1
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Workman RJ, Huang CJ, Lynch GC, Pettitt BM. Peptide diffusion in biomolecular condensates. Biophys J 2024; 123:1668-1675. [PMID: 38751116 PMCID: PMC11213990 DOI: 10.1016/j.bpj.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 05/30/2024] Open
Abstract
Diffusion determines the turnover of biomolecules in liquid-liquid phase-separated condensates. We considered the mean square displacement and thus the diffusion constant for simple model systems of peptides GGGGG, GGQGG, and GGVGG in aqueous solutions after phase separation by simulating atomic-level models. These solutions readily separate into aqueous and peptide-rich droplet phases. We noted the effect of the peptides being in a solvated, surface, or droplet state on the peptide's diffusion coefficients. Both sequence and peptide conformational distribution were found to influence diffusion and condensate turnover in these systems, with sequence dominating the magnitude of the differences. We found that the most compact structures for each sequence diffused the fastest in the peptide-rich condensate phase. This model result may have implications for turnover dynamics in signaling systems.
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Affiliation(s)
- Riley J Workman
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas
| | - Caleb J Huang
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas
| | - Gillian C Lynch
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas
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2
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Takei T, Tsukada M, Tamura K, Hara-Nishimura I, Fukao Y, Kurihara Y, Matsui M, Saze H, Tsuzuki M, Watanabe Y, Hamada T. ARGONAUTE1-binding Tudor domain proteins function in small interfering RNA production for RNA-directed DNA methylation. PLANT PHYSIOLOGY 2024; 195:1333-1346. [PMID: 38446745 DOI: 10.1093/plphys/kiae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
Transposable elements (TEs) contribute to plant evolution, development, and adaptation to environmental changes, but the regulatory mechanisms are largely unknown. RNA-directed DNA methylation (RdDM) is 1 TE regulatory mechanism in plants. Here, we identified that novel ARGONAUTE 1 (AGO1)-binding Tudor domain proteins Precocious dissociation of sisters C/E (PDS5C/E) are involved in 24-nt siRNA production to establish RdDM on TEs in Arabidopsis thaliana. PDS5 family proteins are subunits of the eukaryote-conserved cohesin complex. However, the double mutant lacking angiosperm-specific subfamily PDS5C and PDS5E (pds5c/e) exhibited different developmental phenotypes and transcriptome compared with those of the double mutant lacking eukaryote-conserved subfamily PDS5A and PDS5B (pds5a/b), suggesting that the angiosperm-specific PDS5C/E subfamily has a unique function in angiosperm plants. Proteome and imaging analyses revealed that PDS5C/E interact with AGO1. The pds5c/e double mutant had defects in 24-nt siRNA accumulation and CHH DNA methylation on TEs. In addition, some lncRNAs that accumulated in the pds5c/e mutant were targeted by AGO1-loading 21-nt miRNAs and 21-nt siRNAs. These results indicate that PDS5C/E and AGO1 participate in 24-nt siRNA production for RdDM in the cytoplasm. These findings indicate that angiosperm plants evolved a new regulator, the PDS5C/E subfamily, to control the increase in TEs during angiosperm evolution.
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Affiliation(s)
- Takahito Takei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, Okayama 700-0005, Japan
| | - Michio Tsukada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Kentaro Tamura
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | | | - Yoichiro Fukao
- Graduate School of Life Science, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yukio Kurihara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Nanobioscience, Department of Life and Environmental System Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Masayuki Tsuzuki
- Faculty of Agriculture and Marine Science, Kochi University, Kochi 783-8502, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takahiro Hamada
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, Okayama 700-0005, Japan
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3
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Fan S, Zhang Y, Zhu S, Shen L. Plant RNA-binding proteins: Phase separation dynamics and functional mechanisms underlying plant development and stress responses. MOLECULAR PLANT 2024; 17:531-551. [PMID: 38419328 DOI: 10.1016/j.molp.2024.02.016] [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: 01/03/2024] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
RNA-binding proteins (RBPs) accompany RNA from synthesis to decay, mediating every aspect of RNA metabolism and impacting diverse cellular and developmental processes in eukaryotes. Many RBPs undergo phase separation along with their bound RNA to form and function in dynamic membraneless biomolecular condensates for spatiotemporal coordination or regulation of RNA metabolism. Increasing evidence suggests that phase-separating RBPs with RNA-binding domains and intrinsically disordered regions play important roles in plant development and stress adaptation. Here, we summarize the current knowledge about how dynamic partitioning of RBPs into condensates controls plant development and enables sensing of experimental changes to confer growth plasticity under stress conditions, with a focus on the dynamics and functional mechanisms of RBP-rich nuclear condensates and cytoplasmic granules in mediating RNA metabolism. We also discuss roles of multiple factors, such as environmental signals, protein modifications, and N6-methyladenosine RNA methylation, in modulating the phase separation behaviors of RBPs, and highlight the prospects and challenges for future research on phase-separating RBPs in crops.
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Affiliation(s)
- Sheng Fan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Yu Zhang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Shaobo Zhu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
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4
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Barre-Villeneuve C, Laudié M, Carpentier MC, Kuhn L, Lagrange T, Azevedo-Favory J. The unique dual targeting of AGO1 by two types of PRMT enzymes promotes phasiRNA loading in Arabidopsis thaliana. Nucleic Acids Res 2024; 52:2480-2497. [PMID: 38321923 PMCID: PMC10954461 DOI: 10.1093/nar/gkae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Arginine/R methylation (R-met) of proteins is a widespread post-translational modification (PTM), deposited by a family of protein arginine/R methyl transferase enzymes (PRMT). Regulations by R-met are involved in key biological processes deeply studied in metazoan. Among those, post-transcriptional gene silencing (PTGS) can be regulated by R-met in animals and in plants. It mainly contributes to safeguard processes as protection of genome integrity in germlines through the regulation of piRNA pathway in metazoan, or response to bacterial infection through the control of AGO2 in plants. So far, only PRMT5 has been identified as the AGO/PIWI R-met writer in higher eukaryotes. We uncovered that AGO1, the main PTGS effector regulating plant development, contains unique R-met features among the AGO/PIWI superfamily, and outstanding in eukaryotes. Indeed, AGO1 contains both symmetric (sDMA) and asymmetric (aDMA) R-dimethylations and is dually targeted by PRMT5 and by another type I PRMT in Arabidopsis thaliana. We showed also that loss of sDMA didn't compromise AtAGO1 subcellular trafficking in planta. Interestingly, we underscored that AtPRMT5 specifically promotes the loading of phasiRNA in AtAGO1. All our observations bring to consider this dual regulation of AtAGO1 in plant development and response to environment, and pinpoint the complexity of AGO1 post-translational regulation.
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Affiliation(s)
- Clément Barre-Villeneuve
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Michèle Laudié
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Marie-Christine Carpentier
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg – Esplanade, CNRS FR1589, Université de Strasbourg, IBMC, 2 allée Konrad Roentgen, F-67084 Strasbourg, France
- Fédération de Recherche CNRS FR1589, France
| | - Thierry Lagrange
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Jacinthe Azevedo-Favory
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
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5
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Wang H, Ye T, Guo Z, Yao Y, Tu H, Wang P, Zhang Y, Wang Y, Li X, Li B, Xiong H, Lai X, Xiong L. A double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice. Nat Commun 2024; 15:2514. [PMID: 38514621 PMCID: PMC10957929 DOI: 10.1038/s41467-024-46754-2] [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: 09/19/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Drought stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of drought resistance in rice. Here, through a genome-wide association study, we reveal that natural variations in DROUGHT RESISTANCE GENE 9 (DRG9), encoding a double-stranded RNA (dsRNA) binding protein, contribute to drought resistance. Under drought stress, DRG9 condenses into stress granules (SGs) through liquid-liquid phase separation via a crucial α-helix. DRG9 recruits the mRNAs of OsNCED4, a key gene for the biosynthesis of abscisic acid, into SGs and protects them from degradation. In drought-resistant DRG9 allele, natural variations in the coding region, causing an amino acid substitution (G267F) within the zinc finger domain, increase DRG9's binding ability to OsNCED4 mRNA and enhance drought resistance. Introgression of the drought-resistant DRG9 allele into the elite rice Huanghuazhan significantly improves its drought resistance. Thus, our study underscores the role of a dsRNA-binding protein in drought resistance and its promising value in breeding drought-resistant rice.
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Affiliation(s)
- Huaijun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Tiantian Ye
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zilong Guo
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Bingchen Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haiyan Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuelei Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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6
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Kearly A, Nelson ADL, Skirycz A, Chodasiewicz M. Composition and function of stress granules and P-bodies in plants. Semin Cell Dev Biol 2024; 156:167-175. [PMID: 36464613 DOI: 10.1016/j.semcdb.2022.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Stress Granules (SGs) and Processing-bodies (P-bodies) are biomolecular condensates formed in the cell with the highly conserved purpose of maintaining balance between storage, translation, and degradation of mRNA. This balance is particularly important when cells are exposed to different environmental conditions and adjustments have to be made in order for plants to respond to and tolerate stressful conditions. While P-bodies are constitutively present in the cell, SG formation is a stress-induced event. Typically thought of as protein-RNA aggregates, SGs and P-bodies are formed by a process called liquid-liquid phase separation (LLPS), and both their function and composition are very dynamic. Both foci are known to contain proteins involved in translation, protein folding, and ATPase activity, alluding to their roles in regulating mRNA and protein expression levels. From an RNA perspective, SGs and P-bodies primarily consist of mRNAs, though long non-coding RNAs (lncRNAs) have also been observed, and more focus is now being placed on the specific RNAs associated with these aggregates. Recently, metabolites such as nucleotides and amino acids have been reported in purified plant SGs with implications for the energetic dynamics of these condensates. Thus, even though the field of plant SGs and P-bodies is relatively nascent, significant progress has been made in understanding their composition and biological role in stress responses. In this review, we discuss the most recent discoveries centered around SG and P-body function and composition in plants.
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Affiliation(s)
- Alyssa Kearly
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | | | | | - Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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7
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Blagojevic A, Baldrich P, Schiaffini M, Lechner E, Baumberger N, Hammann P, Elmayan T, Garcia D, Vaucheret H, Meyers BC, Genschik P. Heat stress promotes Arabidopsis AGO1 phase separation and association with stress granule components. iScience 2024; 27:109151. [PMID: 38384836 PMCID: PMC10879784 DOI: 10.1016/j.isci.2024.109151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/17/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role in microRNA (miRNA) and small interfering RNA (siRNA)-mediated silencing. AGO1 associates to the rough endoplasmic reticulum to conduct miRNA-mediated translational repression, mRNA cleavage, and biogenesis of phased siRNAs. Here, we show that a 37°C heat stress (HS) promotes AGO1 protein accumulation in cytosolic condensates where it colocalizes with components of siRNA bodies and of stress granules. AGO1 contains a prion-like domain in its poorly characterized N-terminal Poly-Q domain, which is sufficient to undergo phase separation independently of the presence of SGS3. HS only moderately affects the small RNA repertoire, the loading of AGO1 by miRNAs, and the signatures of target cleavage, suggesting that its localization in condensates protects AGO1 rather than promoting or impairing its activity in reprogramming gene expression during stress. Collectively, our work sheds new light on the impact of high temperature on a main effector of RNA silencing in plants.
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Affiliation(s)
- Aleksandar Blagojevic
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | | | - Marlene Schiaffini
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Esther Lechner
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Nicolas Baumberger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Taline Elmayan
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Damien Garcia
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
| | - Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France
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8
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Liu C, Mentzelopoulou A, Hatzianestis IH, Tzagkarakis E, Skaltsogiannis V, Ma X, Michalopoulou VA, Romero-Campero FJ, Romero-Losada AB, Sarris PF, Marhavy P, Bölter B, Kanterakis A, Gutierrez-Beltran E, Moschou PN. A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes. THE PLANT CELL 2024; 36:559-584. [PMID: 37971938 PMCID: PMC10896293 DOI: 10.1093/plcell/koad288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/18/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.
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Affiliation(s)
- Chen Liu
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Andriani Mentzelopoulou
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Ioannis H Hatzianestis
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | | | - Vasileios Skaltsogiannis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Xuemin Ma
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Vassiliki A Michalopoulou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Francisco J Romero-Campero
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Avenida Reina Mercedes s/n, Seville 41012, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Ana B Romero-Losada
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Avenida Reina Mercedes s/n, Seville 41012, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Panagiotis F Sarris
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
- Biosciences, University of Exeter, Exeter, UK
| | - Peter Marhavy
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Bettina Bölter
- Ludwig Maximilians University Munich, Plant Biochemistry, Großhadernerstr. 2-4, Planegg-Martinsried 82152, Germany
| | - Alexandros Kanterakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Panagiotis N Moschou
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
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9
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Hu S, Zhang Y, Yi Q, Yang C, Liu Y, Bai Y. Time-resolved proteomic profiling reveals compositional and functional transitions across the stress granule life cycle. Nat Commun 2023; 14:7782. [PMID: 38012130 PMCID: PMC10682001 DOI: 10.1038/s41467-023-43470-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Stress granules (SGs) are dynamic, membrane-less organelles. With their formation and disassembly processes characterized, it remains elusive how compositional transitions are coordinated during prolonged stress to meet changing functional needs. Here, using time-resolved proteomic profiling of the acute to prolonged heat-shock SG life cycle, we identify dynamic SG proteins, further segregated into early and late proteins. Comparison of different groups of SG proteins suggests that their biochemical properties help coordinate SG compositional and functional transitions. In particular, early proteins, with high phase-separation-propensity, drive the rapid formation of the initial SG platform, while late proteins are subsequently recruited as discrete modules to further functionalize SGs. This model, supported by immunoblotting and immunofluorescence imaging, provides a conceptual framework for the compositional transitions throughout the acute to prolonged SG life cycle. Additionally, an early SG constituent, non-muscle myosin II, is shown to promote SG formation by increasing SG fusion, underscoring the strength of this dataset in revealing the complexity of SG regulation.
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Affiliation(s)
- Shuyao Hu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yufeng Zhang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Qianqian Yi
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Cuiwei Yang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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10
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Li Y, Gao J, Wang Y, Cai J, Wu D, Wang L, Pu W, Yu F, Zhu S. The functions of a 5' tRNA-Ala-derived fragment in gene expression. PLANT PHYSIOLOGY 2023; 193:1126-1141. [PMID: 37350495 DOI: 10.1093/plphys/kiad361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/04/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Transfer RNA (tRNA) can produce smaller RNA fragments called tRNA-derived fragments (tRFs). tRFs play critical roles in multiple cellular programs, although the functional mechanisms of tRFs remain largely unknown in plants. In this study, we examined the phenotype associated with 5' tRF-Ala (tRF-Ala, produced from tRNA-Ala) overexpression and knockdown lines (tDR-Ala-OE and tDR-Ala-kd, respectively) and the mechanisms by which tRF-Ala affects mRNA levels in Arabidopsis (Arabidopsis thaliana). We investigated the candidate proteins associated with tRF-Ala by quantitative proteomics and confirmed the direct interaction between tRF-Ala and the splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34). A transcriptome sequencing analysis showed that 318 genes among all the genes (786) with substantial alternative splicing (AS) variance in tDR-Ala-OE lines are targets of SR34. tRF-Ala diminished the binding affinity between SR34 and its targets by direct competition for interaction with SR34. These findings reveal the critical roles of tRF-Ala in regulating mRNA levels and splicing.
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Affiliation(s)
- Yuanyuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Junping Gao
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Ying Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Jun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Dousheng Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Wenxuan Pu
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
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11
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Hoffmann G, López-González S, Mahboubi A, Hanson J, Hafrén A. Cauliflower mosaic virus protein P6 is a multivalent node for RNA granule proteins and interferes with stress granule responses during plant infection. THE PLANT CELL 2023; 35:3363-3382. [PMID: 37040611 PMCID: PMC10473198 DOI: 10.1093/plcell/koad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/06/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.
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Affiliation(s)
- Gesa Hoffmann
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Silvia López-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Amir Mahboubi
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Johannes Hanson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Anders Hafrén
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
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12
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Wen J, Qin Z, Sun L, Zhang Y, Wang D, Peng H, Yao Y, Hu Z, Ni Z, Sun Q, Xin M. Alternative splicing of TaHSFA6e modulates heat shock protein-mediated translational regulation in response to heat stress in wheat. THE NEW PHYTOLOGIST 2023; 239:2235-2247. [PMID: 37403528 DOI: 10.1111/nph.19100] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023]
Abstract
Heat stress greatly threatens crop production. Plants have evolved multiple adaptive mechanisms, including alternative splicing, that allow them to withstand this stress. However, how alternative splicing contributes to heat stress responses in wheat (Triticum aestivum) is unclear. We reveal that the heat shock transcription factor gene TaHSFA6e is alternatively spliced in response to heat stress. TaHSFA6e generates two major functional transcripts: TaHSFA6e-II and TaHSFA6e-III. TaHSFA6e-III enhances the transcriptional activity of three downstream heat shock protein 70 (TaHSP70) genes to a greater extent than does TaHSFA6e-II. Further investigation reveals that the enhanced transcriptional activity of TaHSFA6e-III is due to a 14-amino acid peptide at its C-terminus, which arises from alternative splicing and is predicted to form an amphipathic helix. Results show that knockout of TaHSFA6e or TaHSP70s increases heat sensitivity in wheat. Moreover, TaHSP70s are localized in stress granule following exposure to heat stress and are involved in regulating stress granule disassembly and translation re-initiation upon stress relief. Polysome profiling analysis confirms that the translational efficiency of stress granule stored mRNAs is lower at the recovery stage in Tahsp70s mutants than in the wild types. Our finding provides insight into the molecular mechanisms by which alternative splicing improves the thermotolerance in wheat.
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Affiliation(s)
- Jingjing Wen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhen Qin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lv Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yumei Zhang
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Dongli Wang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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13
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Xie Z, Zhao S, Li Y, Deng Y, Shi Y, Chen X, Li Y, Li H, Chen C, Wang X, Liu E, Tu Y, Shi P, Tong J, Gutierrez-Beltran E, Li J, Bozhkov PV, Qian W, Zhou M, Wang W. Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition. NATURE PLANTS 2023; 9:1481-1499. [PMID: 37640933 DOI: 10.1038/s41477-023-01499-6] [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: 12/27/2022] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
Phenolic acids (PAs) secreted by donor plants suppress the growth of their susceptible plant neighbours. However, how structurally diverse ensembles of PAs are perceived by plants to mediate interspecific competition remains a mystery. Here we show that a plant stress granule (SG) marker, RNA-BINDING PROTEIN 47B (RBP47B), is a sensor of PAs in Arabidopsis. PAs, including salicylic acid, 4-hydroxybenzoic acid, protocatechuic acid and so on, directly bind RBP47B, promote its phase separation and trigger SG formation accompanied by global translation inhibition. Salicylic acid-induced global translation inhibition depends on RBP47 family members. RBP47s regulate the proteome rather than the absolute quantity of SG. The rbp47 quadruple mutant shows a reduced sensitivity to the inhibitory effect of the PA mixture as well as to that of PA-rich rice when tested in a co-culturing ecosystem. In this Article, we identified the long sought-after PA sensor as RBP47B and illustrated that PA-induced SG-mediated translational inhibition was one of the PA perception mechanisms.
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Affiliation(s)
- Zhouli Xie
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, China
| | - Shuai Zhao
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, China
| | - Ying Li
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, China
| | - Yuhua Deng
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yabo Shi
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoyuan Chen
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Yue Li
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Haiwei Li
- College of Life Sciences, Capital Normal University, Beijing, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, China
| | - Changtian Chen
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, China
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Xingwei Wang
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Enhui Liu
- College of Life Sciences, Capital Normal University, Beijing, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, China
| | - Yuchen Tu
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Peng Shi
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, China
| | - Jinjin Tong
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, China
| | - Emilio Gutierrez-Beltran
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Instituto de Bioquímica Vegetal y Fotosíntesis, University of Sevilla, Sevilla, Spain
| | - Jiayu Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Weiqiang Qian
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, China
| | - Mian Zhou
- College of Life Sciences, Capital Normal University, Beijing, China.
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, China.
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA.
| | - Wei Wang
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Center for Life Sciences, Beijing, China.
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA.
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14
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Wang W, Wang C, Wang Y, Ma J, Wang T, Tao Z, Liu P, Li S, Hu Y, Gu A, Wang H, Qiu C, Li P. The P-body component DECAPPING5 and the floral repressor SISTER OF FCA regulate FLOWERING LOCUS C transcription in Arabidopsis. THE PLANT CELL 2023; 35:3303-3324. [PMID: 37220754 PMCID: PMC10473201 DOI: 10.1093/plcell/koad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/28/2023] [Accepted: 04/30/2023] [Indexed: 05/25/2023]
Abstract
Flowering is the transition from vegetative to reproductive growth and is critical for plant adaptation and reproduction. FLOWERING LOCUS C (FLC) plays a central role in flowering time control, and dissecting its regulation mechanism provides essential information for crop improvement. Here, we report that DECAPPING5 (DCP5), a component of processing bodies (P-bodies), regulates FLC transcription and flowering time in Arabidopsis (Arabidopsis thaliana). DCP5 and its interacting partner SISTER OF FCA (SSF) undergo liquid-liquid phase separation (LLPS) that is mediated by their prion-like domains (PrDs). Enhancing or attenuating the LLPS of both proteins using transgenic methods greatly affects their ability to regulate FLC and flowering time. DCP5 regulates FLC transcription by modulating RNA polymerase II enrichment at the FLC locus. DCP5 requires SSF for FLC regulation, and loss of SSF or its PrD disrupts DCP5 function. Our results reveal that DCP5 interacts with SSF, and the nuclear DCP5-SSF complex regulates FLC expression at the transcriptional level.
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Affiliation(s)
- Wanyi Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Chuanhong Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yunhe Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Jing Ma
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Tengyue Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Zhen Tao
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Peipei Liu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Shuai Li
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yuanyuan Hu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Aiju Gu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Hui Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Chunhong Qiu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Peijin Li
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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15
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Ruiz-Solaní N, Salguero-Linares J, Armengot L, Santos J, Pallarès I, van Midden KP, Phukkan UJ, Koyuncu S, Borràs-Bisa J, Li L, Popa C, Eisele F, Eisele-Bürger AM, Hill SM, Gutiérrez-Beltrán E, Nyström T, Valls M, Llamas E, Vilchez D, Klemenčič M, Ventura S, Coll NS. Arabidopsis metacaspase MC1 localizes in stress granules, clears protein aggregates, and delays senescence. THE PLANT CELL 2023; 35:3325-3344. [PMID: 37401663 PMCID: PMC10473220 DOI: 10.1093/plcell/koad172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023]
Abstract
Stress granules (SGs) are highly conserved cytoplasmic condensates that assemble in response to stress and contribute to maintaining protein homeostasis. These membraneless organelles are dynamic, disassembling once the stress is no longer present. Persistence of SGs due to mutations or chronic stress has been often related to age-dependent protein-misfolding diseases in animals. Here, we find that the metacaspase MC1 is dynamically recruited into SGs upon proteotoxic stress in Arabidopsis (Arabidopsis thaliana). Two predicted disordered regions, the prodomain and the 360 loop, mediate MC1 recruitment to and release from SGs. Importantly, we show that MC1 has the capacity to clear toxic protein aggregates in vivo and in vitro, acting as a disaggregase. Finally, we demonstrate that overexpressing MC1 delays senescence and this phenotype is dependent on the presence of the 360 loop and an intact catalytic domain. Together, our data indicate that MC1 regulates senescence through its recruitment into SGs and this function could potentially be linked to its remarkable protein aggregate-clearing activity.
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Affiliation(s)
- Nerea Ruiz-Solaní
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona 08028, Spain
| | - Jose Salguero-Linares
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
| | - Laia Armengot
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona 08028, Spain
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Katarina P van Midden
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Ujjal J Phukkan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
| | - Seda Koyuncu
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Júlia Borràs-Bisa
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
| | - Liang Li
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
| | - Crina Popa
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
| | - Frederik Eisele
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Anna Maria Eisele-Bürger
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Sandra Malgrem Hill
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Emilio Gutiérrez-Beltrán
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla and Consejo Superior de Investigaciones Científicas), 41092 Seville, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
| | - Thomas Nyström
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Marc Valls
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona 08028, Spain
| | - Ernesto Llamas
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany
- Faculty of Medicine, University Hospital Cologne, Cologne 50931, Germany
| | - Marina Klemenčič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Nuria S Coll
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08001, Spain
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16
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Solis-Miranda J, Chodasiewicz M, Skirycz A, Fernie AR, Moschou PN, Bozhkov PV, Gutierrez-Beltran E. Stress-related biomolecular condensates in plants. THE PLANT CELL 2023; 35:3187-3204. [PMID: 37162152 PMCID: PMC10473214 DOI: 10.1093/plcell/koad127] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Biomolecular condensates are membraneless organelle-like structures that can concentrate molecules and often form through liquid-liquid phase separation. Biomolecular condensate assembly is tightly regulated by developmental and environmental cues. Although research on biomolecular condensates has intensified in the past 10 years, our current understanding of the molecular mechanisms and components underlying their formation remains in its infancy, especially in plants. However, recent studies have shown that the formation of biomolecular condensates may be central to plant acclimation to stress conditions. Here, we describe the mechanism, regulation, and properties of stress-related condensates in plants, focusing on stress granules and processing bodies, 2 of the most well-characterized biomolecular condensates. In this regard, we showcase the proteomes of stress granules and processing bodies in an attempt to suggest methods for elucidating the composition and function of biomolecular condensates. Finally, we discuss how biomolecular condensates modulate stress responses and how they might be used as targets for biotechnological efforts to improve stress tolerance.
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Affiliation(s)
- Jorge Solis-Miranda
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Monika Chodasiewicz
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Department of Biology, University of Crete, Heraklion 71409, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Emilio Gutierrez-Beltran
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
- Departamento de Bioquimica Vegetal y Biologia Molecular, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
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17
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Hickey K, Nazarov T, Smertenko A. Organellomic gradients in the fourth dimension. PLANT PHYSIOLOGY 2023; 193:98-111. [PMID: 37243543 DOI: 10.1093/plphys/kiad310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/29/2023]
Abstract
Organelles function as hubs of cellular metabolism and elements of cellular architecture. In addition to 3 spatial dimensions that describe the morphology and localization of each organelle, the time dimension describes complexity of the organelle life cycle, comprising formation, maturation, functioning, decay, and degradation. Thus, structurally identical organelles could be biochemically different. All organelles present in a biological system at a given moment of time constitute the organellome. The homeostasis of the organellome is maintained by complex feedback and feedforward interactions between cellular chemical reactions and by the energy demands. Synchronized changes of organelle structure, activity, and abundance in response to environmental cues generate the fourth dimension of plant polarity. Temporal variability of the organellome highlights the importance of organellomic parameters for understanding plant phenotypic plasticity and environmental resiliency. Organellomics involves experimental approaches for characterizing structural diversity and quantifying the abundance of organelles in individual cells, tissues, or organs. Expanding the arsenal of appropriate organellomics tools and determining parameters of the organellome complexity would complement existing -omics approaches in comprehending the phenomenon of plant polarity. To highlight the importance of the fourth dimension, this review provides examples of organellome plasticity during different developmental or environmental situations.
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Affiliation(s)
- Kathleen Hickey
- Institute of Biological Chemistry, College of Agricultural, Human, and Natural Resources Sciences, Washington State University, Pullman, 99164 WA, USA
| | - Taras Nazarov
- Institute of Biological Chemistry, College of Agricultural, Human, and Natural Resources Sciences, Washington State University, Pullman, 99164 WA, USA
| | - Andrei Smertenko
- Institute of Biological Chemistry, College of Agricultural, Human, and Natural Resources Sciences, Washington State University, Pullman, 99164 WA, USA
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18
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Xu W, Jian S, Li J, Wang Y, Zhang M, Xia K. Genomic Identification of CCCH-Type Zinc Finger Protein Genes Reveals the Role of HuTZF3 in Tolerance of Heat and Salt Stress of Pitaya (Hylocereus polyrhizus). Int J Mol Sci 2023; 24:ijms24076359. [PMID: 37047333 PMCID: PMC10094633 DOI: 10.3390/ijms24076359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Pitaya (Hylocereus polyrhizus) is cultivated in a broad ecological range, due to its tolerance to drought, heat, and poor soil. The zinc finger proteins regulate gene expression at the transcriptional and post-transcriptional levels, by interacting with DNA, RNA, and proteins, to play roles in plant growth and development, and stress response. Here, a total of 81 CCCH-type zinc finger protein genes were identified from the pitaya genome. Transcriptomic analysis showed that nine of them, including HuTZF3, responded to both salt and heat stress. RT-qPCR results showed that HuTZF3 is expressed in all tested organs of pitaya, with a high level in the roots and stems, and confirmed that expression of HuTZF3 is induced by salt and heat stress. Subcellular localization showed that HuTZF3 is targeted in the processing bodies (PBs) and stress granules (SGs). Heterologous expression of HuTZF3 could improve both salt and heat tolerance in Arabidopsis, reduce oxidative stress, and improve the activity of catalase and peroxidase. Therefore, HuTZF3 may be involved in post-transcriptional regulation via localizing to PBs and SGs, contributing to both salt and heat tolerance in pitaya.
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Affiliation(s)
- Weijuan Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuguang Jian
- South China National Botanical Garden, Guangzhou 510650, China
- CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jianyi Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yusang Wang
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- Correspondence: (M.Z.); (K.X.); Tel./Fax: +86-20-37252891 (M.Z.)
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- Correspondence: (M.Z.); (K.X.); Tel./Fax: +86-20-37252891 (M.Z.)
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19
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Liu C, Mentzelopoulou A, Muhammad A, Volkov A, Weijers D, Gutierrez-Beltran E, Moschou PN. An actin remodeling role for Arabidopsis processing bodies revealed by their proximity interactome. EMBO J 2023; 42:e111885. [PMID: 36741000 PMCID: PMC10152145 DOI: 10.15252/embj.2022111885] [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: 06/15/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
Cellular condensates can comprise membrane-less ribonucleoprotein assemblies with liquid-like properties. These cellular condensates influence various biological outcomes, but their liquidity hampers their isolation and characterization. Here, we investigated the composition of the condensates known as processing bodies (PBs) in the model plant Arabidopsis thaliana through a proximity-biotinylation proteomics approach. Using in situ protein-protein interaction approaches, genetics and high-resolution dynamic imaging, we show that processing bodies comprise networks that interface with membranes. Surprisingly, the conserved component of PBs, DECAPPING PROTEIN 1 (DCP1), can localize to unique plasma membrane subdomains including cell edges and vertices. We characterized these plasma membrane interfaces and discovered a developmental module that can control cell shape. This module is regulated by DCP1, independently from its role in decapping, and the actin-nucleating SCAR-WAVE complex, whereby the DCP1-SCAR-WAVE interaction confines and enhances actin nucleation. This study reveals an unexpected function for a conserved condensate at unique membrane interfaces.
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Affiliation(s)
- Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Andriani Mentzelopoulou
- Department of Biology, University of Crete, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Amna Muhammad
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.,University Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Andriy Volkov
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Seville, Spain.,Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.,Department of Biology, University of Crete, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
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20
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Lu W, Wen J. H 2S-mediated inhibition of RhoA/ROCK pathway and noncoding RNAs in ischemic stroke. Metab Brain Dis 2023; 38:163-176. [PMID: 36469178 DOI: 10.1007/s11011-022-01130-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/22/2022] [Indexed: 12/11/2022]
Abstract
Ischemic stroke is one of major causes of disability. In the pathological process of ischemic stroke, the up-regulation of Ras homolog gene family, member A (RhoA) and its downstream effector, Ras homolog gene family (Rho)-associated coiled coil-containing kinase (ROCK), contribute to the neuroinflammation, blood-brain barrier (BBB) dysfunction, neuronal apoptosis, axon growth inhibition and astrogliosis. Accumulating evidences have revealed that hydrogen sulphide (H2S) could reduce brain injury in animal model of ischemic stroke via inhibiting the RhoA/ROCK pathway. Recently, noncoding RNAs (ncRNAs) such as circular RNAs (circRNAs), long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) have attracted much attention because of their essential role in adjusting gene expression both in physiological and pathological conditions. Numerous studies have uncovered the role of RhoA/ROCK pathway and ncRNAs in ischemic stroke. In this review, we focused on the role of H2S, RhoA/ROCK pathway and ncRNAs in ischemic stroke and aimed to reveal new strategies for preventing and treating this devastating disease.
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Affiliation(s)
- Weizhuo Lu
- Medical Branch, Hefei Technology College, Hefei, China
| | - Jiyue Wen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
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21
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Abstract
The capacity of cells to organize complex biochemical reactions in intracellular space is a fundamental organizational principle of life. Key to this organization is the compartmentalization of the cytoplasm into distinct organelles, which is frequently achieved through intracellular membranes. Recent evidence, however, has added a new layer of flexibility to cellular compartmentalization. As such, in response to specific stimuli, liquid-liquid phase separations can lead to the rapid rearrangements of the cytoplasm to form membraneless organelles. Stress granules (SGs) are one such type of organelle that form specifically when cells are faced with stress stimuli, to aid cells in coping with stress. Inherently, altered SG formation has been linked to the pathogenesis of diseases associated with stress and inflammatory conditions, including cancer. Exciting discoveries have indicated an intimate link between SGs and tumorigenesis. Several pro-tumorigenic signaling molecules including the RAS oncogene, mTOR, and histone deacetylase 6 (HDAC6) have been shown to upregulate SG formation. Based on these studies, SGs have emerged as structures that can integrate oncogenic signaling and tumor-associated stress stimuli to enhance cancer cell fitness. In addition, growing evidence over the past decade suggests that SGs function not only to regulate the switch between survival and cell death, but also contribute to cancer cell proliferation, invasion, metastasis, and drug resistance. Although much remains to be learned about the role of SGs in tumorigenesis, these studies highlight SGs as a key regulatory hub in cancer and a promising therapeutic target.
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Affiliation(s)
- Min-Seok Song
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Elda Grabocka
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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22
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Workman RJ, Gorle S, Pettitt BM. Effects of Conformational Constraint on Peptide Solubility Limits. J Phys Chem B 2022; 126:10510-10518. [PMID: 36450134 DOI: 10.1021/acs.jpcb.2c06458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Liquid-liquid phase separation of proteins preferentially involves intrinsically disordered proteins or disordered regions. Understanding the solution chemistry of these phase separations is key to learning how to quantify and manipulate systems that involve such processes. Here, we investigate the effect of cyclization on the liquid-liquid phase separation of short polyglycine peptides. We simulated separate aqueous systems of supersaturated cyclic and linear GGGGG and observed spontaneous liquid-liquid phase separation in each of the solutions. The cyclic GGGGG phase separates less robustly than linear GGGGG and has a higher aqueous solubility, even though linear GGGGG has a more favorable single molecule solvation free energy. The versatile and abundant interpeptide contacts formed by the linear GGGGG stabilize the condensed droplet phase, driving the phase separation in this system. In particular, we find that van der Waals close contact interactions are enriched in the droplet phase as opposed to electrostatic interactions. An analysis of the change in backbone conformational entropy that accompanies the phase transition revealed that cyclic peptides lose significantly less entropy in this process as expected. However, we find that the enhanced interaction enthalpy of linear GGGGG in the droplet phase is enough to compensate for a larger decrease in conformational entropy.
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Affiliation(s)
- Riley J Workman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
| | - Suresh Gorle
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
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23
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Berková V, Berka M, Griga M, Kopecká R, Prokopová M, Luklová M, Horáček J, Smýkalová I, Čičmanec P, Novák J, Brzobohatý B, Černý M. Molecular Mechanisms Underlying Flax ( Linum usitatissimum L.) Tolerance to Cadmium: A Case Study of Proteome and Metabolome of Four Different Flax Genotypes. PLANTS (BASEL, SWITZERLAND) 2022; 11:2931. [PMID: 36365383 PMCID: PMC9655427 DOI: 10.3390/plants11212931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Cadmium is one of the most toxic heavy metal pollutants, and its accumulation in the soil is harmful to agriculture. Plants have a higher cadmium tolerance than animals, and some species can be used for phytoremediation. Flax (Linum usitatissimum L.) can accumulate high amounts of cadmium, but the molecular mechanism behind its tolerance is unknown. Here, we employed four genotypes representing two fiber cultivars, an oilseed breeding line, and a transgenic line overexpressing the metallothionein domain for improved cadmium tolerance. We analyzed the proteome of suspensions and the proteome and metabolome of seedling roots in response to cadmium. We identified more than 1400 differentially abundant proteins representing putative mechanisms in cadmium tolerance, including metal-binding proteins and transporters, enzymes of flavonoid, jasmonate, polyamine, glutathione metabolism, and HSP70 proteins. Our data indicated the role of the phytohormone cytokinin in the observed responses. The metabolome profiling found that pipecolinic acid could be a part of the cadmium accumulation mechanism, and the observed accumulation of putrescine, coumaric acid, cinnamic acid, and coutaric acid confirmed the role of polyamines and flavonoids in tolerance to cadmium. In conclusion, our data provide new insight into cadmium tolerance and prospective targets for improving cadmium tolerance in other plants.
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Affiliation(s)
- Veronika Berková
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Miroslav Griga
- Plant Biotechnology Department, Agritec Plant Research, Ltd., 78701 Šumperk, Czech Republic
| | - Romana Kopecká
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Miroslava Prokopová
- Plant Biotechnology Department, Agritec Plant Research, Ltd., 78701 Šumperk, Czech Republic
| | - Markéta Luklová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Jiří Horáček
- Plant Biotechnology Department, Agritec Plant Research, Ltd., 78701 Šumperk, Czech Republic
| | - Iva Smýkalová
- Plant Biotechnology Department, Agritec Plant Research, Ltd., 78701 Šumperk, Czech Republic
| | - Petr Čičmanec
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
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24
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Efficient DNA fluorescence labeling via base excision trapping. Nat Commun 2022; 13:5043. [PMID: 36028479 PMCID: PMC9418136 DOI: 10.1038/s41467-022-32494-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/03/2022] [Indexed: 01/19/2023] Open
Abstract
Fluorescence labeling of DNAs is broadly useful, but methods for labeling are expensive and labor-intensive. Here we describe a general method for fluorescence labeling of oligonucleotides readily and cost-efficiently via base excision trapping (BETr), employing deaminated DNA bases to mark label positions, which are excised by base excision repair enzymes generating AP sites. Specially designed aminooxy-substituted rotor dyes trap the AP sites, yielding high emission intensities. BETr is orthogonal to DNA synthesis by polymerases, enabling multi-uracil incorporation into an amplicon and in situ BETr labeling without washing. BETr also enables labeling of dsDNA such as genomic DNA at a high labeling density in a single tube by use of nick translation. Use of two different deaminated bases facilitates two-color site-specific labeling. Use of a multi-labeled DNA construct as a bright fluorescence tag is demonstrated through the conjugation to an antibody for imaging proteins. Finally, double-strand selectivity of a repair enzyme is harnessed in sensitive reporting on the presence of a target DNA or RNA in a mixture with isothermal turnover and single nucleotide specificity. Overall, the results document a convenient and versatile method for general fluorescence labeling of DNAs.
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25
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Yu H, Chen Q, Pan Y. A bibliometric and emerging trend analysis on stress granules from 2011 to 2020: A systematic review and bibliometrics analysis. Medicine (Baltimore) 2022; 101:e29200. [PMID: 35866775 PMCID: PMC9302325 DOI: 10.1097/md.0000000000029200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Stress granules (SGs) are the dense granules formed in the cytoplasm of eukaryotic cells in response to stress stimuli, such as endoplasmic reticulum stress, heat shock, hypoxia, and arsenate exposure. Although SGs have been attracting a lot of research attention, there is still a lack of systematic analysis of SGs in the literature. METHODS By analyzing the literature published in the Web of Science database using the R software, we extracted all the information related to SGs from the literature and cited references. The following information was included: publications per year, overall citations, top 10 countries, top 10 authors, co-author collaborations, top 10 institutions, critical areas, and top 10 cited research articles. RESULTS A total of 4052 articles related to SGs were selected and screened. These documents have been cited a total of 110,553 times, with an H-index of 126 and an average of 27.28 citations per article. The authors of the literature included in this study were from 89 different countries/regions. The United States and China had the highest number of publications and ranking institutions. CONCLUSIONS This article presents essential insights on the characteristics and influence of SGs, demonstrating their indispensable role in immune regulation and other fields.
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Affiliation(s)
- Haiyang Yu
- Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui Province, China
- The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui Province, China
| | - Qinhao Chen
- Wannan Medical College, Wuhu, Anhui Province, China
| | - Yueyin Pan
- Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui Province, China
- The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui Province, China
- *Correspondence: Yueyin Pan, Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui Province, China (e-mail: )
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26
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Tong J, Ren Z, Sun L, Zhou S, Yuan W, Hui Y, Ci D, Wang W, Fan LM, Wu Z, Qian W. ALBA proteins confer thermotolerance through stabilizing HSF messenger RNAs in cytoplasmic granules. NATURE PLANTS 2022; 8:778-791. [PMID: 35817823 DOI: 10.1038/s41477-022-01175-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 05/23/2022] [Indexed: 05/16/2023]
Abstract
High temperature is one of the major environmental stresses affecting plant growth and fitness. Heat stress transcription factors (HSFs) play critical roles in regulating the expression of heat-responsive genes. However, how HSFs are regulated remains obscure. Here, we show that ALBA4, ALBA5 and ALBA6, which phase separate into stress granules (SGs) and processing bodies (PBs) under heat stress, directly bind selected messenger RNAs, including HSF mRNAs, and recruit them into SGs and PBs to protect them from degradation under heat stress in Arabidopsis. The alba456 triple mutants, but not single and double mutants, display pleiotropic developmental defects and hypersensitivity to heat stress. Mutations in XRN4, a cytoplasmic 5' to 3' exoribonuclease, can rescue the observed developmental and heat-sensitive phenotypes of alba456 seedlings. Our study reveals a new layer of regulation for HSFs whereby HSF mRNAs are stabilized by redundant action of ALBA proteins in SGs and PBs for plant thermotolerance.
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Affiliation(s)
- Jinjin Tong
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Zhitong Ren
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Sixian Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Yuan
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Yufan Hui
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- School of Computing Sciences, University of East Anglia, Norwich, UK
| | - Dong Ci
- School of Life Sciences, Peking University, Beijing, China
| | - Wei Wang
- School of Life Sciences, Peking University, Beijing, China
| | - Liu-Min Fan
- School of Life Sciences, Peking University, Beijing, China
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, China.
- School of Life Sciences, Peking University, Beijing, China.
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27
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Inhibition of RNA Binding in SND1 Increases the Levels of miR-1-3p and Sensitizes Cancer Cells to Navitoclax. Cancers (Basel) 2022; 14:cancers14133100. [PMID: 35804872 PMCID: PMC9265050 DOI: 10.3390/cancers14133100] [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: 02/03/2022] [Revised: 04/29/2022] [Accepted: 06/18/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Despite of decades of intensive research, several cancer types, for example aggressive colon cancers, are still difficult to treat, and life expectancy is low. Since cancer cells are often resilient and tolerate chemical stresses such as cancer drugs efficiently, they have been difficult to treat. Therefore, combined treatment methods that target cancer cells’ stress tolerance may enhance the treatment outcome. Here we have shown that certain cancer drugs are more effective in colon cancer cells when the expression of a protein called SND1, implicated in regulation of stress responses, is prevented in those cells. We also found that a drug compound called suramin binds to a certain “pocket” of an SND1 protein, and this prevents the interaction of SND1 and certain small RNA molecules, called microRNAs. This block of SND1-microRNA interaction reduces the resilience of colon cancer cells and thus sensitizes them to cancer treatment. Abstract SND1 is an RNA-binding protein overexpressed in large variety of cancers. SND1 has been proposed to enhance stress tolerance in cancer cells, but the molecular mechanisms are still poorly understood. We analyzed the expression of 372 miRNAs in the colon carcinoma cell line and show that SND1 silencing increases the expression levels of several tumor suppressor miRNAs. Furthermore, SND1 knockdown showed synergetic effects with cancer drugs through MEK-ERK and Bcl-2 family-related apoptotic pathways. To explore whether the SND1-mediated RNA binding/degradation is responsible for the observed effect, we developed a screening assay to identify small molecules that inhibit the RNA-binding function of SND1. The screen identified P2X purinoreceptor antagonists as the most potent inhibitors. Validation confirmed that the best hit, suramin, inhibits the RNA binding ability of SND1. The binding characteristics and mode of suramin to SND1 were characterized biophysically and by molecular docking that identified positively charged binding cavities in Staphylococcus nuclease domains. Importantly, suramin-mediated inhibition of RNA binding increased the expression of miR-1-3p, and enhanced sensitivity of cancer cells to Bcl-2 inhibitor navitoclax treatment. Taken together, we demonstrate as proof-of-concept a mechanism and an inhibitor compound for SND1 regulation of the survival of cancer cells through tumor suppressor miRNAs.
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28
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Chodasiewicz M, Jang JC, Gutierrez-Beltran E. Editorial: Biology of Stress Granules in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:938654. [PMID: 35755667 PMCID: PMC9218739 DOI: 10.3389/fpls.2022.938654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - J. C. Jang
- Department of Horticulture and Crop Science and Department of Molecular Genetics, Center for Applied Plant Sciences and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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29
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Basak S, Kundu P. Plant metacaspases: Decoding their dynamics in development and disease. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 180:50-63. [PMID: 35390704 DOI: 10.1016/j.plaphy.2022.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/02/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Plant metacaspases were evolved in parallel to well-characterized animal counterpart caspases and retained the similar histidine-cysteine catalytic dyad, leading to functional congruity between these endopeptidases. Although phylogenetic relatedness of the catalytic domain and functional commonality placed these proteases in the caspase family, credible counterarguments predominantly about their distinct substrate specificity raised doubts about the classification. Metacaspases are involved in regulating the PCD during development as well as in senescence. Balancing acts of metacaspase activity also dictate cell fate during defense upon the perception of adverse environmental cues. Accordingly, their activity is tightly regulated, while suppressing spurious activation, by a combination of genetic and post-translational modifications. Structural insights from recent studies provided vital clues on the functionality. This comprehensive review aims to explore the origin of plant metacaspases, and their regulatory and functional diversity in different plants while discussing their analogy to mammalian caspases. Besides, we have presented various modern methodologies for analyzing the proteolytic activity of these indispensable molecules in the healthy or stressed life of a plant. The review would serve as a repository of all the available pieces of evidence indicating metacaspases as the key regulator of PCD across the plant kingdom and highlight the prospect of studying metacaspases for their inclusion in a crop improvement program.
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Affiliation(s)
- Shrabani Basak
- Division of Plant Biology, Bose Institute, EN-80, Sector V, Bidhannagar, Kolkata, 700091, West Bengal, India.
| | - Pallob Kundu
- Division of Plant Biology, Bose Institute, EN-80, Sector V, Bidhannagar, Kolkata, 700091, West Bengal, India.
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30
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Wang W, Gu Y. The emerging role of biomolecular condensates in plant immunity. THE PLANT CELL 2022; 34:1568-1572. [PMID: 34599333 PMCID: PMC9048959 DOI: 10.1093/plcell/koab240] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/22/2021] [Indexed: 05/29/2023]
Abstract
Biomolecular condensates are dynamic nonmembranous structures that seclude and concentrate molecules involved in related biochemical and molecular processes. Recent studies have revealed that a surprisingly large number of fundamentally important cellular processes are driven and regulated by this potentially ancient biophysical principle. Here, we summarize critical findings and new insights from condensate studies that are related to plant immunity. We discuss the role of stress granules and newly identified biomolecular condensates in coordinating plant immune responses and plant-microbe interactions.
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Affiliation(s)
- Wei Wang
- Author for correspondence: (W.W.), (Y.G.)
| | - Yangnan Gu
- Author for correspondence: (W.W.), (Y.G.)
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31
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Chodasiewicz M, Kerber O, Gorka M, Moreno JC, Maruri-Lopez I, Minen RI, Sampathkumar A, Nelson ADL, Skirycz A. 2',3'-cAMP treatment mimics the stress molecular response in Arabidopsis thaliana. PLANT PHYSIOLOGY 2022; 188:1966-1978. [PMID: 35043968 PMCID: PMC8968299 DOI: 10.1093/plphys/kiac013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 05/12/2023]
Abstract
The role of the RNA degradation product 2',3'-cyclic adenosine monophosphate (2',3'-cAMP) is poorly understood. Recent studies have identified 2',3'-cAMP in plant material and determined its role in stress signaling. The level of 2',3'-cAMP increases upon wounding, in the dark, and under heat, and 2',3'-cAMP binding to an RNA-binding protein, Rbp47b, promotes stress granule (SG) assembly. To gain further mechanistic insights into the function of 2',3'-cAMP, we used a multi-omics approach by combining transcriptomics, metabolomics, and proteomics to dissect the response of Arabidopsis (Arabidopsis thaliana) to 2',3'-cAMP treatment. We demonstrated that 2',3'-cAMP is metabolized into adenosine, suggesting that the well-known cyclic nucleotide-adenosine pathway of human cells might also exist in plants. Transcriptomics analysis revealed only minor overlap between 2',3'-cAMP- and adenosine-treated plants, suggesting that these molecules act through independent mechanisms. Treatment with 2',3'-cAMP changed the levels of hundreds of transcripts, proteins, and metabolites, many previously associated with plant stress responses, including protein and RNA degradation products, glucosinolates, chaperones, and SG components. Finally, we demonstrated that 2',3'-cAMP treatment influences the movement of processing bodies, confirming the role of 2',3'-cAMP in the formation and motility of membraneless organelles.
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Affiliation(s)
| | - Olga Kerber
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Michal Gorka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Juan C Moreno
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Israel Maruri-Lopez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Romina I Minen
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Andrew D L Nelson
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
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32
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Matoušek J, Steger G. The Splicing Variant TFIIIA-7ZF of Viroid-Modulated Transcription Factor IIIA Causes Physiological Irregularities in Transgenic Tobacco and Transient Somatic Depression of "Degradome" Characteristic for Developing Pollen. Cells 2022; 11:784. [PMID: 35269406 PMCID: PMC8909551 DOI: 10.3390/cells11050784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Viroids are small, non-coding, pathogenic RNAs with a significant ability of adaptation to several basic cellular processes in plants. TFIIIA-7ZF, a splicing variant of transcription factor IIIA, is involved in replication of nuclear-replicating viroids by DNA-dependent polymerase II. We overexpressed NbTFIIIA-7ZF from Nicotiana benthamiana in tobacco (Nicotiana tabacum) where it caused morphological and physiological deviations like plant stunting, splitting of leaf petioles, pistils or apexes, irregular branching of shoots, formation of double-blade leaves, deformation of main stems, and modification of glandular trichomes. Plant aging and senescence was dramatically delayed in transgenic lines. Factors potentially involved in viroid degradation and elimination in pollen were transiently depressed in transgenic leaves. This depressed "degradome" in young plants involved NtTudor S-like nuclease, dicers, argonoute 5, and pollen extracellular nuclease I showing expression in tobacco anthers and leaves. Analysis of the "degradome" in tobacco leaves transformed with either of two hop viroids confirmed modifications of the "degradome" and TFIIIA expression. Thus, the regulatory network connected to TFIIIA-7ZF could be involved in plant pathogenesis as well as in viroid adaptation to avoid its degradation. These results support the hypothesis on a significant impact of limited TFIIIA-7ZF on viroid elimination in pollen.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic;
| | - Gerhard Steger
- Institutfür Pysikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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34
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Zhu S, Gu J, Yao J, Li Y, Zhang Z, Xia W, Wang Z, Gui X, Li L, Li D, Zhang H, Liu C. Liquid-liquid phase separation of RBGD2/4 is required for heat stress resistance in Arabidopsis. Dev Cell 2022; 57:583-597.e6. [DOI: 10.1016/j.devcel.2022.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 08/24/2021] [Accepted: 02/02/2022] [Indexed: 12/28/2022]
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Yan Y, Gan J, Tao Y, Okita TW, Tian L. RNA-Binding Proteins: The Key Modulator in Stress Granule Formation and Abiotic Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:882596. [PMID: 35783947 PMCID: PMC9240754 DOI: 10.3389/fpls.2022.882596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
To cope with abiotic environmental stress, plants rapidly change their gene expression transcriptionally and post-transcriptionally, the latter by translational suppression of selected proteins and the assembly of cytoplasmic stress granules (SGs) that sequester mRNA transcripts. RNA-binding proteins (RBPs) are the major players in these post-transcriptional processes, which control RNA processing in the nucleus, their export from the nucleus, and overall RNA metabolism in the cytoplasm. Because of their diverse modular domain structures, various RBP types dynamically co-assemble with their targeted RNAs and interacting proteins to form SGs, a process that finely regulates stress-responsive gene expression. This review summarizes recent findings on the involvement of RBPs in adapting plants to various abiotic stresses via modulation of specific gene expression events and SG formation. The relationship of these processes with the stress hormone abscisic acid (ABA) is discussed.
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Affiliation(s)
- Yanyan Yan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Jianghuang Gan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Yilin Tao
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- *Correspondence: Thomas W. Okita,
| | - Li Tian
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
- Li Tian,
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36
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Asadi MR, Moslehian MS, Sabaie H, Poornabi M, Ghasemi E, Hassani M, Hussen BM, Taheri M, Rezazadeh M. Stress Granules in the Anti-Cancer Medications Mechanism of Action: A Systematic Scoping Review. Front Oncol 2021; 11:797549. [PMID: 35004322 PMCID: PMC8739770 DOI: 10.3389/fonc.2021.797549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/08/2021] [Indexed: 12/16/2022] Open
Abstract
Stress granule (SG) formation is a well-known cellular mechanism for minimizing stress-related damage and increasing cell survival. In addition to playing a critical role in the stress response, SGs have emerged as critical mediators in human health. It seems logical that SGs play a key role in cancer cell formation, development, and metastasis. Recent studies have shown that many SG components contribute to the anti-cancer medications' responses through tumor-associated signaling pathways and other mechanisms. SG proteins are known for their involvement in the translation process, control of mRNA stability, and capacity to function in both the cytoplasm and nucleus. The current systematic review aimed to include all research on the impact of SGs on the mechanism of action of anti-cancer medications and was conducted using a six-stage methodological framework and the PRISMA guideline. Prior to October 2021, a systematic search of seven databases for eligible articles was performed. Following the review of the publications, the collected data were subjected to quantitative and qualitative analysis. Notably, Bortezomib, Sorafenib, Oxaliplatin, 5-fluorouracil, Cisplatin, and Doxorubicin accounted for the majority of the medications examined in the studies. Overall, this systematic scoping review attempts to demonstrate and give a complete overview of the function of SGs in the mechanism of action of anti-cancer medications by evaluating all research.
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Affiliation(s)
- Mohammad Reza Asadi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hani Sabaie
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marziye Poornabi
- Student Research Committee, School of Medicine, Shahroud University of Medical Science, Shahroud, Iran
| | - Elham Ghasemi
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Mehdi Hassani
- Student Research Committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Maryam Rezazadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
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37
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Liu Y, Liu S, Shi H, Ma J, Jing M, Han Y. The TSN1 Binding Protein RH31 Is a Component of Stress Granules and Participates in Regulation of Salt-Stress Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:804356. [PMID: 35003193 PMCID: PMC8733394 DOI: 10.3389/fpls.2021.804356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/02/2021] [Indexed: 05/29/2023]
Abstract
Tudor staphylococcal nucleases (TSNs) are evolutionarily conserved RNA binding proteins, which include redundant TSN1 and TSN2 in Arabidopsis. It has been showed TSNs are the components of stress granules (SGs) and regulate plant growth under salt stress. In this study, we find a binding protein of TSN1, RH31, which is a DEAD-box RNA helicase (RH). Subcellular localization studies show that RH31 is mainly located in the nucleus, but under salinity, it translocates to the cytoplasm where it accumulates in cytoplasmic granules. After cycloheximide (CHX) treatment which can block the formation of SGs by interfering with mRNP homeostasis, these cytoplasmic granules disappeared. More importantly, RH31 co-localizes with SGs marker protein RBP47. RH31 deletion results in salt-hypersensitive phenotype, while RH31 overexpression causes more resistant to salt stress. In summary, we demonstrate that RH31, the TSN1 binding protein, is a component of plant SGs and participates in regulation of salt-stress tolerance in Arabidopsis.
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Affiliation(s)
- Yanan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- Wheat Research Institute, Weifang Academy of Agricultural Sciences, Weifang, China
| | - Shijie Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huiying Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | | | - Meng Jing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuzhen Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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38
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Sze H, Palanivelu R, Harper JF, Johnson MA. Holistic insights from pollen omics: co-opting stress-responsive genes and ER-mediated proteostasis for male fertility. PLANT PHYSIOLOGY 2021; 187:2361-2380. [PMID: 34601610 PMCID: PMC8644640 DOI: 10.1093/plphys/kiab463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/01/2021] [Indexed: 05/15/2023]
Abstract
Sexual reproduction in flowering plants takes place without an aqueous environment. Sperm are carried by pollen through air to reach the female gametophyte, though the molecular basis underlying the protective strategy of the male gametophyte is poorly understood. Here we compared the published transcriptomes of Arabidopsis thaliana pollen, and of heat-responsive genes, and uncovered insights into how mature pollen (MP) tolerates desiccation, while developing and germinating pollen are vulnerable to heat stress. Germinating pollen expresses molecular chaperones or "heat shock proteins" in the absence of heat stress. Furthermore, pollen tubes that grew through pistils at basal temperature showed induction of the endoplasmic reticulum (ER) stress response, which is a characteristic of stressed vegetative tissues. Recent studies show MP contains mRNA-protein (mRNP) aggregates that resemble "stress" granules triggered by heat or other stresses to protect cells. Based on these observations, we postulate that mRNP particles are formed in maturing pollen in response to developmentally programmed dehydration. Dry pollen can withstand harsh conditions as it is dispersed in air. We propose that, when pollen lands on a compatible pistil and hydrates, mRNAs stored in particles are released, aided by molecular chaperones, to become translationally active. Pollen responds to osmotic, mechanical, oxidative, and peptide cues that promote ER-mediated proteostasis and membrane trafficking for tube growth and sperm discharge. Unlike vegetative tissues, pollen depends on stress-protection strategies for its normal development and function. Thus, heat stress during reproduction likely triggers changes that interfere with the normal pollen responses, thereby compromising male fertility. This holistic perspective provides a framework to understand the basis of heat-tolerant strains in the reproduction of crops.
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Affiliation(s)
- Heven Sze
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
- Author for communication:
| | | | - Jeffrey F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Mark A Johnson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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39
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Amen T, Guihur A, Zelent C, Ursache R, Wilting J, Kaganovich D. Resveratrol and related stilbene derivatives induce stress granules with distinct clearance kinetics. Mol Biol Cell 2021; 32:ar18. [PMID: 34432484 PMCID: PMC8693967 DOI: 10.1091/mbc.e21-02-0066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Stress granules (SGs) are ribonucleoprotein functional condensates that form under stress conditions in all eukaryotic cells. Although their stress-survival function is far from clear, SGs have been implicated in the regulation of many vital cellular pathways. Consequently, SG dysfunction is thought to be a mechanistic point of origin for many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). Additionally, SGs are thought to play a role in pathogenic pathways as diverse as viral infection and chemotherapy resistance. There is a growing consensus on the hypothesis that understanding the mechanistic regulation of SG physical properties is essential to understanding their function. Although the internal dynamics and condensation mechanisms of SGs have been broadly investigated, there have been fewer investigations into the timing of SG formation and clearance in live cells. Because the lifetime of SG persistence can be a key factor in their function and tendency toward pathological dysregulation, SG clearance mechanisms deserve particular attention. Here we show that resveratrol and its analogues piceatannol, pterostilbene, and 3,4,5,4'-tetramethoxystilbene induce G3BP-dependent SG formation with atypically rapid clearance kinetics. Resveratrol binds to G3BP, thereby reducing its protein-protein association valency. We suggest that altering G3BP valency is a pathway for the formation of uniquely transient SGs.
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Affiliation(s)
- Triana Amen
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37073, Goettingen, Germany
| | - Anthony Guihur
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Christina Zelent
- Department of Anatomy and Cell Biology, University Medical Center Göttingen, 37073, Goettingen, Germany
| | - Robertas Ursache
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Jörg Wilting
- Department of Anatomy and Cell Biology, University Medical Center Göttingen, 37073, Goettingen, Germany
| | - Daniel Kaganovich
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37073, Goettingen, Germany.,1Base Pharmaceuticals, Boston, MA, 02129, USA
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40
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Kimura T, Horikoshi Y, Kuriyagawa C, Niiyama Y. Rho/ROCK Pathway and Noncoding RNAs: Implications in Ischemic Stroke and Spinal Cord Injury. Int J Mol Sci 2021; 22:ijms222111573. [PMID: 34769004 PMCID: PMC8584200 DOI: 10.3390/ijms222111573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/24/2021] [Indexed: 01/18/2023] Open
Abstract
Ischemic strokes (IS) and spinal cord injuries (SCI) are major causes of disability. RhoA is a small GTPase protein that activates a downstream effector, ROCK. The up-regulation of the RhoA/ROCK pathway contributes to neuronal apoptosis, neuroinflammation, blood-brain barrier dysfunction, astrogliosis, and axon growth inhibition in IS and SCI. Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), were previously considered to be non-functional. However, they have attracted much attention because they play an essential role in regulating gene expression in physiological and pathological conditions. There is growing evidence that ROCK inhibitors, such as fasudil and VX-210, can reduce injury in IS and SCI in animal models and clinical trials. Recently, it has been reported that miRNAs are decreased in IS and SCI, while lncRNAs are increased. Inhibiting the Rho/ROCK pathway with miRNAs alleviates apoptosis, neuroinflammation, oxidative stress, and axon growth inhibition in IS and SCI. Further studies are required to explore the significance of ncRNAs in IS and SCI and to establish new strategies for preventing and treating these devastating diseases.
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Affiliation(s)
- Tetsu Kimura
- Correspondence: ; Tel.: +81-18-884-6175; Fax: +81-18-884-6448
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41
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Asadi MR, Rahmanpour D, Moslehian MS, Sabaie H, Hassani M, Ghafouri-Fard S, Taheri M, Rezazadeh M. Stress Granules Involved in Formation, Progression and Metastasis of Cancer: A Scoping Review. Front Cell Dev Biol 2021; 9:745394. [PMID: 34604242 PMCID: PMC8485071 DOI: 10.3389/fcell.2021.745394] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022] Open
Abstract
The assembly of stress granules (SGs) is a well-known cellular strategy for reducing stress-related damage and promoting cell survival. SGs have become important players in human health, in addition to their fundamental role in the stress response. The critical role of SGs in cancer cells in formation, progression, and metastasis makes sense. Recent researchers have found that several SG components play a role in tumorigenesis and cancer metastasis via tumor-associated signaling pathways and other mechanisms. Gene-ontology analysis revealed the role of these protein components in the structure of SGs. Involvement in the translation process, regulation of mRNA stability, and action in both the cytoplasm and nucleus are among the main features of SG proteins. The present scoping review aimed to consider all studies on the effect of SGs on cancer formation, proliferation, and metastasis and performed based on a six-stage methodology structure and the PRISMA guideline. A systematic search of seven databases for qualified articles was conducted before July 2021. Publications were screened, and quantitative and qualitative analysis was performed on the extracted data. Go analysis was performed on seventy-one SGs protein components. Remarkably G3BP1, TIA1, TIAR, and YB1 have the largest share among the proteins considered in the studies. Altogether, this scoping review tries to demonstrate and provide a comprehensive summary of the role of SGs in the formation, progression, and metastasis of cancer by reviewing all studies.
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Affiliation(s)
- Mohammad Reza Asadi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Dara Rahmanpour
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hani Sabaie
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Hassani
- Student Research Committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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42
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Gutierrez‐Beltran E, Elander PH, Dalman K, Dayhoff GW, Moschou PN, Uversky VN, Crespo JL, Bozhkov PV. Tudor staphylococcal nuclease is a docking platform for stress granule components and is essential for SnRK1 activation in Arabidopsis. EMBO J 2021; 40:e105043. [PMID: 34287990 PMCID: PMC8447601 DOI: 10.15252/embj.2020105043] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Tudor staphylococcal nuclease (TSN; also known as Tudor-SN, p100, or SND1) is a multifunctional, evolutionarily conserved regulator of gene expression, exhibiting cytoprotective activity in animals and plants and oncogenic activity in mammals. During stress, TSN stably associates with stress granules (SGs), in a poorly understood process. Here, we show that in the model plant Arabidopsis thaliana, TSN is an intrinsically disordered protein (IDP) acting as a scaffold for a large pool of other IDPs, enriched for conserved stress granule components as well as novel or plant-specific SG-localized proteins. While approximately 30% of TSN interactors are recruited to stress granules de novo upon stress perception, 70% form a protein-protein interaction network present before the onset of stress. Finally, we demonstrate that TSN and stress granule formation promote heat-induced activation of the evolutionarily conserved energy-sensing SNF1-related protein kinase 1 (SnRK1), the plant orthologue of mammalian AMP-activated protein kinase (AMPK). Our results establish TSN as a docking platform for stress granule proteins, with an important role in stress signalling.
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Affiliation(s)
- Emilio Gutierrez‐Beltran
- Instituto de Bioquímica Vegetal y FotosíntesisConsejo Superior de Investigaciones Científicas (CSIC)‐Universidad de SevillaSevillaSpain
- Departamento de Bioquímica Vegetal y Biología MolecularFacultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Pernilla H Elander
- Department of Molecular SciencesUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsalaSweden
| | - Kerstin Dalman
- Department of Molecular SciencesUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsalaSweden
| | - Guy W Dayhoff
- Department of ChemistryCollege of Art and SciencesUniversity of South FloridaTampaFLUSA
| | - Panagiotis N Moschou
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology ‐ HellasHeraklionGreece
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsalaSweden
- Department of BiologyUniversity of CreteHeraklionGreece
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of MedicineUniversity of South FloridaTampaFLUSA
- Institute for Biological Instrumentation of the Russian Academy of SciencesFederal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”PushchinoRussia
| | - Jose L Crespo
- Instituto de Bioquímica Vegetal y FotosíntesisConsejo Superior de Investigaciones Científicas (CSIC)‐Universidad de SevillaSevillaSpain
| | - Peter V Bozhkov
- Department of Molecular SciencesUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsalaSweden
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Maruri-López I, Figueroa NE, Hernández-Sánchez IE, Chodasiewicz M. Plant Stress Granules: Trends and Beyond. FRONTIERS IN PLANT SCIENCE 2021; 12:722643. [PMID: 34434210 PMCID: PMC8381727 DOI: 10.3389/fpls.2021.722643] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/01/2021] [Indexed: 05/20/2023]
Abstract
Stress granules (SGs) are dynamic membrane-less condensates transiently assembled through liquid-liquid phase separation (LLPS) in response to stress. SGs display a biphasic architecture constituted of core and shell phases. The core is a conserved SG fraction fundamental for its assembly and consists primarily of proteins with intrinsically disordered regions and RNA-binding domains, along with translational-related proteins. The shell fraction contains specific SG components that differ among species, cell type, and developmental stage and might include metabolic enzymes, receptors, transcription factors, untranslated mRNAs, and small molecules. SGs assembly positively correlates with stalled translation associated with stress responses playing a pivotal role during the adaptive cellular response, post-stress recovery, signaling, and metabolic rewire. After stress, SG disassembly releases mRNA and proteins to the cytoplasm to reactivate translation and reassume cell growth and development. However, under severe stress conditions or aberrant cellular behavior, SG dynamics are severely disturbed, affecting cellular homeostasis and leading to cell death in the most critical cases. The majority of research on SGs has focused on yeast and mammals as model organism. Nevertheless, the study of plant SGs has attracted attention in the last few years. Genetics studies and adapted techniques from other non-plant models, such as affinity capture coupled with multi-omics analyses, have enriched our understanding of SG composition in plants. Despite these efforts, the investigation of plant SGs is still an emerging field in plant biology research. In this review, we compile and discuss the accumulated progress of plant SGs regarding their composition, organization, dynamics, regulation, and their relation to other cytoplasmic foci. Lastly, we will explore the possible connections among the most exciting findings of SGs from mammalian, yeast, and plants, which might help provide a complete view of the biology of plant SGs in the future.
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Affiliation(s)
| | | | | | - Monika Chodasiewicz
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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44
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Dorone Y, Boeynaems S, Flores E, Jin B, Hateley S, Bossi F, Lazarus E, Pennington JG, Michiels E, De Decker M, Vints K, Baatsen P, Bassel GW, Otegui MS, Holehouse AS, Exposito-Alonso M, Sukenik S, Gitler AD, Rhee SY. A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell 2021; 184:4284-4298.e27. [PMID: 34233164 PMCID: PMC8513799 DOI: 10.1016/j.cell.2021.06.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 03/22/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.
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Affiliation(s)
- Yanniv Dorone
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eduardo Flores
- Department of Chemistry and Chemical Biology, UC Merced, Merced, CA 95340, USA
| | - Benjamin Jin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Shannon Hateley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Flavia Bossi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Elena Lazarus
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Janice G Pennington
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
| | - Emiel Michiels
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Mathias De Decker
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium; KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Katlijn Vints
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
| | - Pieter Baatsen
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Marisa S Otegui
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA; Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, UC Merced, Merced, CA 95340, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
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45
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Arabidopsis thaliana G3BP Ortholog Rescues Mammalian Stress Granule Phenotype across Kingdoms. Int J Mol Sci 2021; 22:ijms22126287. [PMID: 34208100 PMCID: PMC8230867 DOI: 10.3390/ijms22126287] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
Stress granules (SGs) are dynamic RNA–protein complexes localized in the cytoplasm that rapidly form under stress conditions and disperse when normal conditions are restored. The formation of SGs depends on the Ras-GAP SH3 domain-binding protein (G3BP). Formations, interactions and functions of plant and human SGs are strikingly similar, suggesting a conserved mechanism. However, functional analyses of plant G3BPs are missing. Thus, members of the Arabidopsis thaliana G3BP (AtG3BP) protein family were investigated in a complementation assay in a human G3BP knock-out cell line. It was shown that two out of seven AtG3BPs were able to complement the function of their human homolog. GFP-AtG3BP fusion proteins co-localized with human SG marker proteins Caprin-1 and eIF4G1 and restored SG formation in G3BP double KO cells. Interaction between AtG3BP-1 and -7 and known human G3BP interaction partners such as Caprin-1 and USP10 was also demonstrated by co-immunoprecipitation. In addition, an RG/RGG domain exchange from Arabidopsis G3BP into the human G3BP background showed the ability for complementation. In summary, our results support a conserved mechanism of SG function over the kingdoms, which will help to further elucidate the biological function of the Arabidopsis G3BP protein family.
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46
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Abulfaraj AA, Hirt H, Rayapuram N. G3BPs in Plant Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:680710. [PMID: 34177995 PMCID: PMC8222905 DOI: 10.3389/fpls.2021.680710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/14/2021] [Indexed: 05/24/2023]
Abstract
The sessile nature of plants enforces highly adaptable strategies to adapt to different environmental stresses. Plants respond to these stresses by a massive reprogramming of mRNA metabolism. Balancing of mRNA fates, including translation, sequestration, and decay is essential for plants to not only coordinate growth and development but also to combat biotic and abiotic environmental stresses. RNA stress granules (SGs) and processing bodies (P bodies) synchronize mRNA metabolism for optimum functioning of an organism. SGs are evolutionarily conserved cytoplasmic localized RNA-protein storage sites that are formed in response to adverse conditions, harboring mostly but not always translationally inactive mRNAs. SGs disassemble and release mRNAs into a translationally active form upon stress relief. RasGAP SH3 domain binding proteins (G3BPs or Rasputins) are "scaffolds" for the assembly and stability of SGs, which coordinate receptor mediated signal transduction with RNA metabolism. The role of G3BPs in the formation of SGs is well established in mammals, but G3BPs in plants are poorly characterized. In this review, we discuss recent findings of the dynamics and functions of plant G3BPs in response to environmental stresses and speculate on possible mechanisms such as transcription and post-translational modifications that might regulate the function of this important family of proteins.
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Affiliation(s)
- Aala A. Abulfaraj
- Department of Biological Sciences, Science and Arts College, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heribert Hirt
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Naganand Rayapuram
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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47
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Workman RJ, Pettitt BM. Thermodynamic Compensation in Peptides Following Liquid-Liquid Phase Separation. J Phys Chem B 2021; 125:6431-6439. [PMID: 34110175 DOI: 10.1021/acs.jpcb.1c02093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid-liquid phase separation of proteins often incorporates intrinsically disordered proteins or those with disordered regions. Examining these processes via the entropy change is desirable for establishing a quantitative foundation with which to probe and understand these phase transitions. Of interest is the effect of residue sequence on the entropy of the peptide backbone. In this work we model these systems via all atom simulations of liquid-liquid phase separation of peptides. Systems of supersaturated pentapeptides separate into a peptide-dense liquid droplet phase as well as a dilute (saturated) aqueous phase. An analysis of the change in backbone conformational entropy associated with the phase transition was performed. We examined systems of four different pentapeptides (GGGGG, GGQGG, GGNGG, and GGVGG) in order to explore the effect of sequence variation on the conformational entropy, as well as the effect of side chain variation on the physical characteristics of the droplet phases. We find that the loss of conformational entropy that accompanies aqueous → droplet transitions is more than compensated by a decrease in interaction enthalpy as contributions to the free energy change for the process.
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Affiliation(s)
- Riley J Workman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
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48
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Bai JL, Liu D, Wang R. Self-assembly of Amphiphilic Diblock Copolymers Induced by Liquid-Liquid Phase Separation. CHINESE JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1007/s10118-021-2563-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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49
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Xu R, Guo Y, Peng S, Liu J, Li P, Jia W, Zhao J. Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis. Biomolecules 2021; 11:biom11050688. [PMID: 34063698 PMCID: PMC8147800 DOI: 10.3390/biom11050688] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
Cyclic AMP (cAMP) is a pivotal signaling molecule existing in almost all living organisms. However, the mechanism of cAMP signaling in plants remains very poorly understood. Here, we employ the engineered activity of soluble adenylate cyclase to induce cellular cAMP elevation in Arabidopsis thaliana plants and identify 427 cAMP-responsive genes (CRGs) through RNA-seq analysis. Induction of cellular cAMP elevation inhibits seed germination, disturbs phytohormone contents, promotes leaf senescence, impairs ethylene response, and compromises salt stress tolerance and pathogen resistance. A set of 62 transcription factors are among the CRGs, supporting a prominent role of cAMP in transcriptional regulation. The CRGs are significantly overrepresented in the pathways of plant hormone signal transduction, MAPK signaling, and diterpenoid biosynthesis, but they are also implicated in lipid, sugar, K+, nitrate signaling, and beyond. Our results provide a basic framework of cAMP signaling for the community to explore. The regulatory roles of cAMP signaling in plant plasticity are discussed.
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Affiliation(s)
- Ruqiang Xu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: ; Tel.: +86-0371-6778-5095
| | - Yanhui Guo
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Song Peng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Jinrui Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Panyu Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Wenjing Jia
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Junheng Zhao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
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50
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Mussel M, Basser PJ, Horkay F. Ion-Induced Volume Transition in Gels and Its Role in Biology. Gels 2021; 7:20. [PMID: 33670826 PMCID: PMC8005988 DOI: 10.3390/gels7010020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/12/2022] Open
Abstract
Incremental changes in ionic composition, solvent quality, and temperature can lead to reversible and abrupt structural changes in many synthetic and biopolymer systems. In the biological milieu, this nonlinear response is believed to play an important functional role in various biological systems, including DNA condensation, cell secretion, water flow in xylem of plants, cell resting potential, and formation of membraneless organelles. While these systems are markedly different from one another, a physicochemical framework that treats them as polyelectrolytes, provides a means to interpret experimental results and make in silico predictions. This article summarizes experimental results made on ion-induced volume phase transition in a polyelectrolyte model gel (sodium polyacrylate) and observations on the above-mentioned biological systems indicating the existence of a steep response.
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Affiliation(s)
- Matan Mussel
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | | | - Ferenc Horkay
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
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