1
|
Yang F, Vincis Pereira Sanglard L, Lee CP, Ströher E, Singh S, Oh GGK, Millar AH, Small I, Colas des Francs-Small C. Mitochondrial atp1 mRNA knockdown by a custom-designed pentatricopeptide repeat protein alters ATP synthase. PLANT PHYSIOLOGY 2024; 194:2631-2647. [PMID: 38206203 PMCID: PMC10980415 DOI: 10.1093/plphys/kiae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024]
Abstract
Spontaneous mutations are rare in mitochondria and the lack of mitochondrial transformation methods has hindered genetic analyses. We show that a custom-designed RNA-binding pentatricopeptide repeat (PPR) protein binds and specifically induces cleavage of ATP synthase subunit1 (atp1) mRNA in mitochondria, significantly decreasing the abundance of the Atp1 protein and the assembled F1Fo ATP synthase in Arabidopsis (Arabidopsis thaliana). The transformed plants are characterized by delayed vegetative growth and reduced fertility. Five-fold depletion of Atp1 level was accompanied by a decrease in abundance of other ATP synthase subunits and lowered ATP synthesis rate of isolated mitochondria, but no change to mitochondrial electron transport chain complexes, adenylates, or energy charge in planta. Transcripts for amino acid transport and a variety of stress response processes were differentially expressed in lines containing the PPR protein, indicating changes to achieve cellular homeostasis when ATP synthase was highly depleted. Leaves of ATP synthase-depleted lines showed higher respiratory rates and elevated steady-state levels of numerous amino acids, most notably of the serine family. The results show the value of using custom-designed PPR proteins to influence the expression of specific mitochondrial transcripts to carry out reverse genetic studies on mitochondrial gene functions and the consequences of ATP synthase depletion on cellular functions in Arabidopsis.
Collapse
Affiliation(s)
- Fei Yang
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Lilian Vincis Pereira Sanglard
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Chun-Pong Lee
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Elke Ströher
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Swati Singh
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Glenda Guec Khim Oh
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - 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
| |
Collapse
|
2
|
Vincis Pereira Sanglard L, Small ID, Colas des Francs-Small C. Alteration of Mitochondrial Transcript Expression in Arabidopsis thaliana Using a Custom-Made Library of Pentatricopeptide Repeat Proteins. Int J Mol Sci 2023; 24:13233. [PMID: 37686040 PMCID: PMC10487680 DOI: 10.3390/ijms241713233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are considered a potential tool for manipulating organelle gene expression in plants because they can recognise a wide range of different RNA sequences, and the molecular basis for this sequence recognition is partially known and understood. A library of redesigned PPR proteins related to restorer-of-fertility proteins was created and transformed into plants in order to target mitochondrial transcripts. Ninety different variants tested in vivo showed a wide range of phenotypes. One of these lines, which displayed slow growth and downward curled leaves, showed a clear reduction in complex V. The phenotype was due to a specific cleavage of atp1 transcripts induced by a modified PPR protein from the library, validating the use of this library as a source of mitochondrial 'mutants'. This study is a step towards developing specific RNA targeting tools using PPR proteins that can be aimed at desired targets.
Collapse
Affiliation(s)
| | | | - 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
| |
Collapse
|
3
|
Wang C, Blondel L, Quadrado M, Dargel-Graffin C, Mireau H. Pentatricopeptide repeat protein MITOCHONDRIAL STABILITY FACTOR 3 ensures mitochondrial RNA stability and embryogenesis. PLANT PHYSIOLOGY 2022; 190:669-681. [PMID: 35751603 PMCID: PMC9434245 DOI: 10.1093/plphys/kiac309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 05/29/2023]
Abstract
Gene expression in plant mitochondria is predominantly governed at the post-transcriptional level and relies mostly on nuclear-encoded proteins. However, the protein factors involved and the underlying molecular mechanisms are still not well understood. Here, we report on the function of the MITOCHONDRIAL STABILITY FACTOR 3 (MTSF3) protein, previously named EMBRYO DEFECTIVE 2794 (EMB2794), and show that it is essential for accumulation of the mitochondrial NADH dehydrogenase subunit 2 (nad2) transcript in Arabidopsis (Arabidopsis thaliana) but not for splicing of nad2 intron 2 as previously proposed. The MTSF3 gene encodes a pentatricopeptide repeat protein that localizes in the mitochondrion. An MTSF3 null mutation induces embryonic lethality, but viable mtsf3 mutant plants can be generated through partial complementation with the developmentally regulated ABSCISIC ACID INSENSITIVE3 promoter. Genetic analyses revealed growth retardation in rescued mtsf3 plants owing to the specific destabilization of mature nad2 mRNA and a nad2 precursor transcript bearing exons 3 to 5. Biochemical data demonstrate that MTSF3 protein specifically binds to the 3' terminus of nad2. Destabilization of nad2 mRNA induces a substantial decrease in complex I assembly and activity and overexpression of the alternative respiratory pathway. Our results support a role for MTSF3 protein in protecting two nad2 transcripts from degradation by mitochondrial exoribonucleases by binding to their 3' extremities.
Collapse
Affiliation(s)
- Chuande Wang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Lisa Blondel
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Martine Quadrado
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Céline Dargel-Graffin
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | | |
Collapse
|
4
|
The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA. Proc Natl Acad Sci U S A 2021; 118:2105274118. [PMID: 34433671 DOI: 10.1073/pnas.2105274118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The control of messenger RNA (mRNA) translation has been increasingly recognized as a key regulatory step for gene control, but clear examples in eukaryotes are still scarce. Nucleo-cytoplasmic male sterilities (CMS) represent ideal genetic models to dissect genetic interactions between the mitochondria and the nucleus in plants. This trait is determined by specific mitochondrial genes and is associated with a pollen sterility phenotype that can be suppressed by nuclear genes known as restorer-of-fertility (Rf). In this study, we focused on the Ogura CMS system in rapeseed and showed that reversion to male sterility by the PPR-B fertility restorer (also called Rfo) occurs through a specific translation inhibition of the mitochondria-encoded CMS-causing mRNA orf138 We also demonstrate that PPR-B binds within the coding sequence of orf138 and acts as a ribosome blocker to specifically impede translation elongation along the orf138 mRNA. Rfo is the first recognized fertility restorer shown to act this way. These observations will certainly facilitate the development of synthetic fertility restorers for CMS systems in which efficient natural Rfs are lacking.
Collapse
|
5
|
Nguyen TT, Planchard N, Dahan J, Arnal N, Balzergue S, Benamar A, Bertin P, Brunaud V, Dargel-Graffin C, Macherel D, Martin-Magniette ML, Quadrado M, Namy O, Mireau H. A Case of Gene Fragmentation in Plant Mitochondria Fixed by the Selection of a Compensatory Restorer of Fertility-Like PPR Gene. Mol Biol Evol 2021; 38:3445-3458. [PMID: 33878189 PMCID: PMC8321540 DOI: 10.1093/molbev/msab115] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The high mutational load of mitochondrial genomes combined with their uniparental inheritance and high polyploidy favors the maintenance of deleterious mutations within populations. How cells compose and adapt to the accumulation of disadvantageous mitochondrial alleles remains unclear. Most harmful changes are likely corrected by purifying selection, however, the intimate collaboration between mitochondria- and nuclear-encoded gene products offers theoretical potential for compensatory adaptive changes. In plants, cytoplasmic male sterilities are known examples of nucleo-mitochondrial coadaptation situations in which nuclear-encoded restorer of fertility (Rf) genes evolve to counteract the effect of mitochondria-encoded cytoplasmic male sterility (CMS) genes and restore fertility. Most cloned Rfs belong to a small monophyletic group, comprising 26 pentatricopeptide repeat genes in Arabidopsis, called Rf-like (RFL). In this analysis, we explored the functional diversity of RFL genes in Arabidopsis and found that the RFL8 gene is not related to CMS suppression but essential for plant embryo development. In vitro-rescued rfl8 plantlets are deficient in the production of the mitochondrial heme-lyase complex. A complete ensemble of molecular and genetic analyses allowed us to demonstrate that the RFL8 gene has been selected to permit the translation of the mitochondrial ccmFN2 gene encoding a heme-lyase complex subunit which derives from the split of the ccmFN gene, specifically in Brassicaceae plants. This study represents thus a clear case of nuclear compensation to a lineage-specific mitochondrial genomic rearrangement in plants and demonstrates that RFL genes can be selected in response to other mitochondrial deviancies than CMS suppression.
Collapse
Affiliation(s)
- Tan-Trung Nguyen
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Noelya Planchard
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- Paris-Sud University, Université Paris-Saclay, Orsay, France
| | - Jennifer Dahan
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Nadège Arnal
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Sandrine Balzergue
- Unité Mixte de Recherche 1345, Institut de Recherche en Horticulture et Semences, Université d’Angers, Angers, France
| | - Abdelilah Benamar
- Unité Mixte de Recherche 1345, Institut de Recherche en Horticulture et Semences, Université d’Angers, Angers, France
| | - Pierre Bertin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
| | - Céline Dargel-Graffin
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - David Macherel
- Unité Mixte de Recherche 1345, Institut de Recherche en Horticulture et Semences, Université d’Angers, Angers, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
| | - Martine Quadrado
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| |
Collapse
|
6
|
Yamagishi H, Jikuya M, Okushiro K, Hashimoto A, Fukunaga A, Takenaka M, Terachi T. A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility restorer gene, Rfo, in radish. Mol Genet Genomics 2021; 296:705-717. [PMID: 33772345 PMCID: PMC8144145 DOI: 10.1007/s00438-021-01777-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/15/2021] [Indexed: 11/04/2022]
Abstract
Cytoplasmic male sterility (CMS) observed in many plants leads defect in the production of functional pollen, while the expression of CMS is suppressed by a fertility restorer gene in the nuclear genome. Ogura CMS of radish is induced by a mitochondrial orf138, and a fertility restorer gene, Rfo, encodes a P-type PPR protein, ORF687, acting at the translational level. But, the exact function of ORF687 is still unclear. We found a Japanese variety showing male sterility even in the presence of Rfo. We examined the pollen fertility, Rfo expression, and orf138 mRNA in progenies of this variety. The progeny with Type H orf138 and Rfo showed male sterility when their orf138 mRNA was unprocessed within the coding region. By contrast, all progeny with Type A orf138 were fertile though orf138 mRNA remained unprocessed in the coding region, demonstrating that ORF687 functions on Type A but not on Type H. In silico analysis suggested a specific binding site of ORF687 in the coding region, not the 5′ untranslated region estimated previously, of Type A. A single nucleotide substitution in the putative binding site diminishes affinity of ORF687 in Type H and is most likely the cause of the ineffectiveness of ORF687. Furthermore, fertility restoration by RNA processing at a novel site in some progeny plants indicated a new and the third fertility restorer gene, Rfs, for orf138. This study clarified that direct ORF687 binding to the coding region of orf138 is essential for fertility restoration by Rfo.
Collapse
Affiliation(s)
- Hiroshi Yamagishi
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto, 603-8555, Japan.
| | - Megumi Jikuya
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto, 603-8555, Japan
| | - Kanako Okushiro
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto, 603-8555, Japan
| | - Ayako Hashimoto
- Research Center of Botany, Kyoto Sangyo University, Kamigamo, Kita , Kyoto, 603-8555, Japan
| | - Asumi Fukunaga
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto, 603-8555, Japan
| | - Mizuki Takenaka
- Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toru Terachi
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita, Kyoto, 603-8555, Japan
| |
Collapse
|
7
|
Proulex GCR, Meade MJ, Manoylov KM, Cahoon AB. Mitochondrial mRNA Processing in the Chlorophyte Alga Pediastrum duplex and Streptophyte Alga Chara vulgaris Reveals an Evolutionary Branch in Mitochondrial mRNA Processing. PLANTS (BASEL, SWITZERLAND) 2021; 10:576. [PMID: 33803683 PMCID: PMC8003010 DOI: 10.3390/plants10030576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/17/2022]
Abstract
Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing has only been explored in Chlamydomonas reinhardtii (Class: Chlorophyceae) and the mature mRNAs are different than higher plants, having no 5' UnTranslated Regions (UTRs), much shorter and more variable 3' UTRs and polycytidylated mature mRNAs. In this study, we analyzed transcript termini using circular RT-PCR and PacBio Iso-Seq to survey the 3' and 5' UTRs and termini for two green algae, Pediastrum duplex (Class: Chlorophyceae) and Chara vulgaris (Class: Charophyceae). This enabled the comparison of processing in the chlorophyte and charophyte clades of green algae to determine if the differences in mitochondrial mRNA processing pre-date the invasion of land by embryophytes. We report that the 5' mRNA termini and non-template 3' termini additions in P. duplex resemble those of C. reinhardtii, suggesting a conservation of mRNA processing among the chlorophyceae. We also report that C. vulgaris mRNA UTRs are much longer than chlorophytic examples, lack polycytidylation, and are polyadenylated similar to embryophytes. This demonstrates that some mitochondrial mRNA processing events diverged with the split between chlorophytic and streptophytic algae.
Collapse
Affiliation(s)
- Grayson C. R. Proulex
- Department of Natural Sciences, The University of Virginia’s College at Wise, 1 College Ave., Wise, VA 24293, USA; (G.C.R.P.); (M.J.M.)
| | - Marcus J. Meade
- Department of Natural Sciences, The University of Virginia’s College at Wise, 1 College Ave., Wise, VA 24293, USA; (G.C.R.P.); (M.J.M.)
| | - Kalina M. Manoylov
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA 31061, USA;
| | - A. Bruce Cahoon
- Department of Natural Sciences, The University of Virginia’s College at Wise, 1 College Ave., Wise, VA 24293, USA; (G.C.R.P.); (M.J.M.)
| |
Collapse
|
8
|
Durand S, Ricou A, Simon M, Dehaene N, Budar F, Camilleri C. A restorer-of-fertility-like pentatricopeptide repeat protein promotes cytoplasmic male sterility in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:124-135. [PMID: 33098690 DOI: 10.1111/tpj.15045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins form a large family of proteins targeted to organelles, where they post-transcriptionally modulate gene expression through binding to specific RNA sequences. Among them, the mitochondria-targeted restorer-of-fertility (Rf) PPRs inhibit peculiar mitochondrial genes that are detrimental to male gametes and cause cytoplasmic male sterility (CMS). Here, we revealed three nuclear loci involved in CMS in a cross between two distant Arabidopsis thaliana strains, Sha and Cvi-0. We identified the causal gene at one of these loci as RFL24, a conserved gene encoding a PPR protein related to known Rf PPRs. By analysing fertile revertants obtained in a male sterile background, we demonstrate that RFL24 promotes pollen abortion, in contrast with the previously described Rf PPRs, which allow pollen to survive in the presence of a sterilizing cytoplasm. We show that the sterility caused by the RFL24 Cvi-0 allele results from higher expression of the gene during early pollen development. Finally, we predict a binding site for RFL24 upstream of two mitochondrial genes, the CMS gene and the important gene cob. These results suggest that the conservation of RFL24 is linked to a primary role of ensuring a proper functioning of mitochondria, and that it was subsequently diverted by the CMS gene to its benefit.
Collapse
Affiliation(s)
- Stéphanie Durand
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Anthony Ricou
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Matthieu Simon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Noémie Dehaene
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
- Univ. Paris-Sud, Université Paris-Saclay, Orsay, 91405, France
| | - Françoise Budar
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Christine Camilleri
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| |
Collapse
|
9
|
Wang C, Aubé F, Planchard N, Quadrado M, Dargel-Graffin C, Nogué F, Mireau H. The pentatricopeptide repeat protein MTSF2 stabilizes a nad1 precursor transcript and defines the 3΄ end of its 5΄-half intron. Nucleic Acids Res 2017; 45:6119-6134. [PMID: 28334831 PMCID: PMC5449624 DOI: 10.1093/nar/gkx162] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/28/2017] [Indexed: 12/14/2022] Open
Abstract
RNA expression in plant mitochondria implies a large number of post-transcriptional events in which transcript processing and stabilization are essential. In this study, we analyzed the function of the Arabidopsis mitochondrial stability factor 2 gene (MTSF2) and show that the encoded pentatricopeptide repeat protein is essential for the accumulation of stable nad1 mRNA. The production of mature nad1 requires the assembly of three independent RNA precursors via two trans-splicing reactions. Genetic analyses revealed that the lack of nad1 in mtsf2 mutants results from the specific destabilization of the nad1 exons 2-3 precursor transcript. We further demonstrated that MTSF2 binds to its 3΄ extremity with high affinity, suggesting a protective action by blocking exoribonuclease progression. By defining the 3΄ end of nad1 exons 2-3 precursor, MTSF2 concomitantly determines the 3΄ extremity of the first half of the trans-intron found at the end of the transcript. Therefore, binding of the MTSF2 protein to nad1 exons 2-3 precursor evolved both to stabilize the transcript and to define a 3΄ extremity compatible with the trans-splicing reaction needed to reconstitute mature nad1. We thus reveal that the range of transcripts stabilized by association with protective protein on their 3΄ end concerns also mitochondrial precursor transcripts.
Collapse
Affiliation(s)
- Chuande Wang
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- Paris-Sud University, Université Paris-Saclay, 91405 Orsay Cedex, France
- These authors contributed equally to the paper as first authors
| | - Fabien Aubé
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- These authors contributed equally to the paper as first authors
| | - Noelya Planchard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- Paris-Sud University, Université Paris-Saclay, 91405 Orsay Cedex, France
- These authors contributed equally to the paper as first authors
| | - Martine Quadrado
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Céline Dargel-Graffin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- To whom correspondence should be addressed. Tel: +33 130 833 070; Fax: +33 130 833 319;
| |
Collapse
|
10
|
Liu Z, Dong F, Wang X, Wang T, Su R, Hong D, Yang G. A pentatricopeptide repeat protein restores nap cytoplasmic male sterility in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4115-4123. [PMID: 28922764 PMCID: PMC5853434 DOI: 10.1093/jxb/erx239] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/19/2017] [Indexed: 05/20/2023]
Abstract
Two forms of male-sterile cytoplasm, designated nap and pol, are found in the oilseed rape species, Brassica napus. The nap cytoplasm is observed in most B. napus varieties, and it confers male sterility on a limited number of cultivars that lack the corresponding restorer gene, Rfn. In the present study, using linkage analysis in combination with 5652 BC1 progeny derived from a cross between a nap cytoplasmic male sterility (CMS) line 181A and a restorer line H5, we delimited the Rfn gene to a 10.5 kb region on chromosome A09, which contained three putative ORFs. Complementation by transformation rescue revealed that the introduction of ORF2, which encodes a pentatricopeptide repeat (PPR) protein, resulted in the recovery of fertility of nap CMS plants. Expression analysis suggested that the Rfn was highly expressed in flower buds and it was preferentially expressed in the tapetum and meiocytes during anther development. Further RNA gel blots and immunodetection suggested that the Rfn gene may play a complicated role in restoring the nap CMS. Our work laid the foundation for dissecting the molecular basis of CMS fertility restoration and the nuclear-mitochondrial interactions in CMS/Rf systems.
Collapse
Affiliation(s)
- Zhi Liu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- National Research Center of Rapeseed Engineering and Technology, National Rapeseed Genetic Improvement Center (Wuhan Branch), Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Faming Dong
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- National Research Center of Rapeseed Engineering and Technology, National Rapeseed Genetic Improvement Center (Wuhan Branch), Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Xiang Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Tao Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Rui Su
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Dengfeng Hong
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- National Research Center of Rapeseed Engineering and Technology, National Rapeseed Genetic Improvement Center (Wuhan Branch), Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Guangsheng Yang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, PR China
- National Research Center of Rapeseed Engineering and Technology, National Rapeseed Genetic Improvement Center (Wuhan Branch), Huazhong Agricultural University, Wuhan, PR China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
- Correspondence:
| |
Collapse
|
11
|
Stoll K, Jonietz C, Schleicher S, des Francs-Small CC, Small I, Binder S. In Arabidopsis thaliana distinct alleles encoding mitochondrial RNA PROCESSING FACTOR 4 support the generation of additional 5' termini of ccmB transcripts. PLANT MOLECULAR BIOLOGY 2017; 93:659-668. [PMID: 28229269 DOI: 10.1007/s11103-017-0591-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
In plant mitochondria, the 5' ends of many transcripts are generated post-transcriptionally. We show that the pentatricopeptide repeat (PPR) protein RNA PROCESSING FACTOR 4 (RPF4) supports the generation of extra 5' ends of ccmB transcripts in Landsberg erecta (Ler) and a number of other Arabidopsis thaliana ecotypes. RPF4 was identified in Ler applying a forward genetic approach supported by complementation studies of ecotype Columbia (Col), which generates the Ler-type extra ccmB 5' termini only after the introduction of the RPF4 allele from Ler. Studies with chimeric RPF4 proteins composed of various parts of the RPF4 proteins from Ler and Col identified differences in the N-terminal and central PPR motifs that explain ecotype-specific variations in ccmB processing. These results fit well with binding site predictions in ccmB transcripts based on the known determinants of nucleotide base recognition by PPR motifs.
Collapse
Affiliation(s)
- Katrin Stoll
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Christian Jonietz
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Sarah Schleicher
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | - Catherine Colas des Francs-Small
- Australian Research Council 40 Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian Small
- Australian Research Council 40 Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany.
| |
Collapse
|
12
|
Zhang H, Wu J, Dai Z, Qin M, Hao L, Ren Y, Li Q, Zhang L. Allelism analysis of BrRfp locus in different restorer lines and map-based cloning of a fertility restorer gene, BrRfp1, for pol CMS in Chinese cabbage (Brassica rapa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:539-547. [PMID: 27896366 DOI: 10.1007/s00122-016-2833-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 11/18/2016] [Indexed: 05/22/2023]
Abstract
In Chinese cabbage, there are two Rf loci for pol CMS and one of them was mapped to a 12.6-kb region containing a potential candidate gene encoding PPR protein. In Chinese cabbage (Brassica rapa), polima cytoplasmic male sterility (pol CMS) is an important CMS type and is widely used for hybrid breeding. By extensive test crossing in Chinese cabbage, four restorer lines (92s105, 01s325, 00s109, and 88s148) for pol CMS were screened. By analyzing the allelism of the four restorer lines, it was found that 92s105, 01s325, and 00s109 had the same "restorers of fertility" (Rf) locus (designated as BrRfp1), but 88s148 had a different Rf locus (designated as BrRfp2). For fine mapping the BrRfp1 locus of 92s105, a BC1F1 population with 487 individuals and a BC1F2 population with 2485 individuals were successively constructed. Using simple sequence repeat (SSR) markers developed from Brassica rapa reference genome and InDel markers derived from whole-genome resequencing data of 94c9 and 92s105, BrRfp1 was mapped to a 12.6-kb region containing a potential candidate gene encoding pentatricopeptide repeat-containing protein. Based on the nucleotide polymorphisms of the candidate gene sequence between the restoring and nonrestoring alleles, a co-segregating marker SC718 was developed, which would be helpful for hybrid breeding by marker-assisted screening and for detecting new restorer lines.
Collapse
Affiliation(s)
- Huamin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Junqing Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zihui Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Meiling Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lingyu Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanjing Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingfei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lugang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
13
|
Binder S, Stoll K, Stoll B. Maturation of 5' ends of plant mitochondrial RNAs. PHYSIOLOGIA PLANTARUM 2016; 157:280-8. [PMID: 26833432 DOI: 10.1111/ppl.12423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 05/26/2023]
Abstract
The generation of mature RNAs, i.e. mRNAs, rRNAs or tRNAs, is a complex process in all genetic systems. RNA-internal processes such as splicing or RNA editing, but also posttranscriptional processes modulating 5' and 3' termini of transcripts, contribute to RNA maturation. In this article, we focus on the posttranscriptional formation of 5' termini of mitochondrial RNAs in seed plants, with particular emphasis on the model plant species Arabidopsis thaliana (Arabidopsis). We will summarize the progress made in recent studies of proteins involved in this process. In addition, we will evaluate whether 5' processing proceeds endo- or exo-nucleolytically. Despite the considerable progress made, many details of this process remain unsolved. In particular, it is still unclear why there is frequent 5' processing of many mRNAs although impaired processing does not interfere with mitochondrial function and plant fitness. Thus, the importance of 5' processing for plant mitochondria is still puzzling.
Collapse
Affiliation(s)
- Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
| | - Katrin Stoll
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
| | - Birgit Stoll
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
| |
Collapse
|
14
|
Fujii S, Suzuki T, Giegé P, Higashiyama T, Koizuka N, Shikanai T. The Restorer-of-fertility-like 2 pentatricopeptide repeat protein and RNase P are required for the processing of mitochondrial orf291 RNA in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:504-13. [PMID: 27122350 DOI: 10.1111/tpj.13185] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/14/2016] [Indexed: 05/27/2023]
Abstract
Eukaryotes harbor mitochondria obtained via ancient symbiosis events. The successful evolution of energy production in mitochondria has been dependent on the control of mitochondrial gene expression by the nucleus. In flowering plants, the nuclear-encoded pentatricopeptide repeat (PPR) superfamily proteins are widely involved in mitochondrial RNA metabolism. Here, we show that an Arabidopsis nuclear-encoded RNA-binding protein, Restorer-of-fertility-like PPR protein 2 (RFL2), is required for RNA degradation of the mitochondrial orf291 transcript via endonucleolytic cleavage of the transcript in the middle of its reading frame. Both in vivo and in vitro, this RNA cleavage requires the activity of mitochondrial proteinaceous RNase P, which is possibly recruited to the site by RFL2. The site of RNase P cleavage likely forms a tRNA-like structure in the orf291 transcript. This study presents an example of functional collaboration between a PPR protein and an endonuclease in RNA cleavage. Furthermore, we show that the RFL2-binding region within the orf291 gene is hypervariable in the family Brassicaceae, possibly correlated with the rapid evolution of the RNA-recognition interfaces of the RFL proteins.
Collapse
Affiliation(s)
- Sota Fujii
- Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Takamasa Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Japan Science and Technology Agency, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, 12 Rue du Général Zimmer, Strasbourg, 67084, France
| | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Japan Science and Technology Agency, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- WPI-ITbM, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Nobuya Koizuka
- Faculty of Agriculture, Tamagawa University, 6-1-1 Tamagawa-Gakuen, Machida, Tokyo, 194-8610, Japan
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0076, Japan
| |
Collapse
|
15
|
Gaborieau L, Brown GG, Mireau H. The Propensity of Pentatricopeptide Repeat Genes to Evolve into Restorers of Cytoplasmic Male Sterility. FRONTIERS IN PLANT SCIENCE 2016; 7:1816. [PMID: 27999582 PMCID: PMC5138203 DOI: 10.3389/fpls.2016.01816] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/17/2016] [Indexed: 05/18/2023]
Abstract
Cytoplasmic male sterility (CMS) is a widespread phenotype in plants, which present a defect in the production of functional pollen. The male sterilizing factors usually consist of unusual genes or open reading frames encoded by the mitochondrial genome. CMS can be suppressed by specific nuclear genes called restorers of fertility (Rfs). In the majority of cases, Rf genes produce proteins that act directly on the CMS conferring mitochondrial transcripts by binding them specifically and promoting processing events. In this review, we explore the wide array of mechanisms guiding fertility restoration. PPR proteins represent the most frequent protein class among identified Rfs and they exhibit ideal characteristics to evolve into restorer of fertility when the mechanism of restoration implies a post-transcriptional action. Here, we review the literature that highlights those characteristics and help explain why PPR proteins are ideal for the roles they play as restorers of fertility.
Collapse
Affiliation(s)
| | | | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
- *Correspondence: Hakim Mireau,
| |
Collapse
|
16
|
Stoll B, Binder S. Two NYN domain containing putative nucleases are involved in transcript maturation in Arabidopsis mitochondria. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:278-288. [PMID: 26711866 DOI: 10.1111/tpj.13111] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/11/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
Plant mitochondrial transcripts frequently undergo maturation processes at their 5' ends. This almost completely enigmatic process requires the function of several proteins such as RNA processing factors, which are selectively involved in distinct 5' processing events. As RNA processing factors represent pentatricopeptide repeat proteins without apparent enzymatic function, it is hypothesized that a ribonuclease, most likely with endonucleolytic activity is involved in the 5' end maturation. We have now applied a reverse genetic approach to analyze the role of two potential mitochondrial nucleases, MNU1 and MNU2, in Arabidopsis thaliana. Both proteins contain several RNA-binding domains and NYN domains found in other endonucleases. A thorough analysis of various mitochondrial transcripts in MNU1 and MNU2 mutants revealed aberrant transcript pattern characterized by a decrease in mature RNA species often accompanied by an accumulation of larger, 5' extended precursor molecules. In addition, severely reduced amounts of nad9 mRNAs in the rpf2-1/mnu2-1 double mutant indicate a corporate function of RNA processing factor 2 and MNU2 in the maturation of these transcripts. However, the dramatic reduction of the nad9 mRNA is not reflected by the level of the corresponding Nad9 protein, which is found to be only moderately lowered. Collectively, our analysis strongly suggests a function of MNU1 and MNU2 in 5' processing of plant mitochondrial transcripts.
Collapse
Affiliation(s)
- Birgit Stoll
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
| | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Ulm, D-89069, Germany
| |
Collapse
|
17
|
Stoll B, Zendler D, Binder S. RNA processing factor 7 and polynucleotide phosphorylase are necessary for processing and stability of nad2 mRNA in Arabidopsis mitochondria. RNA Biol 2014; 11:968-76. [PMID: 25181358 DOI: 10.4161/rna.29781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Post-transcriptional maturation of plant mitochondrial transcripts requires several steps. Among these, the generation of mature 5' ends is still one of the most enigmatic processes. Toward a characterization of proteins involved in 5' processing of mitochondrial transcripts in Arabidopsis (Arabidopsis thaliana), we now analyzed 5' maturation of nad2 transcripts. Based on natural genetic variation affecting 5' ends of nad2 transcripts in ecotype Can-0 and complementation studies we now identified RNA processing factor 7, which takes part in the generation of the 5' terminus of the mature nad2 mRNA. RPF7 is a relatively short regular P-class pentatricopeptide repeat protein comprising seven canonical P repeats and a single short S repeat. The corresponding allele in Can-0 encodes a truncated version of this protein lacking two C-terminal repeats, which are essential for the function of RPF7. Furthermore we established transgenic plants expressing artifical microRNAs targeting the mitochondrial polynucleotide phosphorylase (PNPase), which results in substantial reduction of the PNPase mRNA levels and strong knockdown of this gene. Detailed quantitative studies of 5' and 3' extended nad2 precursor RNAs in these knockdown plants as well as in the rpf7-1 knockout mutant suggest that 5' processing contributes to the stability of mitochondrial transcripts in plants.
Collapse
Affiliation(s)
- Birgit Stoll
- Institut Molekulare Botanik, Universität Ulm, Germany
| | | | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Germany
| |
Collapse
|