reduction in the abundance and activity of mitochondrial respiration complex I, accompanied by abnormal mitochondrial morphology and energy metabolism. Furthermore, MID1 is associated with other trans-factors involved in NICOTINAMIDE ADENINE DINUCLEOTIDE HYDROGEN (NADH) DEHYDROGENASE SUBUNIT 2 (nad2) intron 1 splicing, and interacts directly with itself and MITOCHONDRIAL STABILITY FACTOR 1 (MTSF1). This suggests that MID1 most likely functions as a dimer for nad2 intron 1 splicing. Together, we characterized a novel PPR protein MID1 for nad2 intron 1 splicing. Mitochondrion, originated from the gram-negative bacterium ancestors, is an essential organelle of eukaryotic organisms that can produce energy and signaling molecules for their growth and development1–3. Most of the mitochondrial genes have been transferred and integrated into nuclear genome during evolutionary progress, and the remaining genes encode a limited number of proteins that mainly make up the respiration complexes and translation machinery4–7.
    [Show full text]
  • The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the Cis-Splicing of Nad4 Intron 1 and Essential to Seed Development in Maize
    International Journal of Molecular Sciences Article The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the cis-Splicing of nad4 Intron 1 and Essential to Seed Development in Maize Rui Liu 1, Shi-Kai Cao 1 , Aqib Sayyed 1, Chunhui Xu 1, Feng Sun 1, Xiaomin Wang 2 and Bao-Cai Tan 1,* 1 Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; [email protected] (R.L.); [email protected] (S.-K.C.); [email protected] (A.S.); [email protected] (C.X.); [email protected] (F.S.) 2 Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; [email protected] * Correspondence: [email protected] Received: 10 May 2020; Accepted: 2 June 2020; Published: 5 June 2020 Abstract: Pentatricopeptide repeat (PPR) protein comprises a large family, participating in various aspects of organellar RNA metabolism in land plants. There are approximately 600 PPR proteins in maize, but the functions of many PPR proteins remain unknown. In this study, we defined the function of PPR18 in the cis-splicing of nad4 intron 1 in mitochondria and seed development in maize. Loss function of PPR18 seriously impairs embryo and endosperm development, resulting in the empty pericarp (emp) phenotype in maize. PPR18 encodes a mitochondrion-targeted P-type PPR protein with 18 PPR motifs. Transcripts analysis indicated that the splicing of nad4 intron 1 is impaired in the ppr18 mutant, resulting in the absence of nad4 transcript, leading to severely reduced assembly and activity of mitochondrial complex I and dramatically reduced respiration rate.
    [Show full text]
  • Yeast Pentatricopeptide Protein Dmr1 (Ccm1) Binds a Repetitive AU-Rich Motif in the Small Subunit Mitochondrial Ribosomal RNA
    Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Yeast pentatricopeptide protein Dmr1 (Ccm1) binds a repetitive AU- rich motif in the small subunit mitochondrial ribosomal RNA Jakub Piątkowski1 and Paweł Golik1,2,* 1 Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland 2 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland * To whom correspondence should be addressed. Tel: +48 (22) 592 3234; Fax: +48 (22) 658 4176; Email: [email protected] ABSTRACT PPR proteins are a diverse family of RNA binding factors found in all Eukaryotic lineages. They perform multiple functions in the expression of organellar genes, mostly on the post-transcriptional level. PPR proteins are also significant determinants of evolutionary nucleo-organellar compatibility. Plant PPR proteins recognize their RNA substrates using a simple modular code. No target sequences recognized by animal or yeast PPR proteins were identified prior to the present study, making it impossible to assess whether this plant PPR code is conserved in other organisms. Dmr1p (Ccm1p, Ygr150cp) is a S. cerevisiae PPR protein essential for mitochondrial gene expression and involved in the stability of 15S ribosomal RNA. We demonstrate that in vitro Dmr1p specifically binds a motif composed of multiple AUA repeats occurring twice in the 15S rRNA sequence as the minimal 14 nucleotide (AUA)4AU or longer (AUA)7 variant. Short RNA fragments containing this motif are protected by Dmr1p from exoribonucleolytic activity in vitro. Presence of the identified motif in mtDNA of different yeast species correlates with the compatibility between their Dmr1p orthologues and S.
    [Show full text]
  • RNA Binding and RNA Remodeling Activities of the Half-A-Tetratricopeptide (HAT) Protein HCF107 Underlie Its Effects on Gene Expression
    RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression Kamel Hammania, William B. Cookb, and Alice Barkana,1 aInstitute of Molecular Biology, University of Oregon, Eugene, OR 97403; and bDepartment of Biology, Midwestern State University, Wichita Falls, TX 76308 Edited by Jennifer A. Doudna, University of California, Berkeley, CA, and approved February 29, 2012 (received for review January 6, 2012) The half-a-tetratricopeptide repeat (HAT) motif is a helical repeat findings obtained with HCF107 are likely to elucidate general motif found in proteins that influence various aspects of RNA mechanisms through which HAT domains act. metabolism, including rRNA biogenesis, RNA splicing, and poly- HCF107 is a nucleus-encoded protein that localizes to the adenylation. This functional association with RNA suggested that chloroplasts of land plants. Mutations in Arabidopsis HCF107 HAT repeat tracts might bind RNA. However, RNA binding activity cause defects in the translation and stabilization of mRNAs psbH has not been reported for any HAT repeat tract, and recent derived from the chloroplast gene (6, 15). Our results show that HCF107 binds ssRNA with specificity for sequences at the 5′ literature has emphasized a protein binding role. In this study, psbH we show that a chloroplast-localized HAT protein, HCF107, is end of the processed mRNA isoforms that require HCF107 fi for their accumulation. In addition, we show that bound HCF107 a sequence-speci c RNA binding protein. HCF107 consists of 11 i ′ → ′ tandem HAT repeats and short flanking regions that are also ( ) blocks a 5 3 exonuclease in vitro, accounting for its ability to stabilize psbH RNA in vivo, and (ii) remodels local RNA predicted to form helical hairpins.
    [Show full text]
  • Two Interacting PPR Proteins Are Major Arabidopsis Editing Factors In
    Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria Damien Guillaumot, Mauricio Lopez Obando, Kévin Baudry, Alexandra Launay-Avon, Guillem Rigaill, A. F. de Longevialle, B. Broche, M. Takenaka, Richard Berthomé, G. de Jaeger, et al. To cite this version: Damien Guillaumot, Mauricio Lopez Obando, Kévin Baudry, Alexandra Launay-Avon, Guillem Rigaill, et al.. Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria. Proceedings of the National Academy of Sciences of the United States of America , Na- tional Academy of Sciences, 2017, 114 (33), pp.8877-8882. 10.1073/pnas.1705780114. hal-01606226 HAL Id: hal-01606226 https://hal.archives-ouvertes.fr/hal-01606226 Submitted on 25 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria Damien Guillaumota,b,1, Mauricio Lopez-Obandoa,b,1,2, Kevin Baudrya,b, Alexandra Avona,b, Guillem Rigailla,b,c, Andéol Falcon de Longeviallea,b,3,
    [Show full text]
  • The Novel E-Subgroup Pentatricopeptide Repeat Protein
    Ren et al. BMC Plant Biology (2020) 20:553 https://doi.org/10.1186/s12870-020-02765-x RESEARCH ARTICLE Open Access The novel E-subgroup pentatricopeptide repeat protein DEK55 is responsible for RNA editing at multiple sites and for the splicing of nad1 and nad4 in maize Ru Chang Ren1†, Xu Wei Yan1†, Ya Jie Zhao1†, Yi Ming Wei1, Xiaoduo Lu2, Jie Zang1, Jia Wen Wu1, Guang Ming Zheng1, Xin Hua Ding3, Xian Sheng Zhang1 and Xiang Yu Zhao1* Abstract Background: Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown. Results: In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel (dek) 55 (dek55). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at + 449 bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in dek55 kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of nad1 introns 1 and 4 and nad4 intron 1 significantly decreased in dek55 compared with the wild type (WT).
    [Show full text]
  • Self-Analysis of Repeat Proteins Reveals Evolutionarily Conserved
    Merski et al. BMC Bioinformatics (2020) 21:179 https://doi.org/10.1186/s12859-020-3493-y RESEARCH ARTICLE Open Access Self-analysis of repeat proteins reveals evolutionarily conserved patterns Matthew Merski1*† , Krzysztof Młynarczyk1†, Jan Ludwiczak2,3, Jakub Skrzeczkowski1, Stanisław Dunin-Horkawicz2 and Maria W. Górna1* * Correspondence: merski@gmail. com; [email protected] Abstract †Matthew Merski and Krzysztof Młynarczyk contributed equally to Background: Protein repeats can confound sequence analyses because the this work. repetitiveness of their amino acid sequences lead to difficulties in identifying whether 1Structural Biology Group, Biological similar repeats are due to convergent or divergent evolution. We noted that the and Chemical Research Centre, “ ” Department of Chemistry, University patterns derived from traditional dot plot protein sequence self-similarity analysis of Warsaw, Warsaw, Poland tended to be conserved in sets of related repeat proteins and this conservation could Full list of author information is be quantitated using a Jaccard metric. available at the end of the article Results: Comparison of these dot plots obviated the issues due to sequence similarity for analysis of repeat proteins. A high Jaccard similarity score was suggestive of a conserved relationship between closely related repeat proteins. The dot plot patterns decayed quickly in the absence of selective pressure with an expected loss of 50% of Jaccard similarity due to a loss of 8.2% sequence identity. To perform method testing, we assembled a standard set of 79 repeat proteins representing all the subgroups in RepeatsDB. Comparison of known repeat and non-repeat proteins from the PDB suggested that the information content in dot plots could be used to identify repeat proteins from pure sequence with no requirement for structural information.
    [Show full text]