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Feng L, Yan W, Tang X, Wu H, Pan Y, Lu D, Ling-Hu Q, Liu Y, Liu Y, Song X, Ali M, Fang L, Guo H, Li B. Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis. Commun Biol 2024; 7:474. [PMID: 38637717 PMCID: PMC11026412 DOI: 10.1038/s42003-024-06142-4] [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: 11/10/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Coding transcript-derived siRNAs (ct-siRNAs) produced from specific endogenous loci can suppress the translation of their source genes to balance plant growth and stress response. In this study, we generated Arabidopsis mutants with deficiencies in RNA decay and/or post-transcriptional gene silencing (PTGS) pathways and performed comparative sRNA-seq analysis, revealing that multiple RNA decay and PTGS factors impede the ct-siRNA selective production. Genes that produce ct-siRNAs often show increased or unchanged expression and typically have higher GC content in sequence composition. The growth and development of plants can perturb the dynamic accumulation of ct-siRNAs from different gene loci. Two nitrate reductase genes, NIA1 and NIA2, produce massive amounts of 22-nt ct-siRNAs and are highly expressed in a subtype of mesophyll cells where DCL2 exhibits higher expression relative to DCL4, suggesting a potential role of cell-specific expression of ct-siRNAs. Overall, our findings unveil the multifaceted factors and features involved in the selective production and regulation of ct-siRNAs and enrich our understanding of gene silencing process in plants.
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Affiliation(s)
- Li Feng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Wei Yan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Xianli Tang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Huihui Wu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yajie Pan
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Dongdong Lu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Qianyan Ling-Hu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yuelin Liu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yongqi Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiehai Song
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Muhammad Ali
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Liang Fang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
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2
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Chery M, Berrissou C, Humbert N, Hummel G, Mely Y, Salinas-Giegé T, Drouard L. The Arabidopsis tDR Ala forms G-quadruplex structures that can be unwound by the DExH1 DEA(D/H)-box RNA helicase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:124-140. [PMID: 38113339 DOI: 10.1111/tpj.16596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/05/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
As in many other organisms, tRNA-derived RNAs (tDRs) exist in plants and likely have multiple functions. We previously showed that tDRs are present in Arabidopsis under normal growth conditions, and that the ones originating from alanine tRNAs are the most abundant in leaves. We also showed that tDRs Ala of 20 nt produced from mature tRNAAla (AGC) can block in vitro protein translation. Here, we report that first, these tDRs Ala (AGC) can be found within peculiar foci in the cell that are neither P-bodies nor stress granules and, second, that they assemble into intermolecular RNA G-quadruplex (rG4) structures. Such tDR Ala rG4 structures can specifically interact with an Arabidopsis DEA(D/H) RNA helicase, the DExH1 protein, and unwind them. The rG4-DExH1 protein interaction relies on a glycine-arginine domain with RGG/RG/GR/GRR motifs present at the N-terminal extremity of the protein. Mutations on the four guanine residues located at the 5' extremity of the tDR Ala abolish its rG4 structure assembly, association with the DExH1 protein, and foci formation, but they do not prevent protein translation inhibition in vitro. Our data suggest that the sequestration of tDRs Ala into rG4 complexes might represent a way to modulate accessible and functional tDRs for translation inhibition within the plant cell via the activity of a specific RNA helicase, DExH1.
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Affiliation(s)
- Marjorie Chery
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
| | - Christina Berrissou
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
| | - Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies - CNRS, UMR 7021, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France
| | - Guillaume Hummel
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies - CNRS, UMR 7021, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France
| | - Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
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3
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Vaucheret H, Voinnet O. The plant siRNA landscape. THE PLANT CELL 2024; 36:246-275. [PMID: 37772967 PMCID: PMC10827316 DOI: 10.1093/plcell/koad253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Whereas micro (mi)RNAs are considered the clean, noble side of the small RNA world, small interfering (si)RNAs are often seen as a noisy set of molecules whose barbarian acronyms reflect a large diversity of often elusive origins and functions. Twenty-five years after their discovery in plants, however, new classes of siRNAs are still being identified, sometimes in discrete tissues or at particular developmental stages, making the plant siRNA world substantially more complex and subtle than originally anticipated. Focusing primarily on the model Arabidopsis, we review here the plant siRNA landscape, including transposable elements (TE)-derived siRNAs, a vast array of non-TE-derived endogenous siRNAs, as well as exogenous siRNAs produced in response to invading nucleic acids such as viruses or transgenes. We primarily emphasize the extraordinary sophistication and diversity of their biogenesis and, secondarily, the variety of their known or presumed functions, including via non-cell autonomous activities, in the sporophyte, gametophyte, and shortly after fertilization.
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Affiliation(s)
- Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH-Zurich), 8092 Zürich, Switzerland
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4
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Kang L, Li C, Qin A, Liu Z, Li X, Zeng L, Yu H, Wang Y, Song J, Chen R. Identification and Expression Analysis of the Nucleotidyl Transferase Protein (NTP) Family in Soybean ( Glycine max) under Various Abiotic Stresses. Int J Mol Sci 2024; 25:1115. [PMID: 38256188 PMCID: PMC10816777 DOI: 10.3390/ijms25021115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Nucleotidyl transferases (NTPs) are common transferases in eukaryotes and play a crucial role in nucleotide modifications at the 3' end of RNA. In plants, NTPs can regulate RNA stability by influencing 3' end modifications, which in turn affect plant growth, development, stress responses, and disease resistance. Although the functions of NTP family members have been extensively studied in Arabidopsis, rice, and maize, there is limited knowledge about NTP genes in soybeans. In this study, we identified 16 members of the NTP family in soybeans, including two subfamilies (G1 and G2) with distinct secondary structures, conserved motifs, and domain distributions at the protein level. Evolutionary analysis of genes in the NTP family across multiple species and gene collinearity analysis revealed a relatively conserved evolutionary pattern. Analysis of the tertiary structure of the proteins showed that NTPs have three conserved aspartic acids that bind together to form a possible active site. Tissue-specific expression analysis indicated that some NTP genes exhibit tissue-specific expression, likely due to their specific functions. Stress expression analysis showed significant differences in the expression levels of NTP genes under high salt, drought, and cold stress. Additionally, RNA-seq analysis of soybean plants subjected to salt and drought stress further confirmed the association of soybean NTP genes with abiotic stress responses. Subcellular localization experiments revealed that GmNTP2 and GmNTP14, which likely have similar functions to HESO1 and URT1, are located in the nucleus. These research findings provide a foundation for further investigations into the functions of NTP family genes in soybeans.
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Affiliation(s)
- Liqing Kang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Changgen Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Aokang Qin
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Zehui Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Xuanyue Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Liming Zeng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Hongyang Yu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Yihua Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Jianbo Song
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Rongrong Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
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5
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Giraudo P, Simonnot Q, Pflieger D, Peter J, Gagliardi D, Zuber H. Nano3'RACE: A Method to Analyze Poly(A) Tail Length and Nucleotide Additions at the 3' Extremity of Selected mRNAs Using Nanopore Sequencing. Methods Mol Biol 2024; 2723:233-252. [PMID: 37824074 DOI: 10.1007/978-1-0716-3481-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Deadenylation is a major process that regulates gene expression by shaping the length of mRNA poly(A) tails. Deadenylation is controlled by factors in trans that recruit or impede deadenylases, by the incorporation of non-adenosines during poly(A) tail synthesis, and by the posttranscriptional addition of 3' nucleotides to poly(A) tails. Deciphering the regulation of poly(A) tail shortening requires both transcriptome-wide approaches and more targeted methodologies, allowing deep analyses of specific mRNAs. In this chapter, we present Nano3'RACE, a nanopore-based cDNA sequencing method that allows in-depth analysis to precisely measure poly(A) tail length and detect 3' terminal nucleotide addition, such as uridylation, for mRNAs of interest.
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Affiliation(s)
- Pietro Giraudo
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Quentin Simonnot
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jackson Peter
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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6
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Tomecki R, Drazkowska K, Kobylecki K, Tudek A. SKI complex: A multifaceted cytoplasmic RNA exosome cofactor in mRNA metabolism with links to disease, developmental processes, and antiviral responses. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1795. [PMID: 37384835 DOI: 10.1002/wrna.1795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 07/01/2023]
Abstract
RNA stability and quality control are integral parts of gene expression regulation. A key factor shaping eukaryotic transcriptomes, mainly via 3'-5' exoribonucleolytic trimming or degradation of diverse transcripts in nuclear and cytoplasmic compartments, is the RNA exosome. Precise exosome targeting to various RNA molecules requires strict collaboration with specialized auxiliary factors, which facilitate interactions with its substrates. The predominant class of cytoplasmic RNA targeted by the exosome are protein-coding transcripts, which are carefully scrutinized for errors during translation. Normal, functional mRNAs are turned over following protein synthesis by the exosome or by Xrn1 5'-3'-exonuclease, acting in concert with Dcp1/2 decapping complex. In turn, aberrant transcripts are eliminated by dedicated surveillance pathways, triggered whenever ribosome translocation is impaired. Cytoplasmic 3'-5' mRNA decay and surveillance are dependent on the tight cooperation between the exosome and its evolutionary conserved co-factor-the SKI (superkiller) complex (SKIc). Here, we summarize recent findings from structural, biochemical, and functional studies of SKIc roles in controlling cytoplasmic RNA metabolism, including links to various cellular processes. Mechanism of SKIc action is illuminated by presentation of its spatial structure and details of its interactions with exosome and ribosome. Furthermore, contribution of SKIc and exosome to various mRNA decay pathways, usually converging on recycling of ribosomal subunits, is delineated. A crucial physiological role of SKIc is emphasized by describing association between its dysfunction and devastating human disease-a trichohepatoenteric syndrome (THES). Eventually, we discuss SKIc functions in the regulation of antiviral defense systems, cell signaling and developmental transitions, emerging from interdisciplinary investigations. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karolina Drazkowska
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Kamil Kobylecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Tudek
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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7
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Kairouani A, Pontier D, Picart C, Mounet F, Martinez Y, Le-Bot L, Fanuel M, Hammann P, Belmudes L, Merret R, Azevedo J, Carpentier MC, Gagliardi D, Couté Y, Sibout R, Bies-Etheve N, Lagrange T. Cell-type-specific control of secondary cell wall formation by Musashi-type translational regulators in Arabidopsis. eLife 2023; 12:RP88207. [PMID: 37773033 PMCID: PMC10541177 DOI: 10.7554/elife.88207] [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] [Indexed: 09/30/2023] Open
Abstract
Deciphering the mechanism of secondary cell wall/SCW formation in plants is key to understanding their development and the molecular basis of biomass recalcitrance. Although transcriptional regulation is essential for SCW formation, little is known about the implication of post-transcriptional mechanisms in this process. Here we report that two bonafide RNA-binding proteins homologous to the animal translational regulator Musashi, MSIL2 and MSIL4, function redundantly to control SCW formation in Arabidopsis. MSIL2/4 interactomes are similar and enriched in proteins involved in mRNA binding and translational regulation. MSIL2/4 mutations alter SCW formation in the fibers, leading to a reduction in lignin deposition, and an increase of 4-O-glucuronoxylan methylation. In accordance, quantitative proteomics of stems reveal an overaccumulation of glucuronoxylan biosynthetic machinery, including GXM3, in the msil2/4 mutant stem. We showed that MSIL4 immunoprecipitates GXM mRNAs, suggesting a novel aspect of SCW regulation, linking post-transcriptional control to the regulation of SCW biosynthesis genes.
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Affiliation(s)
- Alicia Kairouani
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, INP, UMR5546Castanet-TolosanFrance
| | - Yves Martinez
- FRAIB-CNRS Plateforme ImagerieCastanet-TolosanFrance
| | - Lucie Le-Bot
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
| | - Mathieu Fanuel
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
- PROBE research infrastructure, BIBS Facility, INRAENantesFrance
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade de CNRS, Université de StrasbourgStrasbourgFrance
| | - Lucid Belmudes
- Université Grenoble Alpes, INSERM, UA13 BGE, CNRS, CEA, FR2048GrenobleFrance
| | - Remy Merret
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Jacinthe Azevedo
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, IBMP, CNRS, Université de StrasbourgStrasbourgFrance
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, UA13 BGE, CNRS, CEA, FR2048GrenobleFrance
| | - Richard Sibout
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
| | - Natacha Bies-Etheve
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
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8
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Joly AC, Garcia S, Hily JM, Koechler S, Demangeat G, Garcia D, Vigne E, Lemaire O, Zuber H, Gagliardi D. An extensive survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns. PLANT PHYSIOLOGY 2023; 193:271-290. [PMID: 37177985 PMCID: PMC10469402 DOI: 10.1093/plphys/kiad278] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023]
Abstract
Viral RNAs can be uridylated in eukaryotic hosts. However, our knowledge of uridylation patterns and roles remains rudimentary for phytoviruses. Here, we report global 3' terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses. We detected uridylation in all 47 viral RNAs investigated here, revealing its prevalence. Yet, uridylation levels of viral RNAs varied from 0.2% to 90%. Unexpectedly, most poly(A) tails of grapevine fanleaf virus (GFLV) RNAs, including encapsidated tails, were strictly monouridylated, which corresponds to an unidentified type of viral genomic RNA extremity. This monouridylation appears beneficial for GFLV because it became dominant when plants were infected with nonuridylated GFLV transcripts. We found that GFLV RNA monouridylation is independent of the known terminal uridylyltransferases (TUTases) HEN1 SUPPRESSOR 1 (HESO1) and UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) in Arabidopsis (Arabidopsis thaliana). By contrast, both TUTases can uridylate other viral RNAs like turnip crinkle virus (TCV) and turnip mosaic virus (TuMV) RNAs. Interestingly, TCV and TuMV degradation intermediates were differentially uridylated by HESO1 and URT1. Although the lack of both TUTases did not prevent viral infection, we detected degradation intermediates of TCV RNA at higher levels in an Arabidopsis heso1 urt1 mutant, suggesting that uridylation participates in clearing viral RNA. Collectively, our work unveils an extreme diversity of uridylation patterns across phytoviruses and constitutes a valuable resource to further decipher pro- and antiviral roles of uridylation.
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Affiliation(s)
- Anne Caroline Joly
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Shahinez Garcia
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
| | - Jean-Michel Hily
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
- Institut Français de la Vigne et du Vin, Le Grau-Du-Roi 30240, France
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Gérard Demangeat
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
| | - Damien Garcia
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Emmanuelle Vigne
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
| | - Olivier Lemaire
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
| | - Hélène Zuber
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
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9
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Kupriyanova E, Manakhov A, Ezhova T. PARG1 and EXA1 genes as possible components of the facultative epigenetic control of plant development. PHYSIOLOGIA PLANTARUM 2023; 175:e13959. [PMID: 37350155 DOI: 10.1111/ppl.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
Plants are able to adjust their developmental program in response to incremental environmental changes by reprogramming the epigenomes of the cells. This process, known as facultative epigenetic developmental control, underlies plant developmental plasticity and the amazing diversity of morphotypes, which arises from the changes in cell fates. How plants determine when epigenome reprogramming should occur is largely unclear. Here, we show that the Arabidopsis PARG1 and EXA1 genes, encoding poly(ADP-ribose) glycohydrolase and GYF domain protein involved in nonsense-mediated mRNA decay, respectively, act synergistically in maintaining leaf cell identity. Loss of their function in Arabidopsis tae mutant triggers autoimmunity and wounding response, alters transcription of a number of epigenetic regulators, initiates the acquisition of pluripotency by cells of the developed leaf and ectopic outgrowths and buds formation. The dependence of the cell fate on the activity level of PARG1 and EXA1 genes indicates that these interacting genes may function as an important regulator of facultative epigenetic control of plant development.
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Affiliation(s)
- Evgenia Kupriyanova
- Faculty of Biology, Department of Genetics, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey Manakhov
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Ezhova
- Faculty of Biology, Department of Genetics, Lomonosov Moscow State University, Moscow, Russia
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10
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Lee S, Jee D, Srivastava S, Yang A, Ramidi A, Shang R, Bortolamiol-Becet D, Pfeffer S, Gu S, Wen J, Lai EC. Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals. Cell Rep 2023; 42:112111. [PMID: 36800291 PMCID: PMC10508058 DOI: 10.1016/j.celrep.2023.112111] [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: 06/28/2022] [Revised: 11/16/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Canonical microRNA (miRNA) hairpins are processed by the RNase III enzymes Drosha and Dicer into ∼22 nt RNAs loaded into an Argonaute (Ago) effector. In addition, splicing generates numerous intronic hairpins that bypass Drosha (mirtrons) to yield mature miRNAs. Here, we identify hundreds of previously unannotated, splicing-derived hairpins in intermediate-length (∼50-100 nt) but not small (20-30 nt) RNA data. Since we originally defined mirtrons from small RNA duplexes, we term this larger set as structured splicing-derived RNAs (ssdRNAs). These associate with Dicer and/or Ago complexes, but generally accumulate modestly and are poorly conserved. We propose they contaminate the canonical miRNA pathway, which consequently requires defense against the siege of splicing-derived substrates. Accordingly, ssdRNAs/mirtrons comprise dominant hairpin substrates for 3' tailing by multiple terminal nucleotidyltransferases, notably TUT4/7 and TENT2. Overall, the rampant proliferation of young mammalian mirtrons/ssdRNAs, coupled with an inhibitory molecular defense, comprises a Red Queen's race of intragenomic conflict.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - David Jee
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sid Srivastava
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; High Technology High School, Lincroft, NJ 07738, USA
| | - Acong Yang
- RNA Biology Laboratory, Center for Cancer Research, 8 National Cancer Institute, Frederick, MD 21702, USA
| | - Abhinav Ramidi
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; High Technology High School, Lincroft, NJ 07738, USA
| | - Renfu Shang
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - Diane Bortolamiol-Becet
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 Allée Konrad Roentgen, 67084 Strasbourg, France
| | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 Allée Konrad Roentgen, 67084 Strasbourg, France
| | - Shuo Gu
- RNA Biology Laboratory, Center for Cancer Research, 8 National Cancer Institute, Frederick, MD 21702, USA
| | - Jiayu Wen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
| | - Eric C Lai
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA; Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA.
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11
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Vaucheret H. Epigenetic management of self and non-self: lessons from 40 years of transgenic plants. C R Biol 2023; 345:149-174. [PMID: 36847123 DOI: 10.5802/crbiol.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022]
Abstract
Plant varieties exhibiting unstable or variegated phenotypes, or showing virus recovery have long remained a mystery. It is only with the development of transgenic plants 40 years ago that the epigenetic features underlying these phenomena were elucidated. Indeed, the study of transgenic plants that did not express the introduced sequences revealed that transgene loci sometimes undergo transcriptional gene silencing (TGS) or post-transcriptional gene silencing (PTGS) by activating epigenetic defenses that naturally control transposable elements, duplicated genes or viruses. Even when they do not trigger TGS or PTGS spontaneously, stably expressed transgenes driven by viral promoters set apart from endogenous genes in their epigenetic regulation. As a result, transgenes driven by viral promoters are capable of undergoing systemic PTGS throughout the plant, whereas endogenous genes can only undergo local PTGS in cells where RNA quality control is impaired. Together, these results indicate that the host genome distinguishes self from non-self at the epigenetic level, allowing PTGS to eliminate non-self, and preventing PTGS to become systemic and kill the plant when it is locally activated against deregulated self.
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12
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Zhang X, Qin L, Lu J, Xia Y, Tang X, Lu X, Xia S. Genome-Wide Identification of GYF-Domain Encoding Genes in Three Brassica Species and Their Expression Responding to Sclerotinia sclerotiorum in Brassica napus. Genes (Basel) 2023; 14:224. [PMID: 36672966 PMCID: PMC9858701 DOI: 10.3390/genes14010224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
GYF (glycine-tyrosine-phenylalanine)-domain-containing proteins, which were reported to participate in many aspects of biological processes in yeast and animals, are highly conserved adaptor proteins existing in almost all eukaryotes. Our previous study revealed that GYF protein MUSE11/EXA1 is involved in nucleotide-binding leucine-rich repeat (NLR) receptor-mediated defense in Arabidopsis thaliana. However, the GYF-domain encoding homologous genes are still not clear in other plants. Here, we performed genome-wide identification of GYF-domain encoding genes (GYFs) from Brassica napus and its parental species, Brassica rapa and Brassica oleracea. As a result, 26 GYFs of B. napus (BnaGYFs), 11 GYFs of B. rapa (BraGYFs), and 14 GYFs of B. oleracea (BolGYFs) together with 10 A. thaliana (AtGYFs) were identified, respectively. We, then, conducted gene structure, motif, cis-acting elements, duplication, chromosome localization, and phylogenetic analysis of these genes. Gene structure analysis indicated the diversity of the exon numbers of these genes. We found that the defense and stress responsiveness element existed in 23 genes and also identified 10 motifs in these GYF proteins. Chromosome localization exhibited a similar distribution of BnaGYFs with BraGYFs or BolGYFs in their respective genomes. The phylogenetic and gene collinearity analysis showed the evolutionary conservation of GYFs among B. napus and its parental species as well as Arabidopsis. These 61 identified GYF domain proteins can be classified into seven groups according to their sequence similarity. Expression of BnaGYFs induced by Sclerotinia sclerotiorum provided five highly upregulated genes and five highly downregulated genes, which might be candidates for further research of plant-fungal interaction in B. napus.
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Affiliation(s)
- Xiaobo Zhang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Junxing Lu
- College of Life Science, Chongqing Normal University, Chongqing 400047, China
| | - Yunong Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xianyu Tang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xun Lu
- Agricultural Science Academy of Xiangxi Tujia and Miao Autonomous Prefecture, Xiangxi 416000, China
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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Kuhn L, Vincent T, Hammann P, Zuber H. Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts. Methods Mol Biol 2023; 2426:243-265. [PMID: 36308692 DOI: 10.1007/978-1-0716-1967-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Immunoprecipitation mass spectrometry (IP-MS) is a popular method for the identification of protein-protein interactions. This approach is particularly powerful when information is collected without a priori knowledge and has been successively used as a first key step for the elucidation of many complex protein networks. IP-MS consists in the affinity purification of a protein of interest and of its interacting proteins followed by protein identification and quantification by mass spectrometry analysis. We developed an R package, named IPinquiry, dedicated to IP-MS analysis and based on the spectral count quantification method. The main purpose of this package is to provide a simple R pipeline with a limited number of processing steps to facilitate data exploration for biologists. This package allows to perform differential analysis of protein accumulation between two groups of IP experiments, to retrieve protein annotations, to export results, and to create different types of graphics. Here we describe the step-by-step procedure for an interactome analysis using IPinquiry from data loading to result export and plot production.
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Affiliation(s)
- Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Timothée Vincent
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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14
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Christie M, Igreja C. eIF4E-homologous protein (4EHP): a multifarious cap-binding protein. FEBS J 2023; 290:266-285. [PMID: 34758096 DOI: 10.1111/febs.16275] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 02/05/2023]
Abstract
The cap-binding protein 4EHP/eIF4E2 has been a recent object of interest in the field of post-transcriptional gene regulation and translational control. From ribosome-associated quality control, to RNA decay and microRNA-mediated gene silencing, this member of the eIF4E protein family regulates gene expression through numerous pathways. Low in abundance but ubiquitously expressed, 4EHP interacts with different binding partners to form multiple protein complexes that regulate translation in a variety of biological contexts. Documented functions of 4EHP primarily relate to its role as a translational repressor, but recent findings indicate that it might also participate in the activation of translation in specific settings. In this review, we discuss the known functions, properties and mechanisms that involve 4EHP in the control of gene expression. We also discuss our current understanding of how 4EHP processes are regulated in eukaryotic cells, and the diseases implicated with dysregulation of 4EHP-mediated translational control.
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Affiliation(s)
- Mary Christie
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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15
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Qi Y, Wang L, Li W, Xie Y, Zhao W, Dang Z, Li W, Zhao L, Zhang J. Phenotypic analysis of Longya-10 × pale flax hybrid progeny and identification of candidate genes regulating prostrate/erect growth in flax plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1044415. [PMID: 36561460 PMCID: PMC9763623 DOI: 10.3389/fpls.2022.1044415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Flax is a dual-purpose crop that is important for oil and fiber production. The growth habit is one of the crucial targets of selection during flax domestication. Wild hybridization between cultivated flax and wild flax can produce superior germplasms for flax breeding and facilitate the study of the genetic mechanism underlying agronomically important traits. In this study, we used pale flax, Linum grandiflorum, and L. perenne to pollinate Longya-10. Only pale flax interspecific hybrids were obtained, and the trait analysis of the F1 and F2 generations showed that the traits analyzed in this study exhibited disparate genetic characteristics. In the F1 generation, only one trait, i.e., the number of capsules per plant (140) showed significant heterosis, while the characteristics of other traits were closely associated with those of the parents or a decline in hybrid phenotypes. The traits of the F2 generation were widely separated, and the variation coefficient ranged from 9.96% to 146.15%. The quantitative trait locus underlying growth habit was preliminarily found to be situated on chromosome 2 through Bulked-segregant analysis sequencing. Then linkage mapping analysis was performed to fine-map GH2.1 to a 23.5-kb interval containing 4 genes. Among them, L.us.o.m.scaffold22.109 and L.us.o.m.scaffold22.112 contained nonsynonymous SNPs with Δindex=1. Combined with the qRT-PCR results, the two genes might be possible candidate genes for GH2.1. This study will contribute to the development of important germplasms for flax breeding, which would facilitate the elucidation of the genetic mechanisms regulating the growth habit and development of an ideal architecture for the flax plant.
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16
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Qin Y, Long Y, Zhai J. Genome-wide characterization of nascent RNA processing in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102294. [PMID: 36063636 DOI: 10.1016/j.pbi.2022.102294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Following transcription initiation, RNA polymerase II (Pol II) elongates through the genic region and terminates after the polyadenylation signal. This process is accompanied by splicing, 3' cleavage, and polyadenylation, to eventually form a mature mRNA. Recent advances in short-read and long-read high-throughput sequencing methods have shed light on the global landscape of these co-transcriptional events at nucleotide resolution. In this mini review, we summarize recent developments in genome-wide approaches that broadened our understanding of nascent RNA processing in plants.
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Affiliation(s)
- Yuwei Qin
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Yanping Long
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Jixian Zhai
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China.
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17
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Hemono M, Salinas‐Giegé T, Roignant J, Vingadassalon A, Hammann P, Ubrig E, Ngondo P, Duchêne A. FRIENDLY (FMT) is an RNA binding protein associated with cytosolic ribosomes at the mitochondrial surface. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:309-321. [PMID: 36050837 PMCID: PMC9826127 DOI: 10.1111/tpj.15962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The spatial organization of protein synthesis in the eukaryotic cell is essential for maintaining the integrity of the proteome and the functioning of the cell. Translation on free polysomes or on ribosomes associated with the endoplasmic reticulum has been studied for a long time. More recent data have revealed selective translation of mRNAs in other compartments, in particular at the surface of mitochondria. Although these processes have been described in many organisms, particularky in plants, the mRNA targeting and localized translation mechanisms remain poorly understood. Here, the Arabidopsis thaliana Friendly (FMT) protein is shown to be a cytosolic RNA binding protein that associates with cytosolic ribosomes at the surface of mitochondria. FMT knockout delays seedling development and causes mitochondrial clustering. The mutation also disrupts the mitochondrial proteome, as well as the localization of nuclear transcripts encoding mitochondrial proteins at the surface of mitochondria. These data indicate that FMT participates in the localization of mRNAs and their translation at the surface of mitochondria.
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Affiliation(s)
- Mickaele Hemono
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Thalia Salinas‐Giegé
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Jeanne Roignant
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Audrey Vingadassalon
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
- Université des Antilles, COVACHIM M2E (EA 3592), UFR SEN, Campus de FouilloleF‐97 110Pointe‐à‐PitreFrance
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg‐EsplanadeInstitut de Biologie Moléculaire et CellulaireFR1589 du CNRS, 2 Allée Konrad Roentgen67084Strasbourg CedexFrance
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Patryk Ngondo
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
- Institut de Biologie Moléculaire et Cellulaire, UPR 9002 du CNRS, Université de Strasbourg2 Allée Konrad Roentgen67 084Strasbourg CedexFrance
| | - Anne‐Marie Duchêne
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
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18
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Hu Q, Yang H, Li M, Zhu L, Lv M, Li F, Zhang Z, Ren G, Gong Q. Molecular mechanism underlying the di-uridylation activity of Arabidopsis TUTase URT1. Nucleic Acids Res 2022; 50:10614-10625. [PMID: 36177876 PMCID: PMC9561377 DOI: 10.1093/nar/gkac839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/09/2022] [Accepted: 09/19/2022] [Indexed: 11/14/2022] Open
Abstract
In Arabidopsis, HESO1 and URT1 act cooperatively on unmethylated miRNA and mRNA uridylation to induce their degradation. Their collaboration significantly impacts RNA metabolism in plants. However, the molecular mechanism determining the functional difference and complementarity of these two enzymes remains unclear. We previously solved the three-dimensional structure of URT1 in the absence and presence of UTP. In this study, we further determined the structure of URT1 in complex with a 5′-AAAU-3′ RNA stretch that mimics the post-catalytic state of the mRNA poly(A) tail after the addition of the first uridine. Structural analysis and enzymatic assays revealed that L527 and Y592 endow URT1 with a preference to interact with purine over pyrimidine at the -1 RNA binding position, thus controlling the optimal number of uridine added to the 3′ extremity of poly(A) as two. In addition, we observed that a large-scale conformational rearrangement in URT1 occurs upon binding with RNA from an ‘open’ to a ‘closed’ state. Molecular dynamic simulation supports an open-closed conformational selection mechanism employed by URT1 to interact with RNA substrates and maintain distributive enzymatic activity. Based on the above results, a model regarding the catalytic cycle of URT1 is proposed to explain its di-uridylation activity.
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Affiliation(s)
- Qian Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Huiru Yang
- State Key Laboratory of Genetic Engineering, Zhangjiang mRNA Innovation and Translation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Mingwei Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Lingru Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Mengqi Lv
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Fudong Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Zhiyong Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Zhangjiang mRNA Innovation and Translation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qingguo Gong
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
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19
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RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
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Uridylation and the SKI complex orchestrate the Calvin cycle of photosynthesis through RNA surveillance of TKL1 in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:e2205842119. [PMID: 36095196 PMCID: PMC9499578 DOI: 10.1073/pnas.2205842119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA uridylation, catalyzed by terminal uridylyl transferases (TUTases), represents a conserved and widespread posttranscriptional RNA modification in eukaryotes that affects RNA metabolism. In plants, several TUTases, including HEN1 SUPPRESSOR 1 (HESO1) and UTP: RNA URIDYLYLTRANSFERASE (URT1), have been characterized through genetic and biochemical approaches. However, little is known about their physiological significance during plant development. Here, we show that HESO1 and URT1 act cooperatively with the cytoplasmic 3'-5' exoribonucleolytic machinery component SUPERKILLER 2 (SKI2) to regulate photosynthesis through RNA surveillance of the Calvin cycle gene TRANSKETOLASE 1 (TKL1) in Arabidopsis. Simultaneous dysfunction of HESO1, URT1, and SKI2 resulted in leaf etiolation and reduced photosynthetic efficiency. In addition, we detected massive illegitimate short interfering RNAs (siRNAs) from the TKL1 locus in heso1 urt1 ski2, accompanied by reduced TKL1/2 expression and attenuated TKL activities. Consequently, the metabolic analysis revealed that the abundance of many Calvin cycle intermediates is dramatically disturbed in heso1 urt1 ski2. Importantly, all these molecular and physiological defects were largely rescued by the loss-of-function mutation in RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), demonstrating illegitimate siRNA-mediated TKL silencing. Taken together, our results suggest that HESO1- and URT1-mediated RNA uridylation connects to the cytoplasmic RNA degradation pathway for RNA surveillance, which is crucial for TKL expression and photosynthesis in Arabidopsis.
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21
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Jia J, Lu W, Liu B, Fang H, Yu Y, Mo W, Zhang H, Jin X, Shu Y, Long Y, Pei Y, Zhai J. An atlas of plant full-length RNA reveals tissue-specific and monocots-dicots conserved regulation of poly(A) tail length. NATURE PLANTS 2022; 8:1118-1126. [PMID: 35982302 DOI: 10.1038/s41477-022-01224-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Poly(A) tail is a hallmark of eukaryotic messenger RNA and its length plays an essential role in regulating mRNA metabolism. However, a comprehensive resource for plant poly(A) tail length has yet to be established. Here, we applied a poly(A)-enrichment-free, nanopore-based method to profile full-length RNA with poly(A) tail information in plants. Our atlas contains over 120 million polyadenylated mRNA molecules from seven different tissues of Arabidopsis, as well as the shoot tissue of maize, soybean and rice. In most tissues, the size of plant poly(A) tails shows peaks at approximately 20 and 45 nucleotides, while the poly(A) tails in pollen exhibit a distinct pattern with strong peaks centred at 55 and 80 nucleotides. Moreover, poly(A) tail length is regulated in a gene-specific manner-mRNAs with short half-lives in general have long poly(A) tails, while mRNAs with long half-lives are featured with relatively short poly(A) tails that peak at ~45 nucleotides. Across species, poly(A) tails in the nucleus are almost twice as long as in the cytoplasm. Our comprehensive dataset lays the groundwork for future functional and evolutionary studies on poly(A) tail length regulation in plants.
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Affiliation(s)
- Jinbu Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Wenqin Lu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Bo Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Huihui Fang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Yiming Yu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Weipeng Mo
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Hong Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Xianhao Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Yi Shu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Yanping Long
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Yanxi Pei
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China.
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China.
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22
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Krzyszton M, Kufel J. Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana. Sci Rep 2022; 12:1474. [PMID: 35087200 PMCID: PMC8795450 DOI: 10.1038/s41598-022-05574-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/14/2022] [Indexed: 02/05/2023] Open
Abstract
Defects in RNA maturation and RNA decay factors may generate substrates for the RNA interference machinery. This phenomenon was observed in plants where mutations in some RNA-related factors lead to the production of RNA-quality control small interfering RNAs and several mutants show enhanced silencing of reporter transgenes. To assess the potential of RNAi activation on endogenous transcripts, we sequenced small RNAs from a set of Arabidopsis thaliana mutants with defects in various RNA metabolism pathways. We observed a global production of siRNAs caused by inefficient pre-mRNA cleavage and polyadenylation leading to read-through transcription into downstream antisense genes. In addition, in the lsm1a lsm1b double mutant, we identified NIA1, SMXL5, and several miRNA-targeted mRNAs as producing siRNAs, a group of transcripts suggested being especially sensitive to deficiencies in RNA metabolism. However, in most cases, RNA metabolism perturbations do not lead to the widespread production of siRNA derived from mRNA molecules. This observation is contrary to multiple studies based on reporter transgenes and suggests that only a very high accumulation of defective mRNA species caused by specific mutations or substantial RNA processing defects trigger RNAi pathways.
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Affiliation(s)
- Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Joanna Kufel
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
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23
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Vigh ML, Bressendorff S, Thieffry A, Arribas-Hernández L, Brodersen P. Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis. Nucleic Acids Res 2022; 50:1396-1415. [PMID: 35037064 PMCID: PMC8860578 DOI: 10.1093/nar/gkab1289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/13/2021] [Accepted: 01/03/2022] [Indexed: 11/14/2022] Open
Abstract
Amplification of short interfering RNA (siRNAs) via RNA-dependent RNA polymerases (RdRPs) is of fundamental importance in RNA silencing. Plant microRNA (miRNA) action generally does not involve engagement of RdRPs, in part thanks to a poorly understood activity of the cytoplasmic exosome adaptor SKI2. Here, we show that inactivation of the exosome subunit RRP45B and SKI2 results in similar patterns of miRNA-induced siRNA production. Furthermore, loss of the nuclear exosome adaptor HEN2 leads to secondary siRNA production from miRNA targets largely distinct from those producing siRNAs in ski2. Importantly, mutation of the Release Factor paralogue PELOTA1 required for subunit dissociation of stalled ribosomes causes siRNA production from miRNA targets overlapping with, but distinct from, those affected in ski2 and rrp45b mutants. We also show that in exosome mutants, miRNA targets can be sorted into producers and non-producers of illicit secondary siRNAs based on trigger miRNA levels and miRNA:target affinity rather than on presence of 5′-cleavage fragments. We propose that stalled RNA-Induced Silencing Complex (RISC) and ribosomes, but not mRNA cleavage fragments released from RISC, trigger siRNA production, and that the exosome limits siRNA amplification by reducing RISC dwell time on miRNA target mRNAs while PELOTA1 does so by reducing ribosome stalling.
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Affiliation(s)
- Maria L Vigh
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simon Bressendorff
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Axel Thieffry
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Laura Arribas-Hernández
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Brodersen
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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24
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Sajeev N, Baral A, America AHP, Willems LAJ, Merret R, Bentsink L. The mRNA-binding proteome of a critical phase transition during Arabidopsis seed germination. THE NEW PHYTOLOGIST 2022; 233:251-264. [PMID: 34643285 PMCID: PMC9298696 DOI: 10.1111/nph.17800] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/01/2021] [Indexed: 05/22/2023]
Abstract
Arabidopsis thaliana seed germination is marked by extensive translational control at two critical phase transitions. The first transition refers to the start of hydration, the hydration translational shift. The second shift, the germination translational shift (GTS) is the phase between testa rupture and radicle protrusion at which the seed makes the all or nothing decision to germinate. The mechanism behind the translational regulation at these phase transitions is unknown. RNA binding proteins (RBPs) are versatile players in the post-transcriptional control of messenger RNAs (mRNAs) and as such candidates for regulating translation during seed germination. Here, we report the mRNA binding protein repertoire of seeds during the GTS. Thirty seed specific RBPs and 22 dynamic RBPs were identified during the GTS, like the putative RBP Vacuolar ATPase subunit A and RBP HSP101. Several stress granule markers were identified in this study, which suggests that seeds are prepared to quickly adapt the translation of specific mRNAs in response to changes in environmental conditions during the GTS. Taken together this study provides a detailed insight into the world of RBPs during seed germination and their possible regulatory role during this developmentally regulated process.
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Affiliation(s)
- Nikita Sajeev
- Laboratory of PhysiologyWageningen Seed Science CentreWageningen UniversityWageningen6708PBthe Netherlands
| | - Anirban Baral
- Laboratory of PhysiologyWageningen Seed Science CentreWageningen UniversityWageningen6708PBthe Netherlands
| | | | - Leo A. J. Willems
- Laboratory of PhysiologyWageningen Seed Science CentreWageningen UniversityWageningen6708PBthe Netherlands
| | - Rémy Merret
- Laboratoire Génome et Développement des PlantesCNRS‐LGDP UMR 5096Perpignan66860France
| | - Leónie Bentsink
- Laboratory of PhysiologyWageningen Seed Science CentreWageningen UniversityWageningen6708PBthe Netherlands
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