1
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Peng Q, Jiao B, Cheng Y, Yuan B, Zhou J, Cai J, Jiang N, Lin H, Xi D. NtG3BPL1 confers resistance to chilli veinal mottle virus through promoting the degradation of 6K2 in tobacco. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38713838 DOI: 10.1111/tpj.16789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/01/2024] [Accepted: 04/10/2024] [Indexed: 05/09/2024]
Abstract
The RNA regulatory network is a complex and dynamic regulation in plant cells involved in mRNA modification, translation, and degradation. Ras-GAP SH3 domain-binding protein (G3BP) is a scaffold protein for the assembly of stress granules (SGs) and is considered an antiviral component in mammals. However, the function of G3BP during virus infection in plants is still largely unknown. In this study, four members of the G3BP-like proteins (NtG3BPLs) were identified in Nicotiana tabacum and the expression levels of NtG3BPL1 were upregulated during chilli veinal mottle virus (ChiVMV) infection. NtG3BPL1 was localized in the nucleus and cytoplasm, forming cytoplasmic granules under transient high-temperature treatment, whereas the abundance of cytoplasmic granules was decreased under ChiVMV infection. Overexpression of NtG3BPL1 inhibited ChiVMV infection and delayed the onset of symptoms, whereas knockout of NtG3BPL1 promoted ChiVMV infection. In addition, NtG3BPL1 directly interacted with ChiVMV 6K2 protein, whereas 6K2 protein had no effect on NtG3BPL1-derived cytoplasmic granules. Further studies revealed that the expression of NtG3BPL1 reduced the chloroplast localization of 6K2-GFP and the NtG3BPL1-6K2 interaction complex was localized in the cytoplasm. Furthermore, NtG3BPL1 promoted the degradation of 6K2 through autophagy pathway, and the accumulation of 6K2 and ChiVMV was affected by autophagy activation or inhibition in plants. Taken together, our results demonstrate that NtG3BPL1 plays a positive role in tobacco resistance against ChiVMV infection, revealing a novel mechanism of plant G3BP in antiviral strategy.
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Affiliation(s)
- Qiding Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Bolei Jiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Yongchao Cheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Bowen Yuan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Jingya Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Jingliu Cai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Ning Jiang
- Agronomic Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, P.R. China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Dehui Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
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2
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Liang Y, Zhang X, Wu B, Wang S, Kang L, Deng Y, Xie L, Li Z. Actomyosin-driven motility and coalescence of phase-separated viral inclusion bodies are required for efficient replication of a plant rhabdovirus. THE NEW PHYTOLOGIST 2023; 240:1990-2006. [PMID: 37735952 DOI: 10.1111/nph.19255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023]
Abstract
Phase separation has emerged as a fundamental principle for organizing viral and cellular membraneless organelles. Although these subcellular compartments have been recognized for decades, their biogenesis and mechanisms of regulation are poorly understood. Here, we investigate the formation of membraneless inclusion bodies (IBs) induced during the infection of a plant rhabdovirus, tomato yellow mottle-associated virus (TYMaV). We generated recombinant TYMaV encoding a fluorescently labeled IB constituent protein and employed live-cell imaging to characterize the intracellular dynamics and maturation of viral IBs in infected Nicotiana benthamiana cells. We show that TYMaV IBs are phase-separated biomolecular condensates and that viral nucleoprotein and phosphoprotein are minimally required for IB formation in vivo and in vitro. TYMaV IBs move along the microfilaments, likely through the anchoring of viral phosphoprotein to myosin XIs. Furthermore, pharmacological disruption of microfilaments or inhibition of myosin XI functions suppresses IB motility, resulting in arrested IB growth and inefficient virus replication. Our study establishes phase separation as a process driving the formation of liquid viral factories and emphasizes the role of the cytoskeletal system in regulating the dynamics of condensate maturation.
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Affiliation(s)
- Yan Liang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoyan Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Binyan Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shuo Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Lihua Kang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Yinlu Deng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Li Xie
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
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3
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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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4
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Field S, Jang GJ, Dean C, Strader LC, Rhee SY. Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development. THE PLANT CELL 2023; 35:3173-3186. [PMID: 36879427 PMCID: PMC10473230 DOI: 10.1093/plcell/koad062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.
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Affiliation(s)
- Sterling Field
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Geng-Jen Jang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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5
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Murase Y, Yamagishi M, Okada N, Toya M, Yajima J, Hamada T, Sato M. Fission yeast Dis1 is an unconventional TOG/XMAP215 that induces microtubule catastrophe to drive chromosome pulling. Commun Biol 2022; 5:1298. [PMID: 36435910 PMCID: PMC9701203 DOI: 10.1038/s42003-022-04271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/16/2022] [Indexed: 11/28/2022] Open
Abstract
The shortening of microtubules attached to kinetochores is the driving force of chromosome movement during cell division. Specific kinesins are believed to shorten microtubules but are dispensable for viability in yeast, implying the existence of additional factors responsible for microtubule shortening. Here, we demonstrate that Dis1, a TOG/XMAP215 ortholog in fission yeast, promotes microtubule shortening to carry chromosomes. Although TOG/XMAP215 orthologs are generally accepted as microtubule polymerases, Dis1 promoted microtubule catastrophe in vitro and in vivo. Notably, microtubule catastrophe was promoted when the tip was attached to kinetochores, as they steadily anchored Dis1 at the kinetochore-microtubule interface. Engineered Dis1 oligomers artificially tethered at a chromosome arm region induced the shortening of microtubules in contact, frequently pulling the chromosome arm towards spindle poles. This effect was not brought by oligomerised Alp14. Thus, unlike Alp14 and other TOG/XMAP215 orthologs, Dis1 plays an unconventional role in promoting microtubule catastrophe, thereby driving chromosome movement.
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Affiliation(s)
- Yuichi Murase
- grid.5290.e0000 0004 1936 9975Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480 Japan
| | - Masahiko Yamagishi
- grid.26999.3d0000 0001 2151 536XDepartment of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, 153-8902 Tokyo Japan
| | - Naoyuki Okada
- grid.5290.e0000 0004 1936 9975Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480 Japan ,grid.5808.50000 0001 1503 7226Instituto de Biologia Molecular e Celular, Instituto de Investigacao e Inovacao em Saude (i3S), Universidade do Porto, 208 Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Mika Toya
- grid.5290.e0000 0004 1936 9975Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480 Japan ,grid.5290.e0000 0004 1936 9975Global Center for Science and Engineering, Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555 Japan ,grid.5290.e0000 0004 1936 9975Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555 Japan
| | - Junichiro Yajima
- grid.26999.3d0000 0001 2151 536XDepartment of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, 153-8902 Tokyo Japan ,grid.26999.3d0000 0001 2151 536XKomaba Institute for Science, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, 153-8902 Tokyo Japan ,grid.26999.3d0000 0001 2151 536XResearch Center for Complex Systems Biology, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, 153-8902 Tokyo Japan
| | - Takahiro Hamada
- grid.444568.f0000 0001 0672 2184Department of Bioscience, Faculty of Life Science, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama-shi 700-0005 Japan
| | - Masamitsu Sato
- grid.5290.e0000 0004 1936 9975Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480 Japan ,grid.5290.e0000 0004 1936 9975Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555 Japan ,grid.5290.e0000 0004 1936 9975Institute for Medical-Oriented Structural Biology, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480 Japan
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6
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Londoño Vélez V, Alquraish F, Tarbiyyah I, Rafique F, Mao D, Chodasiewicz M. Landscape of biomolecular condensates in heat stress responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1032045. [PMID: 36311142 PMCID: PMC9601738 DOI: 10.3389/fpls.2022.1032045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/21/2022] [Indexed: 06/06/2023]
Abstract
High temperature is one of the abiotic stresses that plants face and acts as a major constraint on crop production and food security. Plants have evolved several mechanisms to overcome challenging environments and respond to internal and external stimuli. One significant mechanism is the formation of biomolecular condensates driven by liquid-liquid phase separation. Biomolecular condensates have received much attention in the past decade, especially with regard to how plants perceive temperature fluctuations and their involvement in stress response and tolerance. In this review, we compile and discuss examples of plant biomolecular condensates regarding their composition, localization, and functions triggered by exposure to heat. Bioinformatic tools can be exploited to predict heat-induced biomolecular condensates. As the field of biomolecular condensates has emerged in the study of plants, many intriguing questions have arisen that have yet to be solved. Increased knowledge of biomolecular condensates will help in securing crop production and overcoming limitations caused by heat stress.
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7
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Xu M, Risse J, Kormelink R. Cap-snatching as a possible contributor to photosynthesis shut-off. J Gen Virol 2022; 103. [PMID: 35947091 DOI: 10.1099/jgv.0.001763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cap-snatching is a mechanism applied by segmented, negative strand (-) RNA viruses (NSVs) to initiate genome transcription. So far, the cap donor source of cytoplasmic-replicating NSVs has remained elusive. Recently, studies pointed to processing body (P body, PB) as the potential source for providing capped RNAs but conclusive evidence is still lacking. To attempt identifying these sources, here the 5' non-viral leader sequences of Tomato spotted wilt virus (TSWV) N mRNAs were analysed by high-throughput sequencing (HTS) from plants subjected to normal and heat-stress conditions, and subsequently mapped on host donor transcripts. The majority of non-viral heterogenous, host-derived leader sequences ranged in size between ~10-20 nt and contained A or AG residues at the cleavage site and the presence of certain sequence motifs. Mapping the capped-leader sequences to the 5' UTR region of genes encoded by the Nicotiana tabacum genome, identified 348 donor genes and which were specifically enriched in cellular photosynthesis pathway. Nineteen of those were clearly expressed differentially at normal condition versus heat-stress conditions. Although the results did not point towards snatching of capped-RNA leader sequences from certain cytoplasmic RNA granules in particular, they indicated photosynthesis downregulation (and development of disease symptoms) partially result from cap-snatching.
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Affiliation(s)
- Min Xu
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Judith Risse
- Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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8
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De Jaeger-Braet J, Krause L, Buchholz A, Schnittger A. Heat stress reveals a specialized variant of the pachytene checkpoint in meiosis of Arabidopsis thaliana. THE PLANT CELL 2022; 34:433-454. [PMID: 34718750 PMCID: PMC8846176 DOI: 10.1093/plcell/koab257] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/14/2021] [Indexed: 05/25/2023]
Abstract
Plant growth and fertility strongly depend on environmental conditions such as temperature. Remarkably, temperature also influences meiotic recombination and thus, the current climate change will affect the genetic make-up of plants. To better understand the effects of temperature on meiosis, we followed male meiocytes in Arabidopsis thaliana by live cell imaging under three temperature regimes: at 21°C; at heat shock conditions of 30°C and 34°C; after an acclimatization phase of 1 week at 30°C. This work led to a cytological framework of meiotic progression at elevated temperature. We determined that an increase from 21°C to 30°C speeds up meiosis with specific phases being more amenable to heat than others. An acclimatization phase often moderated this effect. A sudden increase to 34°C promoted a faster progression of early prophase compared to 21°C. However, the phase in which cross-overs mature was prolonged at 34°C. Since mutants involved in the recombination pathway largely did not show the extension of this phase at 34°C, we conclude that the delay is recombination-dependent. Further analysis also revealed the involvement of the ATAXIA TELANGIECTASIA MUTATED kinase in this prolongation, indicating the existence of a pachytene checkpoint in plants, yet in a specialized form.
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Affiliation(s)
- Joke De Jaeger-Braet
- Department of Developmental Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Linda Krause
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anika Buchholz
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arp Schnittger
- Department of Developmental Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
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9
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Náprstková A, Malínská K, Záveská Drábková L, Billey E, Náprstková D, Sýkorová E, Bousquet-Antonelli C, Honys D. Characterization of ALBA Family Expression and Localization in Arabidopsis thaliana Generative Organs. Int J Mol Sci 2021; 22:1652. [PMID: 33562109 PMCID: PMC7914821 DOI: 10.3390/ijms22041652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
ALBA DNA/RNA-binding proteins form an ancient family, which in eukaryotes diversified into two Rpp25-like and Rpp20-like subfamilies. In most studied model organisms, their function remains unclear, but they are usually associated with RNA metabolism, mRNA translatability and stress response. In plants, the enriched number of ALBA family members remains poorly understood. Here, we studied ALBA dynamics during reproductive development in Arabidopsis at the levels of gene expression and protein localization, both under standard conditions and following heat stress. In generative tissues, ALBA proteins showed the strongest signal in mature pollen where they localized predominantly in cytoplasmic foci, particularly in regions surrounding the vegetative nucleus and sperm cells. Finally, we demonstrated the involvement of two Rpp25-like subfamily members ALBA4 and ALBA6 in RNA metabolism in mature pollen supported by their co-localization with poly(A)-binding protein 3 (PABP3). Collectively, we demonstrated the engagement of ALBA proteins in male reproductive development and the heat stress response, highlighting the involvement of ALBA4 and ALBA6 in RNA metabolism, storage and/or translational control in pollen upon heat stress. Such dynamic re-localization of ALBA proteins in a controlled, developmentally and environmentally regulated manner, likely reflects not only their redundancy but also their possible functional diversification in plants.
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Affiliation(s)
- Alena Náprstková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Kateřina Malínská
- Imaging Facility, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic;
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Elodie Billey
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; (E.B.); (C.B.-A.)
- LGDP-UMR5096, Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Dagmar Náprstková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Eva Sýkorová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská, 612 00 Brno, Czech Republic;
| | - Cécile Bousquet-Antonelli
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; (E.B.); (C.B.-A.)
- LGDP-UMR5096, Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
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10
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Koppers M, Özkan N, Farías GG. Complex Interactions Between Membrane-Bound Organelles, Biomolecular Condensates and the Cytoskeleton. Front Cell Dev Biol 2020; 8:618733. [PMID: 33409284 PMCID: PMC7779554 DOI: 10.3389/fcell.2020.618733] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane-bound and membraneless organelles/biomolecular condensates ensure compartmentalization into functionally distinct units enabling proper organization of cellular processes. Membrane-bound organelles form dynamic contacts with each other to enable the exchange of molecules and to regulate organelle division and positioning in coordination with the cytoskeleton. Crosstalk between the cytoskeleton and dynamic membrane-bound organelles has more recently also been found to regulate cytoskeletal organization. Interestingly, recent work has revealed that, in addition, the cytoskeleton and membrane-bound organelles interact with cytoplasmic biomolecular condensates. The extent and relevance of these complex interactions are just beginning to emerge but may be important for cytoskeletal organization and organelle transport and remodeling. In this review, we highlight these emerging functions and emphasize the complex interplay of the cytoskeleton with these organelles. The crosstalk between membrane-bound organelles, biomolecular condensates and the cytoskeleton in highly polarized cells such as neurons could play essential roles in neuronal development, function and maintenance.
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Affiliation(s)
| | | | - Ginny G. Farías
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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11
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Urquidi-Camacho RA, Lokdarshi A, von Arnim AG. Translational gene regulation in plants: A green new deal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1597. [PMID: 32367681 PMCID: PMC9258721 DOI: 10.1002/wrna.1597] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/09/2023]
Abstract
The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants. This article is categorized under: Translation > Translation Regulation RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Ricardo A. Urquidi-Camacho
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Ansul Lokdarshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology and UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
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12
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Emenecker RJ, Holehouse AS, Strader LC. Emerging Roles for Phase Separation in Plants. Dev Cell 2020; 55:69-83. [PMID: 33049212 PMCID: PMC7577370 DOI: 10.1016/j.devcel.2020.09.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022]
Abstract
The plant cell internal environment is a dynamic, intricate landscape composed of many intracellular compartments. Cells organize some cellular components through formation of biomolecular condensates-non-stoichiometric assemblies of protein and/or nucleic acids. In many cases, phase separation appears to either underly or contribute to the formation of biomolecular condensates. Many canonical membraneless compartments within animal cells form in a manner that is at least consistent with phase separation, including nucleoli, stress granules, Cajal bodies, and numerous additional bodies, regulated by developmental and environmental stimuli. In this Review, we examine the emerging roles for phase separation in plants. Further, drawing on studies carried out in other organisms, we identify cellular phenomenon in plants that might also arise via phase separation. We propose that plants make use of phase separation to a much greater extent than has been previously appreciated, implicating phase separation as an evolutionarily ancient mechanism for cellular organization.
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Affiliation(s)
- Ryan J Emenecker
- Department of Biology, Washington University, St. Louis, MO 63130, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA; Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130, 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 Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA.
| | - Lucia C Strader
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA; Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130, USA; Department of Biology, Duke University, Durham, NC 27708, USA.
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13
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Abstract
Stress granules (SGs) are ubiquitous nonmembrane-bound assemblies of protein and mRNA formed under stress conditions associated with stalled translation. SGs are evolutionarily conserved across eukaryotes. The canonical function of SGs is to selectively protect mRNAs and proteins from unfolding and prevent degradation induced by diverse environmental stresses. Moreover, sequestration into SGs provides an elegant way to regulate protein activities. Disassembly of SGs upon stress recovery is accompanied by the reactivation of protein translation and protein activities. The regulatory importance of SGs has been corroborated by recent studies describing the multiomics analysis of the composition of SGs from yeast, animal, and plant cells. Herein, we describe an isolation protocol of SGs that allows for the identification of proteins, mRNA, and metabolites sequestered into SG cores. Furthermore, the described protocols can be used to isolate other SG-like foci. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of SG-enriched fraction from plant material Basic Protocol 2: Affinity purification to isolate SGs Basic Protocol 3: Simultaneous extraction of proteins and metabolites from affinity-purified beads Basic Protocol 4: Protein digestion on affinity-purified beads Basic Protocol 5: Data analysis.
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Affiliation(s)
- Monika Kosmacz
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
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14
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Jang GJ, Jang JC, Wu SH. Dynamics and Functions of Stress Granules and Processing Bodies in Plants. PLANTS 2020; 9:plants9091122. [PMID: 32872650 PMCID: PMC7570210 DOI: 10.3390/plants9091122] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/23/2022]
Abstract
RNA granules, such as stress granules and processing bodies, can balance the storage, degradation, and translation of mRNAs in diverse eukaryotic organisms. The sessile nature of plants demands highly versatile strategies to respond to environmental fluctuations. In this review, we discuss recent findings of the dynamics and functions of these RNA granules in plants undergoing developmental reprogramming or responding to environmental stresses. Special foci include the dynamic assembly, disassembly, and regulatory roles of these RNA granules in determining the fate of mRNAs.
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Affiliation(s)
- Geng-Jen Jang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA;
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
- Correspondence: ; Tel.: +886-2-2787-1178
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15
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Lawrence R, Kaplinsky N. Arabidopsis Heat Shock Granules exhibit dynamic cellular behavior and can form in response to protein misfolding in the absence of elevated temperatures. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000285. [PMID: 32760882 PMCID: PMC7396158 DOI: 10.17912/micropub.biology.000285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - Nick Kaplinsky
- Swarthmore College,
Correspondence to: Nick Kaplinsky ()
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Chodasiewicz M, Sokolowska EM, Nelson-Dittrich AC, Masiuk A, Beltran JCM, Nelson ADL, Skirycz A. Identification and Characterization of the Heat-Induced Plastidial Stress Granules Reveal New Insight Into Arabidopsis Stress Response. FRONTIERS IN PLANT SCIENCE 2020; 11:595792. [PMID: 33224174 PMCID: PMC7674640 DOI: 10.3389/fpls.2020.595792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/07/2020] [Indexed: 05/06/2023]
Abstract
Plants exhibit different physiological and molecular responses to adverse changes in their environment. One such molecular response is the sequestration of proteins, RNAs, and metabolites into cytoplasmic bodies called stress granules (cSGs). Here we report that, in addition to cSGs, heat stress also induces the formation of SG-like foci (cGs) in the chloroplasts of the model plant Arabidopsis thaliana. Similarly to the cSGs, (i) cpSG assemble rapidly in response to stress and disappear when the stress ceases, (ii) cpSG formation is inhibited by treatment with a translation inhibitor (lincomycin), and (iii) cpSG are composed of a stable core and a fluid outer shell. A previously published protocol for cSG extraction was successfully adapted to isolate cpSG, followed by protein, metabolite, and RNA analysis. Analogously to the cSGs, cpSG sequester proteins essential for SG formation, dynamics, and function, also including RNA-binding proteins with prion-like domain, ATPases and chaperones, and the amino acids proline and glutamic acid. However, the most intriguing observation relates to the cpSG localization of proteins, such as a complete magnesium chelatase complex, which is involved in photosynthetic acclimation to stress. These data suggest that cpSG have a role in plant stress tolerance.
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Affiliation(s)
- Monika Chodasiewicz
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Monika Chodasiewicz, ;
| | | | | | | | | | | | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- *Correspondence: Monika Chodasiewicz, ;
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Matsui A, Nakaminami K, Seki M. Biological Function of Changes in RNA Metabolism in Plant Adaptation to Abiotic Stress. PLANT & CELL PHYSIOLOGY 2019; 60:1897-1905. [PMID: 31093678 DOI: 10.1093/pcp/pcz068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/08/2019] [Indexed: 05/28/2023]
Abstract
Plant growth and productivity are greatly impacted by environmental stresses. Therefore, plants have evolved various sophisticated mechanisms for adaptation to nonoptimal environments. Recent studies using RNA metabolism-related mutants have revealed that RNA processing, RNA decay and RNA stability play an important role in regulating gene expression at a post-transcriptional level in response to abiotic stresses. Studies indicate that RNA metabolism is a unified network, and modification of stress adaptation-related transcripts at multiple steps of RNA metabolism is necessary to control abiotic stress-related gene expression. Recent studies have also demonstrated the important role of noncoding RNAs (ncRNAs) in regulating abiotic stress-related gene expression and revealed their involvement in various biological functions through their regulation of DNA methylation, DNA structural modifications, histone modifications and RNA-RNA interactions. ncRNAs regulate mRNA transcription and their synthesis is affected by mRNA processing and degradation. In the present review, recent findings pertaining to the role of the metabolic regulation of mRNAs and ncRNAs in abiotic stress adaptation are summarized and discussed.
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Affiliation(s)
- Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, Japan
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