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Timcheva K, Dufour S, Touat-Todeschini L, Burnard C, Carpentier MC, Chuffart F, Merret R, Helsmoortel M, Ferré S, Grézy A, Couté Y, Rousseaux S, Khochbin S, Vourc'h C, Bousquet-Antonelli C, Kiernan R, Seigneurin-Berny D, Verdel A. Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression. Cell Rep 2022; 41:111784. [PMID: 36516773 DOI: 10.1016/j.celrep.2022.111784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/01/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Heat stress (HS) induces a cellular response leading to profound changes in gene expression. Here, we show that human YTHDC1, a reader of N6-methyladenosine (m6A) RNA modification, mostly associates to the chromatin fraction and that HS induces a redistribution of YTHDC1 across the genome, including to heat-induced heat shock protein (HSP) genes. YTHDC1 binding to m6A-modified HSP transcripts co-transcriptionally promotes expression of HSPs. In parallel, hundreds of the genes enriched in YTHDC1 during HS have their transcripts undergoing YTHDC1- and m6A-dependent intron retention. Later, YTHDC1 concentrates within nuclear stress bodies (nSBs) where it binds to m6A-modified SATIII non-coding RNAs, produced in an HSF1-dependent manner upon HS. These findings reveal that YTHDC1 plays a central role in a chromatin-associated m6A-based reprogramming of gene expression during HS. Furthermore, they support the model where the subsequent and temporary sequestration of YTHDC1 within nSBs calibrates the timing of this YTHDC1-dependent gene expression reprogramming.
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Affiliation(s)
- Kalina Timcheva
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Solenne Dufour
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Leila Touat-Todeschini
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Callum Burnard
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Marie-Christine Carpentier
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Florent Chuffart
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Rémy Merret
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Marion Helsmoortel
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Sabrina Ferré
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Aude Grézy
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Yohann Couté
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Sophie Rousseaux
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Saadi Khochbin
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Claire Vourc'h
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Cécile Bousquet-Antonelli
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Rosemary Kiernan
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Daphné Seigneurin-Berny
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
| | - André Verdel
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
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Abstract
RNA binding proteins, through control of mRNA fate and expression, are key players of organism development. The LARP family of RBPs sharing the La motif, are largely present in eukaryotes. They classify into five subfamilies which members acquired specific additional domains, including the RRM1 moiety which teams up with the La motif to form a versatile RNA binding unit. The LARP6 subfamily has had a peculiar history during plant evolution. While containing a single LARP6 in algae and non-vascular plants, they expanded and neofunctionalized into three subclusters in vascular plants. Studies from Arabidopsis thaliana, support that they acquired specific RNA binding properties and physiological roles. In particular LARP6C participates, through spatiotemporal control of translation, to male fertilization, a role seemingly conserved in maize. Interestingly, human LARP6 also acts in translation control and mRNA transport and similarly to LARP6C which is required for pollen tube guided elongation, is necessary to cell migration, through protrusion extension. This opens the possibility that some cellular and molecular functions of LARP6 were retained across eukaryote evolution. With their peculiar evolutionary history, plants provide a unique opportunity to uncover how La-module RNA binding properties evolved and identify species specific and basal roles of the LARP6 function. Deciphering of how LARP6, in particular LARP6C, acts at the molecular level, will foster novel knowledge on translation regulation and dynamics in changing cellular contexts. Considering the seemingly conserved function of LARP6C in male reproduction, it should fuel studies aimed at deriving crop species with improved seed yields.
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Affiliation(s)
- Cécile Bousquet-Antonelli
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France
- Université de Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France
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3
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Billey E, Hafidh S, Cruz-Gallardo I, Litholdo CG, Jean V, Carpentier MC, Picart C, Kumar V, Kulichova K, Maréchal E, Honys D, Conte MR, Deragon JM, Bousquet-Antonelli C. LARP6C orchestrates posttranscriptional reprogramming of gene expression during hydration to promote pollen tube guidance. Plant Cell 2021; 33:2637-2661. [PMID: 34124761 DOI: 10.1101/2020.11.27.401307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/06/2021] [Indexed: 05/19/2023]
Abstract
Increasing evidence suggests that posttranscriptional regulation is a key player in the transition between mature pollen and the progamic phase (from pollination to fertilization). Nonetheless, the actors in this messenger RNA (mRNA)-based gene expression reprogramming are poorly understood. We demonstrate that the evolutionarily conserved RNA-binding protein LARP6C is necessary for the transition from dry pollen to pollen tubes and the guided growth of pollen tubes towards the ovule in Arabidopsis thaliana. In dry pollen, LARP6C binds to transcripts encoding proteins that function in lipid synthesis and homeostasis, vesicular trafficking, and polarized cell growth. LARP6C also forms cytoplasmic granules that contain the poly(A) binding protein and possibly represent storage sites for translationally silent mRNAs. In pollen tubes, the loss of LARP6C negatively affects the quantities and distribution of storage lipids, as well as vesicular trafficking. In Nicotiana benthamiana leaf cells and in planta, analysis of reporter mRNAs designed from the LARP6C target MGD2 provided evidence that LARP6C can shift from a repressor to an activator of translation when the pollen grain enters the progamic phase. We propose that LARP6C orchestrates the timely posttranscriptional regulation of a subset of mRNAs in pollen during the transition from the quiescent to active state and along the progamic phase to promote male fertilization in plants.
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Affiliation(s)
- Elodie Billey
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Celso G Litholdo
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Viviane Jean
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Katarina Kulichova
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS, CEA, INRAE, Université Grenoble Alpes, IRIG, CEA Grenoble, 38054 Grenoble, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Jean-Marc Deragon
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Institut Universitaire de France, 75231 Paris Cedex 5, France
| | - Cécile Bousquet-Antonelli
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
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Billey E, Hafidh S, Cruz-Gallardo I, Litholdo CG, Jean V, Carpentier MC, Picart C, Kumar V, Kulichova K, Maréchal E, Honys D, Conte MR, Deragon JM, Bousquet-Antonelli C. LARP6C orchestrates posttranscriptional reprogramming of gene expression during hydration to promote pollen tube guidance. Plant Cell 2021; 33:2637-2661. [PMID: 34124761 PMCID: PMC8408461 DOI: 10.1093/plcell/koab131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/06/2021] [Indexed: 05/15/2023]
Abstract
Increasing evidence suggests that posttranscriptional regulation is a key player in the transition between mature pollen and the progamic phase (from pollination to fertilization). Nonetheless, the actors in this messenger RNA (mRNA)-based gene expression reprogramming are poorly understood. We demonstrate that the evolutionarily conserved RNA-binding protein LARP6C is necessary for the transition from dry pollen to pollen tubes and the guided growth of pollen tubes towards the ovule in Arabidopsis thaliana. In dry pollen, LARP6C binds to transcripts encoding proteins that function in lipid synthesis and homeostasis, vesicular trafficking, and polarized cell growth. LARP6C also forms cytoplasmic granules that contain the poly(A) binding protein and possibly represent storage sites for translationally silent mRNAs. In pollen tubes, the loss of LARP6C negatively affects the quantities and distribution of storage lipids, as well as vesicular trafficking. In Nicotiana benthamiana leaf cells and in planta, analysis of reporter mRNAs designed from the LARP6C target MGD2 provided evidence that LARP6C can shift from a repressor to an activator of translation when the pollen grain enters the progamic phase. We propose that LARP6C orchestrates the timely posttranscriptional regulation of a subset of mRNAs in pollen during the transition from the quiescent to active state and along the progamic phase to promote male fertilization in plants.
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Affiliation(s)
- Elodie Billey
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Celso G. Litholdo
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Viviane Jean
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Katarina Kulichova
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS, CEA, INRAE, Université Grenoble Alpes, IRIG, CEA Grenoble, 38054 Grenoble, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Jean-Marc Deragon
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Institut Universitaire de France, 75231 Paris Cedex 5, France
| | - Cécile Bousquet-Antonelli
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
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Carpentier MC, Bousquet-Antonelli C, Merret R. Fast and Efficient 5'P Degradome Library Preparation for Analysis of Co-Translational Decay in Arabidopsis. Plants (Basel) 2021; 10:plants10030466. [PMID: 33804539 PMCID: PMC7998949 DOI: 10.3390/plants10030466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022]
Abstract
The recent development of high-throughput technologies based on RNA sequencing has allowed a better description of the role of post-transcriptional regulation in gene expression. In particular, the development of degradome approaches based on the capture of 5′monophosphate decay intermediates allows the discovery of a new decay pathway called co-translational mRNA decay. Thanks to these approaches, ribosome dynamics could now be revealed by analysis of 5′P reads accumulation. However, library preparation could be difficult to set-up for non-specialists. Here, we present a fast and efficient 5′P degradome library preparation for Arabidopsis samples. Our protocol was designed without commercial kit and gel purification and can be easily done in one working day. We demonstrated the robustness and the reproducibility of our protocol. Finally, we present the bioinformatic reads-outs necessary to assess library quality control.
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Affiliation(s)
- Marie-Christine Carpentier
- CNRS-LGDP UMR 5096, 58 avenue Paul Alduy, 66860 Perpignan, France; (M.-C.C.); (C.B.-A.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 58 avenue Paul Alduy, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- CNRS-LGDP UMR 5096, 58 avenue Paul Alduy, 66860 Perpignan, France; (M.-C.C.); (C.B.-A.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 58 avenue Paul Alduy, 66860 Perpignan, France
| | - Rémy Merret
- CNRS-LGDP UMR 5096, 58 avenue Paul Alduy, 66860 Perpignan, France; (M.-C.C.); (C.B.-A.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 58 avenue Paul Alduy, 66860 Perpignan, France
- Correspondence:
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Náprstková A, Malínská K, Záveská Drábková L, Billey E, Náprstková D, Sýkorová E, Bousquet-Antonelli C, Honys D. Characterization of ALBA Family Expression and Localization in Arabidopsis thaliana Generative Organs. Int J Mol Sci 2021; 22:1652. [PMID: 33562109 PMCID: PMC7914821 DOI: 10.3390/ijms22041652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
ALBA DNA/RNA-binding proteins form an ancient family, which in eukaryotes diversified into two Rpp25-like and Rpp20-like subfamilies. In most studied model organisms, their function remains unclear, but they are usually associated with RNA metabolism, mRNA translatability and stress response. In plants, the enriched number of ALBA family members remains poorly understood. Here, we studied ALBA dynamics during reproductive development in Arabidopsis at the levels of gene expression and protein localization, both under standard conditions and following heat stress. In generative tissues, ALBA proteins showed the strongest signal in mature pollen where they localized predominantly in cytoplasmic foci, particularly in regions surrounding the vegetative nucleus and sperm cells. Finally, we demonstrated the involvement of two Rpp25-like subfamily members ALBA4 and ALBA6 in RNA metabolism in mature pollen supported by their co-localization with poly(A)-binding protein 3 (PABP3). Collectively, we demonstrated the engagement of ALBA proteins in male reproductive development and the heat stress response, highlighting the involvement of ALBA4 and ALBA6 in RNA metabolism, storage and/or translational control in pollen upon heat stress. Such dynamic re-localization of ALBA proteins in a controlled, developmentally and environmentally regulated manner, likely reflects not only their redundancy but also their possible functional diversification in plants.
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Affiliation(s)
- Alena Náprstková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Kateřina Malínská
- Imaging Facility, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic;
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Elodie Billey
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; (E.B.); (C.B.-A.)
- LGDP-UMR5096, Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Dagmar Náprstková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Eva Sýkorová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská, 612 00 Brno, Czech Republic;
| | - Cécile Bousquet-Antonelli
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; (E.B.); (C.B.-A.)
- LGDP-UMR5096, Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
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Carpentier MC, Deragon JM, Jean V, Be SHV, Bousquet-Antonelli C, Merret R. Monitoring of XRN4 Targets Reveals the Importance of Cotranslational Decay during Arabidopsis Development. Plant Physiol 2020; 184:1251-1262. [PMID: 32913043 PMCID: PMC7608176 DOI: 10.1104/pp.20.00942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/02/2020] [Indexed: 05/31/2023]
Abstract
RNA turnover is a general process that maintains appropriate mRNA abundance at the posttranscriptional level. Although long thought to be antagonistic to translation, discovery of the 5' to 3' cotranslational mRNA decay pathway demonstrated that both processes are intertwined. Cotranslational mRNA decay globally shapes the transcriptome in different organisms and in response to stress; however, the dynamics of this process during plant development is poorly understood. In this study, we used a multiomics approach to reveal the global landscape of cotranslational mRNA decay during Arabidopsis (Arabidopsis thaliana) seedling development. We demonstrated that cotranslational mRNA decay is regulated by developmental cues. Using the EXORIBONUCLEASE4 (XRN4) loss-of-function mutant, we showed that XRN4 poly(A+) mRNA targets are largely subject to cotranslational decay during plant development. As cotranslational mRNA decay is interconnected with translation, we also assessed its role in translation efficiency. We discovered that clusters of transcripts were specifically subjected to cotranslational decay in a developmental-dependent manner to modulate their translation efficiency. Our approach allowed the determination of a cotranslational decay efficiency that could be an alternative to other methods to assess transcript translation efficiency. Thus, our results demonstrate the prevalence of cotranslational mRNA decay in plant development and its role in translational control.
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Affiliation(s)
- Marie-Christine Carpentier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
| | - Jean-Marc Deragon
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
- Institut Universitaire de France, 75231 Paris cedex 05, France
| | - Viviane Jean
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
| | - Seng Hour Vichet Be
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
| | - Rémy Merret
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
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Merret R, Bousquet-Antonelli C. Immunity gate-keepers. Nat Plants 2020; 6:608-609. [PMID: 32483331 DOI: 10.1038/s41477-020-0679-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Rémy Merret
- CNRS-UMR5096, Plant Genome and Development Laboratory, Perpignan, France
- UPVD-UMR5096, Plant Genome and Development Laboratory, Perpignan, France
| | - Cécile Bousquet-Antonelli
- CNRS-UMR5096, Plant Genome and Development Laboratory, Perpignan, France.
- UPVD-UMR5096, Plant Genome and Development Laboratory, Perpignan, France.
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9
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Berlivet S, Scutenaire J, Deragon JM, Bousquet-Antonelli C. Readers of the m 6A epitranscriptomic code. Biochim Biophys Acta Gene Regul Mech 2019; 1862:329-342. [PMID: 30660758 DOI: 10.1016/j.bbagrm.2018.12.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 12/20/2018] [Accepted: 12/28/2018] [Indexed: 12/21/2022]
Abstract
N6-methyl adenosine (m6A) is the most prevalent and evolutionarily conserved, modification of polymerase II transcribed RNAs. By post-transcriptionally controlling patterns of gene expression, m6A deposition is crucial for organism reproduction, development and likely stress responses. m6A mostly mediates its effect by recruiting reader proteins that either directly accommodate the modified residue in a hydrophobic pocket formed by their YTH domain, or otherwise have their affinity positively influenced by the presence of m6A. We firstly describe here the evolutionary history, and review known molecular and physiological roles of eukaryote YTH readers. In the second part, we present non YTH-proteins whose roles as m6A readers largely remain to be explored. The diversity and multiplicity of m6A readers together with the possibility to regulate their expression and function in response to various cues, offers a multitude of possible combinations to rapidly and finely tune gene expression patterns and hence cellular plasticity. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Soizik Berlivet
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France
| | - Jérémy Scutenaire
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France
| | - Jean-Marc Deragon
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France; Institut Universitaire de France (IUF), 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Cécile Bousquet-Antonelli
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France.
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10
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Scutenaire J, Deragon JM, Jean V, Benhamed M, Raynaud C, Favory JJ, Merret R, Bousquet-Antonelli C. The YTH Domain Protein ECT2 Is an m 6A Reader Required for Normal Trichome Branching in Arabidopsis. Plant Cell 2018; 30:986-1005. [PMID: 29618631 PMCID: PMC6002185 DOI: 10.1105/tpc.17.00854] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/01/2018] [Accepted: 04/04/2018] [Indexed: 05/14/2023]
Abstract
Methylations at position N6 of internal adenosines (m6As) are the most abundant and widespread mRNA modifications. These modifications play crucial roles in reproduction, growth, and development by controlling gene expression patterns at the posttranscriptional level. Their function is decoded by readers that share the YTH domain, which forms a hydrophobic pocket that directly accommodates the m6A residues. While the physiological and molecular functions of YTH readers have been extensively studied in animals, little is known about plant readers, even though m6As are crucial for plant survival and development. Viridiplantae contains high numbers of YTH domain proteins. Here, we performed comprehensive evolutionary analysis of YTH domain proteins and demonstrated that they are highly likely to be actual readers with redundant as well as specific functions. We also show that the ECT2 protein from Arabidopsis thaliana binds to m6A-containing RNAs in vivo and that this property relies on the m6A binding pocket carried by its YTH domain. ECT2 is cytoplasmic and relocates to stress granules upon heat exposure, suggesting that it controls mRNA fate in the cytosol. Finally, we demonstrate that ECT2 acts to decode the m6A signal in the trichome and is required for their normal branching through controlling their ploidy levels.
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Affiliation(s)
- Jérémy Scutenaire
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Jean-Marc Deragon
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Institut Universitaire de France, 75231 Paris Cedex 05, France
| | - Viviane Jean
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Moussa Benhamed
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Jean-Jacques Favory
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Rémy Merret
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- LGDP-UMR5096, CNRS, 66860 Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
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11
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Merret R, Carpentier MC, Favory JJ, Picart C, Descombin J, Bousquet-Antonelli C, Tillard P, Lejay L, Deragon JM, Charng YY. Heat Shock Protein HSP101 Affects the Release of Ribosomal Protein mRNAs for Recovery after Heat Shock. Plant Physiol 2017; 174:1216-1225. [PMID: 28381501 PMCID: PMC5462041 DOI: 10.1104/pp.17.00269] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/03/2017] [Indexed: 05/21/2023]
Abstract
Heat shock (HS) is known to have a profound impact on gene expression at different levels, such as inhibition of protein synthesis, in which HS blocks translation initiation and induces the sequestration of mRNAs into stress granules (SGs) or P-bodies for storage and/or decay. SGs prevent the degradation of the stored mRNAs, which can be reengaged into translation in the recovery period. However, little is known on the mRNAs stored during the stress, how these mRNAs are released from SGs afterward, and what the functional importance is of this process. In this work, we report that Arabidopsis HEAT SHOCK PROTEIN101 (HSP101) knockout mutant (hsp101) presented a defect in translation recovery and SG dissociation after HS Using RNA sequencing and RNA immunoprecipitation approaches, we show that mRNAs encoding ribosomal proteins (RPs) were preferentially stored during HS and that these mRNAs were released and translated in an HSP101-dependent manner during recovery. By 15N incorporation and polysome profile analyses, we observed that these released mRNAs contributed to the production of new ribosomes to enhance translation. We propose that, after HS, HSP101 is required for the efficient release of RP mRNAs from SGs resulting in a rapid restoration of the translation machinery by producing new RPs.
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Affiliation(s)
- Rémy Merret
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.);
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.);
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.);
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Marie-Christine Carpentier
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Jean-Jacques Favory
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Claire Picart
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Julie Descombin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Cécile Bousquet-Antonelli
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Pascal Tillard
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Laurence Lejay
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Jean-Marc Deragon
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.)
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.)
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
| | - Yee-Yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529, Republic of China (R.M., Y.-y.C.);
- CNRS-LGDP UMR 5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.);
- Université de Perpignan Via Domitia, LGDP-UMR5096, 66860 Perpignan, France (R.M., M.-C.C., J.-J.F., C.P., J.D., C.B.-A., J.-M.D.);
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon,' UMR CNRS/INRA/SupAgro/UM2, 34060 Montpellier cedex, France (P.T., L.L.); and
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris cedex 05, France (J.-M.D.)
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12
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Clavel M, Pélissier T, Montavon T, Tschopp MA, Pouch-Pélissier MN, Descombin J, Jean V, Dunoyer P, Bousquet-Antonelli C, Deragon JM. Evolutionary history of double-stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis. Plant Mol Biol 2016; 91:131-47. [PMID: 26858002 DOI: 10.1007/s11103-016-0448-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/03/2016] [Indexed: 05/27/2023]
Abstract
In this work, we retrace the evolutionary history of plant double-stranded RNA binding proteins (DRBs), a group of non-catalytic factors containing one or more double-stranded RNA binding motif (dsRBM) that play important roles in small RNA biogenesis and functions. Using a phylogenetic approach, we show that multiple dsRBM DRBs are systematically composed of two different types of dsRBMs evolving under different constraints and likely fulfilling complementary functions. In vascular plants, four distinct clades of multiple dsRBM DRBs are always present with the exception of Brassicaceae species, that do not possess member of the newly identified clade we named DRB6. We also identified a second new and highly conserved DRB family (we named DRB7) whose members possess a single dsRBM that shows concerted evolution with the most C-terminal dsRBM domain of the Dicer-like 4 (DCL4) proteins. Using a BiFC approach, we observed that Arabidopsis thaliana DRB7.2 (AtDRB7.2) can directly interact with AtDRB4 but not with AtDCL4 and we provide evidence that both AtDRB7.2 and AtDRB4 participate in the epigenetically activated siRNAs pathway.
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Affiliation(s)
- Marion Clavel
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Thierry Pélissier
- UMR 6293 CNRS - INSERM U1103 - GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171, Aubière Cedex, France
| | - Thomas Montavon
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Marie-Aude Tschopp
- Department of Biology LFW D17/D18, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Marie-Noëlle Pouch-Pélissier
- UMR 6293 CNRS - INSERM U1103 - GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171, Aubière Cedex, France
| | - Julie Descombin
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Viviane Jean
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Patrice Dunoyer
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Cécile Bousquet-Antonelli
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Jean-Marc Deragon
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
- CNRS UMR5096 LGDP, Perpignan Cedex, France.
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13
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Lahr RM, Mack SM, Héroux A, Blagden SP, Bousquet-Antonelli C, Deragon JM, Berman AJ. The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence. Nucleic Acids Res 2015; 43:8077-88. [PMID: 26206669 PMCID: PMC4652764 DOI: 10.1093/nar/gkv748] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/09/2015] [Accepted: 07/11/2015] [Indexed: 12/20/2022] Open
Abstract
La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.
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Affiliation(s)
- Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Seshat M Mack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Annie Héroux
- Photon Sciences Directorate, Bldg 745 L107 Brookhaven National Laboratory Upton, NY 11973, USA
| | - Sarah P Blagden
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Cécile Bousquet-Antonelli
- CNRS-UMR5096 LGDP, 66860 Perpignan, France Université de Perpignan-UMR5096 LGDP, 66860 Perpignan, France
| | - Jean-Marc Deragon
- CNRS-UMR5096 LGDP, 66860 Perpignan, France Université de Perpignan-UMR5096 LGDP, 66860 Perpignan, France
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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14
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Deragon JM, Bousquet-Antonelli C. The role of LARP1 in translation and beyond. Wiley Interdiscip Rev RNA 2015; 6:399-417. [PMID: 25892282 DOI: 10.1002/wrna.1282] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 12/11/2022]
Abstract
The LARP1 proteins form an evolutionarily homogeneous subgroup of the eukaryotic superfamily of La-Motif (LAM) containing factors. Members of the LARP1 family are found in most protists, fungi, plants, and animals. We review here evidence suggesting that LARP1 are key versatile messenger RNA (mRNA)-binding proteins involved in regulating important biological processes such as gametogenesis, embryogenesis, sex determination, and cell division in animals, as well as acclimation to stress in yeasts and plants. LARP1 proteins perform all these essential tasks likely by binding to key mRNAs and regulating their stability and/or translation. In human, the impact of LARP1 over cell division and proliferation is potentially under the control of the TORC1 complex. We review data suggesting that LARP1 is a direct target of this master signaling hub. TOR-dependent LARP1 phosphorylation could specifically enhance the translation of TOP mRNAs providing a way to promote translation, growth, and proliferation. Consequently, LARP1 is found to be significantly upregulated in many malignant cell types. In plants, LARP1 was found to act as a cofactor of the heat-induced mRNA degradation process, an essential acclimation strategy leading to the degradation of more than 4500 mRNAs coding for growth and development housekeeping functions. In Saccharomyces cerevisiae, the LARP1 proteins (Slf1p and Sro9p) are important, among other things, for copper resistance and oxidative stress survival. LARP1 proteins are therefore emerging as critical ancient mRNA-binding factors that evolved common as well as specific targets and regulatory functions in all eukaryotic lineages.
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Affiliation(s)
- Jean-Marc Deragon
- CNRS, LGDP-UMR5096, Perpignan, France.,University of Perpignan, LGDP-UMR5096, Perpignan, France
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15
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Merret R, Nagarajan VK, Carpentier MC, Park S, Favory JJ, Descombin J, Picart C, Charng YY, Green PJ, Deragon JM, Bousquet-Antonelli C. Heat-induced ribosome pausing triggers mRNA co-translational decay in Arabidopsis thaliana. Nucleic Acids Res 2015; 43:4121-32. [PMID: 25845591 PMCID: PMC4417158 DOI: 10.1093/nar/gkv234] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 03/06/2015] [Indexed: 12/24/2022] Open
Abstract
The reprogramming of gene expression in heat stress is a key determinant to organism survival. Gene expression is downregulated through translation initiation inhibition and release of free mRNPs that are rapidly degraded or stored. In mammals, heat also triggers 5′-ribosome pausing preferentially on transcripts coding for HSC/HSP70 chaperone targets, but the impact of such phenomenon on mRNA fate remains unknown. Here, we provide evidence that, in Arabidopsis thaliana, heat provokes 5′-ribosome pausing leading to the XRN4-mediated 5′-directed decay of translating mRNAs. We also show that hindering HSC/HSP70 activity at 20°C recapitulates heat effects by inducing ribosome pausing and co-translational mRNA turnover. Strikingly, co-translational decay targets encode proteins with high HSC/HSP70 binding scores and hydrophobic N-termini, two characteristics that were previously observed for transcripts most prone to pausing in animals. This work suggests for the first time that stress-induced variation of translation elongation rate is an evolutionarily conserved process leading to the polysomal degradation of thousands of ‘non-aberrant’ mRNAs.
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Affiliation(s)
- Rémy Merret
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Vinay K Nagarajan
- University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Marie-Christine Carpentier
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Sunhee Park
- University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Jean-Jacques Favory
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Julie Descombin
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Claire Picart
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Yee-Yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, 128 Academia Road Section 2, Taipei, Taiwan 11529, ROC
| | - Pamela J Green
- University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Jean-Marc Deragon
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
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Clavel M, Pélissier T, Descombin J, Jean V, Picart C, Charbonel C, Saez-Vásquez J, Bousquet-Antonelli C, Deragon JM. Parallel action of AtDRB2 and RdDM in the control of transposable element expression. BMC Plant Biol 2015; 15:70. [PMID: 25849103 PMCID: PMC4351826 DOI: 10.1186/s12870-015-0455-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 02/13/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND In plants and animals, a large number of double-stranded RNA binding proteins (DRBs) have been shown to act as non-catalytic cofactors of DICERs and to participate in the biogenesis of small RNAs involved in RNA silencing. We have previously shown that the loss of Arabidopsis thaliana's DRB2 protein results in a significant increase in the population of RNA polymerase IV (p4) dependent siRNAs, which are involved in the RNA-directed DNA methylation (RdDM) process. RESULTS Surprisingly, despite this observation, we show in this work that DRB2 is part of a high molecular weight complex that does not involve RdDM actors but several chromatin regulator proteins, such as MSI4, PRMT4B and HDA19. We show that DRB2 can bind transposable element (TE) transcripts in vivo but that drb2 mutants do not have a significant variation in TE DNA methylation. CONCLUSION We propose that DRB2 is part of a repressive epigenetic regulator complex involved in a negative feedback loop, adjusting epigenetic state to transcription level at TE loci, in parallel of the RdDM pathway. Loss of DRB2 would mainly result in an increased production of TE transcripts, readily converted in p4-siRNAs by the RdDM machinery.
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Affiliation(s)
- Marion Clavel
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
- />Present address: IBMP, UPR 2357, 12, rue du général Zimmer, 67084 Strasbourg cedex, France
| | - Thierry Pélissier
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
- />Present address: UMR6293 CNRS - INSERM U1103 – GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171 Aubière Cedex, France
| | - Julie Descombin
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Viviane Jean
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Claire Picart
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Cyril Charbonel
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Julio Saez-Vásquez
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Cécile Bousquet-Antonelli
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Jean-Marc Deragon
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
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Merret R, Descombin J, Juan YT, Favory JJ, Carpentier MC, Chaparro C, Charng YY, Deragon JM, Bousquet-Antonelli C. XRN4 and LARP1 Are Required for a Heat-Triggered mRNA Decay Pathway Involved in Plant Acclimation and Survival during Thermal Stress. Cell Rep 2013; 5:1279-93. [DOI: 10.1016/j.celrep.2013.11.019] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 10/08/2013] [Accepted: 11/09/2013] [Indexed: 01/22/2023] Open
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Sement FM, Ferrier E, Zuber H, Merret R, Alioua M, Deragon JM, Bousquet-Antonelli C, Lange H, Gagliardi D. Uridylation prevents 3' trimming of oligoadenylated mRNAs. Nucleic Acids Res 2013; 41:7115-27. [PMID: 23748567 PMCID: PMC3737552 DOI: 10.1093/nar/gkt465] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Degradation of mRNAs is usually initiated by deadenylation, the shortening of long poly(A) tails to oligo(A) tails of 12–15 As. Deadenylation leads to decapping and to subsequent 5′ to 3′ degradation by XRN proteins, or alternatively 3′ to 5′ degradation by the exosome. Decapping can also be induced by uridylation as shown for the non-polyadenylated histone mRNAs in humans and for several mRNAs in Schizosaccharomyces pombe and Aspergillus nidulans. Here we report a novel role for uridylation in preventing 3′ trimming of oligoadenylated mRNAs in Arabidopsis. We show that oligo(A)-tailed mRNAs are uridylated by the cytosolic UTP:RNA uridylyltransferase URT1 and that URT1 has no major impact on mRNA degradation rates. However, in absence of uridylation, oligo(A) tails are trimmed, indicating that uridylation protects oligoadenylated mRNAs from 3′ ribonucleolytic attacks. This conclusion is further supported by an increase in 3′ truncated transcripts detected in urt1 mutants. We propose that preventing 3′ trimming of oligo(A)-tailed mRNAs by uridylation participates in establishing the 5′ to 3′ directionality of mRNA degradation. Importantly, uridylation prevents 3′ shortening of mRNAs associated with polysomes, suggesting that a key biological function of uridylation is to confer 5′ to 3′ polarity in case of co-translational mRNA decay.
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Affiliation(s)
- François Michaël Sement
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du général Zimmer, 67084 Strasbourg Cedex, France
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Merret R, Martino L, Bousquet-Antonelli C, Fneich S, Descombin J, Billey É, Conte MR, Deragon JM. The association of a La module with the PABP-interacting motif PAM2 is a recurrent evolutionary process that led to the neofunctionalization of La-related proteins. RNA 2013; 19:36-50. [PMID: 23148093 PMCID: PMC3527725 DOI: 10.1261/rna.035469.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/12/2012] [Indexed: 05/27/2023]
Abstract
La-related proteins (LARPs) are largely uncharacterized factors, well conserved throughout evolution. Recent reports on the function of human LARP4 and LARP6 suggest that these proteins fulfill key functions in mRNA metabolism and/or translation. We report here a detailed evolutionary history of the LARP4 and 6 families in eukaryotes. Genes coding for LARP4 and 6 were duplicated in the common ancestor of the vertebrate lineage, but one LARP6 gene was subsequently lost in the common ancestor of the eutherian lineage. The LARP6 gene was also independently duplicated several times in the vascular plant lineage. We observed that vertebrate LARP4 and plant LARP6 duplication events were correlated with the acquisition of a PABP-interacting motif 2 (PAM2) and with a significant reorganization of their RNA-binding modules. Using isothermal titration calorimetry (ITC) and immunoprecipitation methods, we show that the two plant PAM2-containing LARP6s (LARP6b and c) can, indeed, interact with the major plant poly(A)-binding protein (PAB2), while the third plant LARP6 (LARP6a) is unable to do so. We also analyzed the RNA-binding properties and the subcellular localizations of the two types of plant LARP6 proteins and found that they display nonredundant characteristics. As a whole, our results support a model in which the acquisition by LARP4 and LARP6 of a PAM2 allowed their targeting to mRNA 3' UTRs and led to their neofunctionalization.
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Affiliation(s)
- Rémy Merret
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, United Kingdom
| | - Cécile Bousquet-Antonelli
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Sara Fneich
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Julie Descombin
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Élodie Billey
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, United Kingdom
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
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20
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Abstract
The extremely well-conserved La motif (LAM), in synergy with the immediately following RNA recognition motif (RRM), allows direct binding of the (genuine) La autoantigen to RNA polymerase III primary transcripts. This motif is not only found on La homologs, but also on La-related proteins (LARPs) of unrelated function. LARPs are widely found amongst eukaryotes and, although poorly characterized, appear to be RNA-binding proteins fulfilling crucial cellular functions. We searched the fully sequenced genomes of 83 eukaryotic species scattered along the tree of life for the presence of LAM-containing proteins. We observed that these proteins are absent from archaea and present in all eukaryotes (except protists from the Plasmodium genus), strongly suggesting that the LAM is an ancestral motif that emerged early after the archaea-eukarya radiation. A complete evolutionary and structural analysis of these proteins resulted in their classification into five families: the genuine La homologs and four LARP families. Unexpectedly, in each family a conserved domain representing either a classical RRM or an RRM-like motif immediately follows the LAM of most proteins. An evolutionary analysis of the LAM-RRM/RRM-L regions shows that these motifs co-evolved and should be used as a single entity to define the functional region of interaction of LARPs with their substrates. We also found two extremely well conserved motifs, named LSA and DM15, shared by LARP6 and LARP1 family members, respectively. We suggest that members of the same family are functional homologs and/or share a common molecular mode of action on different RNA baits.
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21
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Fleurdépine S, Deragon JM, Devic M, Guilleminot J, Bousquet-Antonelli C. A bona fide La protein is required for embryogenesis in Arabidopsis thaliana. Nucleic Acids Res 2007; 35:3306-21. [PMID: 17459889 PMCID: PMC1904278 DOI: 10.1093/nar/gkm200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 03/21/2007] [Accepted: 03/21/2007] [Indexed: 01/28/2023] Open
Abstract
Searches in the Arabidopsis thaliana genome using the La motif as query revealed the presence of eight La or La-like proteins. Using structural and phylogenetic criteria, we identified two putative genuine La proteins (At32 and At79) and showed that both are expressed throughout plant development but at different levels and under different regulatory conditions. At32, but not At79, restores Saccharomyces cerevisiae La nuclear functions in non-coding RNAs biogenesis and is able to bind to plant 3'-UUU-OH RNAs. We conclude that these La nuclear functions are conserved in Arabidopsis and supported by At32, which we renamed as AtLa1. Consistently, AtLa1 is predominantly localized to the plant nucleoplasm and was also detected in the nucleolar cavity. The inactivation of AtLa1 in Arabidopsis leads to an embryonic-lethal phenotype with deficient embryos arrested at early globular stage of development. In addition, mutant embryonic cells display a nucleolar hypertrophy suggesting that AtLa1 is required for normal ribosome biogenesis. The identification of two distantly related proteins with all structural characteristics of genuine La proteins suggests that these factors evolved to a certain level of specialization in plants. This unprecedented situation provides a unique opportunity to dissect the very different aspects of this crucial cellular activity.
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Affiliation(s)
- Sophie Fleurdépine
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Jean-Marc Deragon
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Martine Devic
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Jocelyne Guilleminot
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- CNRS UMR6547 GEEM, Université Blaise Pascal, 63177 Aubière, France and CNRS UMR5096 LGDP, Université de Perpignan Via Domitia, 66860 Perpignan, France
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Sun FJ, Fleurdépine S, Bousquet-Antonelli C, Caetano-Anollés G, Deragon JM. Common evolutionary trends for SINE RNA structures. Trends Genet 2006; 23:26-33. [PMID: 17126948 DOI: 10.1016/j.tig.2006.11.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 10/10/2006] [Accepted: 11/10/2006] [Indexed: 10/23/2022]
Abstract
Short interspersed elements (SINEs) and long interspersed elements (LINEs) are transposable elements in eukaryotic genomes that mobilize through an RNA intermediate. Understanding their evolution is important because of their impact on the host genome. Most eukaryotic SINEs are ancestrally related to tRNA genes, although the typical tRNA cloverleaf structure is not apparent for most SINE consensus RNAs. Using a cladistic method where RNA structural components were coded as polarized and ordered multistate characters, we showed that related structural motifs are present in most SINE RNAs from mammals, fishes and plants, suggesting common selective constraints imposed at the SINE RNA structural level. Based on these results, we propose a general multistep model for the evolution of tRNA-related SINEs in eukaryotes.
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Affiliation(s)
- Feng-Jie Sun
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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23
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Lenoir A, Pélissier T, Bousquet-Antonelli C, Deragon JM. Comparative evolution history of SINEs in Arabidopsis thaliana and Brassica oleracea: evidence for a high rate of SINE loss. Cytogenet Genome Res 2005; 110:441-7. [PMID: 16093696 DOI: 10.1159/000084976] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Accepted: 10/16/2003] [Indexed: 11/19/2022] Open
Abstract
Brassica oleracea and Arabidopsis thaliana belong to the Brassicaceae(Cruciferae) family and diverged 16 to 19 million years ago. Although the genome size of B. oleracea (approximately 600 million base pairs) is more than four times that of A. thaliana (approximately 130 million base pairs), their gene content is believed to be very similar with more than 85% sequence identity in the coding region. Therefore, this important difference in genome size is likely to reflect a different rate of non-coding DNA accumulation. Transposable elements (TEs) constitute a major fraction of non-coding DNA in plant species. A different rate in TE accumulation between two closely related species can result in significant genome size variations in a short evolutionary period. Short interspersed elements (SINEs) are non-autonomous retroposons that have invaded the genome of most eukaryote species. Several SINE families are present in B. oleracea and A. thaliana and we found that two of them (called RathE1 and RathE2) are present in both species. In this study, the tempo of evolution of RathE1 and RathE2 SINE families in both species was compared. We observed that most B. oleracea RathE2 SINEs are "young" (close to the consensus sequence) and abundant while elements from this family are more degenerated and much less abundant in A. thaliana. However, the situation is different for the RathE1 SINE family for which the youngest elements are found in A. thaliana. Surprisingly, no SINE was found to occupy the same (orthologous) genomic locus in both species suggesting that either these SINE families were not amplified at a significant rate in the common ancestor of the two species or that older elements were lost and only the recent (lineage-specific) insertions remain. To test this latter hypothesis, loci containing a recently inserted SINE in the A. thaliana col-0 ecotype were selected and characterized in several other A. thaliana ecotypes. In addition to the expected SINE containing allele and the pre-integrative allele (i.e. the "empty" allele), we observed in the different ecotypes, alleles with truncated portions of the SINE (up to the complete loss of the element) and of the immediate genomic flanking sequences. The absence of SINEs in orthologous positions between B. oleracea and A. thaliana and the presence in recently diverged A. thaliana ecotypes of alleles containing severely truncated SINEs suggest a very high rate of SINE loss in these species.
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Affiliation(s)
- A Lenoir
- CNRS UMR6547 Biomove, Université Blaise Pascal, Aubière, France
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24
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Pélissier T, Bousquet-Antonelli C, Lavie L, Deragon JM. Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana. Nucleic Acids Res 2004; 32:3957-66. [PMID: 15282328 PMCID: PMC506818 DOI: 10.1093/nar/gkh738] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite the ubiquitous distribution of tRNA-related short interspersed elements (SINEs) in eukaryotic species, very little is known about the synthesis and processing of their RNAs. In this work, we have characterized in detail the different RNA populations resulting from the expression of a tRNA-related SINE S1 founder copy in Arabidopsis thaliana. The main population is composed of poly(A)-ending (pa) SINE RNAs, while two minor populations correspond to full-length (fl) or poly(A) minus [small cytoplasmic (sc)] SINE RNAs. Part of the poly(A) minus RNAs is modified by 3'-terminal addition of C or CA nucleotides. All three RNA populations accumulate in the cytoplasm. Using a mutagenesis approach, we show that the poly(A) region and the 3' end unique region, present at the founder locus, are both important for the maturation and the steady-state accumulation of the different S1 RNA populations. The observation that primary SINE transcripts can be post-transcriptionally processed in vivo into a poly(A)-ending species introduces the possibility that this paRNA is used as a retroposition intermediate.
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MESH Headings
- 3' Untranslated Regions
- Arabidopsis/genetics
- Base Sequence
- Cytoplasm/metabolism
- Gene Expression Regulation, Plant
- Molecular Sequence Data
- Polyadenylation
- RNA Processing, Post-Transcriptional
- RNA, Plant/biosynthesis
- RNA, Plant/chemistry
- RNA, Plant/metabolism
- RNA, Transfer/biosynthesis
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Regulatory Sequences, Ribonucleic Acid
- Short Interspersed Nucleotide Elements
- Transcription, Genetic
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Affiliation(s)
- Thierry Pélissier
- CNRS UMR 6547 BIOMOVE and GDR 2157, Université Blaise Pascal Clermont-Ferrand II, 63177 Aubière Cedex, France
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Vanrobays E, Gleizes PE, Bousquet-Antonelli C, Noaillac-Depeyre J, Caizergues-Ferrer M, Gélugne JP. Processing of 20S pre-rRNA to 18S ribosomal RNA in yeast requires Rrp10p, an essential non-ribosomal cytoplasmic protein. EMBO J 2001; 20:4204-13. [PMID: 11483523 PMCID: PMC149176 DOI: 10.1093/emboj/20.15.4204] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Numerous non-ribosomal trans-acting factors involved in pre-ribosomal RNA processing have been characterized, but none of them is specifically required for the last cytoplasmic steps of 18S rRNA maturation. Here we demonstrate that Rio1p/Rrp10p is such a factor. Previous studies showed that the RIO1 gene is essential for cell viability and conserved from archaebacteria to man. We isolated a RIO1 mutant in a screen for mutations synthetically lethal with a mutant allele of GAR1, an essential gene required for 18S rRNA production and rRNA pseudouridylation. We show that RIO1 encodes a cytoplasmic non-ribosomal protein, and that depletion of Rio1p blocks 18S rRNA production leading to 20S pre-rRNA accumulation. In situ hybridization reveals that, in Rio1p depleted cells, 20S pre-rRNA localizes in the cytoplasm, demonstrating that its accumulation is not due to an export defect. This strongly suggests that Rio1p is involved in the cytoplasmic cleavage of 20S pre-rRNA at site D, producing mature 18S rRNA. Thus, Rio1p has been renamed Rrp10p (ribosomal RNA processing #10). Rio1p/Rrp10p is the first non-ribosomal factor characterized specifically required for 20S pre-rRNA processing.
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Affiliation(s)
| | | | - Cécile Bousquet-Antonelli
- LBME du CNRS, 118 route de Narbonne, 31062 Toulouse cedex 04, France
Present address: Institute of Cell and Molecular Biology, University of Edinburgh, King’s Buildings, Edinburgh EH9 3JR, UK Corresponding author e-mail:
| | | | | | - Jean-Paul Gélugne
- LBME du CNRS, 118 route de Narbonne, 31062 Toulouse cedex 04, France
Present address: Institute of Cell and Molecular Biology, University of Edinburgh, King’s Buildings, Edinburgh EH9 3JR, UK Corresponding author e-mail:
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26
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Abstract
We have identified a nuclear pathway that rapidly degrades unspliced pre-mRNAs in yeast. This involves 3'-->5' degradation by the exosome complex and 5'-->3' degradation by the exonuclease Rat1p. 3'-->5' degradation is normally the major pathway and is regulated in response to carbon source. Inhibition of pre-mRNA degradation resulted in increased levels of pre-mRNAs and spliced mRNAs. When splicing was inhibited by mutation of a splicing factor, inhibition of turnover resulted in 20- to 50-fold accumulation of pre-mRNAs, accompanied by increased mRNA production. Splicing of a reporter construct with a 3' splice site mutation was also increased on inhibition of turnover, showing competition between degradation and splicing. We propose that nuclear pre-mRNA turnover represents a novel step in the regulation of gene expression.
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Bousquet-Antonelli C, Vanrobays E, Gélugne JP, Caizergues-Ferrer M, Henry Y. Rrp8p is a yeast nucleolar protein functionally linked to Gar1p and involved in pre-rRNA cleavage at site A2. RNA 2000; 6:826-43. [PMID: 10864042 PMCID: PMC1369961 DOI: 10.1017/s1355838200992288] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Chemical modifications and processing of the 18S, 5.8S, and 25S ribosomal RNAs from the 35S pre-ribosomal RNA depend on an important set of small nucleolar ribonucleoprotein particles (snoRNPs). Genetic depletion of yeast Gar1p, an essential common component of H/ACA snoRNPs, leads to inhibition of uridine isomerizations to pseudo-uridines on the 35S pre-rRNA and of the early pre-rRNA cleavages at sites A1 and A2, resulting in a loss of mature 18S rRNA synthesis. To identify Gar1p functional partners, we screened for mutations that are synthetically lethal with a gar1 mutant allele encoding a Gar1p mutant protein lacking its two glycine/arginine-rich (GAR) domains. We identified a previously uncharacterized Saccharomyces cerevisiae open reading frame, YDR083W (now designated RRP8), that encodes a highly conserved protein containing motifs found in methyltransferases. Rrp8p localizes to the nucleolus. A yeast strain lacking this protein is viable at 30 degrees C but displays strong growth impairment at lower temperatures. In this strain, cleavage of the pre-rRNA at site A2 is strongly affected whereas cleavages at sites A0 and A1 are only slightly inhibited or delayed.
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Affiliation(s)
- C Bousquet-Antonelli
- Laboratoire de Biologie Moléculaire Eucaryote du Centre National de la Recherche Scientifique, Toulouse, France
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Henras A, Henry Y, Bousquet-Antonelli C, Noaillac-Depeyre J, Gélugne JP, Caizergues-Ferrer M. Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J 1998; 17:7078-90. [PMID: 9843512 PMCID: PMC1171055 DOI: 10.1093/emboj/17.23.7078] [Citation(s) in RCA: 186] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The small nucleolar ribonucleoprotein particles containing H/ACA-type snoRNAs (H/ACA snoRNPs) are crucial trans-acting factors intervening in eukaryotic ribosome biogenesis. Most of these particles generate the site-specific pseudouridylation of rRNAs while a subset are required for 18S rRNA synthesis. To understand in detail how these particles carry out these functions, all of their protein components have to be characterized. For that purpose, we have affinity-purified complexes containing epitope-tagged Gar1p protein, previously shown to be part of H/ACA snoRNPs. Under the conditions used, three polypeptides of 65, 22 and 10 kDa apparent molecular weight specifically copurify with epitope-tagged Gar1p. The 22 and 10 kDa polypeptides were identified as Nhp2p and a novel protein we termed Nop10p, respectively. Both proteins are conserved, essential and present in the dense fibrillar component of the nucleolus. Nhp2p and Nop10p are specifically associated with all H/ACA snoRNAs and are essential to the function of H/ACA snoRNPs. Cells lacking Nhp2p or Nop10p are impaired in global rRNA pseudouridylation and in the A1 and A2 cleavage steps of the pre-rRNA required for the synthesis of mature 18S rRNA. These phenotypes are probably a direct consequence of the instability of H/ACA snoRNAs and Gar1p observed in cells deprived of Nhp2p or Nop10p. Our results suggest that Nhp2p and Nop10p, together with Cbf5p, constitute the core of H/ACA snoRNPs.
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Affiliation(s)
- A Henras
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, 118 route de Narbonne, 31062 Toulouse Cedex 04, France
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29
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Lafontaine DL, Bousquet-Antonelli C, Henry Y, Caizergues-Ferrer M, Tollervey D. The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev 1998; 12:527-37. [PMID: 9472021 PMCID: PMC316522 DOI: 10.1101/gad.12.4.527] [Citation(s) in RCA: 282] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many or all of the sites of pseudouridine (Psi) formation in eukaryotic rRNA are selected by site-specific base-pairing with members of the box H + ACA class of small nucleolar RNAs (snoRNAs). Database searches previously identified strong homology between the rat nucleolar protein Nap57p, its yeast homolog Cbf5p, and the Escherichia coli Psi synthase truB/P35. We therefore tested whether Cbf5p is required for synthesis of Psi in the yeast rRNA. After genetic depletion of Cbf5p, formation of Psi in the pre-rRNA is dramatically inhibited, resulting in accumulation of the unmodified rRNA. Protein A-tagged Cbf5p coprecipitates all tested members of the box H + ACA snoRNAs but not box C + D snoRNAs or other RNA species. Genetic depletion of Cbf5p leads to depletion of all box H + ACA snoRNAs. These include snR30, which is required for pre-rRNA processing. Depletion of Cbf5p also results in a pre-rRNA processing defect similar to that seen on depletion of snR30. We conclude that Cbf5p is likely to be the rRNA Psi synthase and is an integral component of the box H + ACA class of snoRNPs, which function to target the enzyme to its site of action.
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Affiliation(s)
- D L Lafontaine
- Institute of Cell and Molecular Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
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30
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Bousquet-Antonelli C, Henry Y, G'elugne JP, Caizergues-Ferrer M, Kiss T. A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs. EMBO J 1997; 16:4770-6. [PMID: 9303321 PMCID: PMC1170103 DOI: 10.1093/emboj/16.15.4770] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic rRNAs possess numerous post-transcriptionally modified nucleotides. The most abundant modifications, 2'-O-ribose methylation and pseudouridylation, occur in the nucleolus during rRNA processing. The nucleolus contains a large number of small nucleolar RNAs (snoRNAs) most of which can be classified into two distinct families defined by conserved sequence boxes and common associated proteins. The C and D box-containing snoRNAs are associated with fibrillarin, and most of them function as guide RNAs in site-specific ribose methylation of rRNAs. The nucleolar function of the other class of snoRNAs, which share box H and ACA elements and are associated with a glycine- and arginine-rich nucleolar protein, Gar1p, remains elusive. Here we demonstrate that the yeast Saccharomyces cerevisiae Gar1 snoRNP protein plays an essential and specific role in the overall pseudouridylation of yeast rRNAs. These results establish a novel function for Gar1 protein and indicate that the box H/ACA snoRNAs, or at least a subset of these snoRNAs, function in the site-specific pseudouridylation of rRNAs.
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Affiliation(s)
- C Bousquet-Antonelli
- Laboratoire de Biologie Mol'eculaire Eucaryote du CNRS, Universit'e Paul Sabatier, Toulouse, France
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Venema J, Bousquet-Antonelli C, Gelugne JP, Caizergues-Ferrer M, Tollervey D. Rok1p is a putative RNA helicase required for rRNA processing. Mol Cell Biol 1997; 17:3398-407. [PMID: 9154839 PMCID: PMC232193 DOI: 10.1128/mcb.17.6.3398] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The synthesis of ribosomes involves many small nucleolar ribonucleoprotein particles (snoRNPs) as transacting factors. Yeast strains lacking the snoRNA, snR10, are viable but are impaired in growth and delayed in the early pre-rRNA cleavages at sites A0, A1, and A2, which lead to the synthesis of 18S rRNA. The same cleavages are inhibited by genetic depletion of the essential snoRNP protein Gar1p. Screens for mutations showing synthetic lethality with deletion of the SNR10 gene or with a temperature-sensitive gar1 allele both identified the ROK1 gene, encoding a putative, ATP-dependent RNA helicase of the DEAD-box family. The ROK1 gene is essential for viability, and depletion of Rok1p inhibits pre-rRNA processing at sites A0, A1, and A2, thereby blocking 18S rRNA synthesis. Indirect immunofluorescence by using a ProtA-Rok1p construct shows the protein to be predominantly nucleolar. These results suggest that Rok1p is required for the function of the snoRNP complex carrying out the early pre-rRNA cleavage reactions.
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Affiliation(s)
- J Venema
- European Molecular Biology Laboratory, Heidelberg, Germany.
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