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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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Wei H, Wang X, Wang K, Tang X, Zhang N, Si H. Transcription factors as molecular switches regulating plant responses to drought stress. PHYSIOLOGIA PLANTARUM 2024; 176:e14366. [PMID: 38812034 DOI: 10.1111/ppl.14366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024]
Abstract
Plants often experience abiotic stress, which severely affects their growth. With the advent of global warming, drought stress has become a pivotal factor affecting crop yield and quality. Increasing numbers of studies have focused on elucidating the molecular mechanisms underlying plant responses to drought stress. As molecular switches, transcription factors (TFs) are key participants in drought-resistance regulatory networks in crops. TFs regulate the transcription of downstream genes and are regulated by various upstream regulatory factors. Therefore, understanding the mechanisms of action of TFs in regulating drought stress can help enhance the adaptive capacity of crops under drought conditions. In this review, we summarize the structural characteristics of several common TFs, their multiple drought-response pathways, and recently employed research strategies. We describe the application of new technologies such as analysis of stress granule dynamics and function, multi-omics data, gene editing, and molecular crosstalk between TFs in drought resistance. This review aims to familiarize readers with the regulatory network of TFs in drought resistance and to provide a reference for examining the molecular mechanisms of drought resistance in plants and improving agronomic traits.
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Affiliation(s)
- Han Wei
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Xiao Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Kaitong Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
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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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Zhao HM, Huang HB, Zhan ZX, Ye YY, Cheng JL, Xiang L, Li YW, Cai QY, Xie Y, Mo CH. Insights into the molecular network underlying phytotoxicity and phytoaccumulation of ciprofloxacin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169392. [PMID: 38104812 DOI: 10.1016/j.scitotenv.2023.169392] [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: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Ciprofloxacin (CIP) is frequently detected in agricultural soils and can be accumulated by crops, causing phytotoxicities and food safety concerns. However, the molecular basis of its phytotoxicity and phytoaccumulation is hardly known. Here, we analyzed physiological and molecular responses of choysum (Brassica parachinensis) to CIP stress by comparing low CIP accumulation variety (LAV) and high accumulation variety (HAV). Results showed that the LAV suffered more severe inhibition of growth and photosynthesis than the HAV, exhibiting a lower tolerance to CIP toxicity. Integrated transcriptome and proteome analyses suggested that more differentially expressed genes/proteins (DEGs/DEPs) involved in basic metabolic processes were downregulated to a larger extent in the LAV, explaining its lower CIP tolerance at molecular level. By contrast, more DEGs/DEPs involved in defense responses were upregulated to a larger extent in the HAV, showing the molecular basis of its stronger CIP tolerance. Further, a CIP phytotoxicity-responsive molecular network was constructed for the two varieties to better understand the molecular mechanisms underlying the variety-specific CIP tolerance and accumulation. The results present the first comprehensive molecular profile of plant response to CIP stress for molecular-assisted breeding to improve CIP tolerance and minimize CIP accumulation in crops.
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Affiliation(s)
- Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - He-Biao Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhen-Xuan Zhan
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yao-Yao Ye
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ji-Liang Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yunchang Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Zhu T, Yang SL, De Smet I. It is time to move: Heat-induced translocation events. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102406. [PMID: 37354735 DOI: 10.1016/j.pbi.2023.102406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/26/2023]
Abstract
Climate change-induced temperature fluctuations impact agricultural productivity through short-term intense heat waves or long-term heat stress. Plants have evolved sophisticated strategies to deal with heat stress. Understanding perception and transduction of heat signals from outside to inside cells is essential to improve plant thermotolerance. In this review, we will focus on translocation of molecules and proteins associated with signal transduction to understand how plant cells decode signals from the environment to trigger a suitable response.
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Affiliation(s)
- Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Shao-Li Yang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium.
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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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7
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Wei Y, Sandhu E, Yang X, Yang J, Ren Y, Gao X. Bidirectional Functional Effects of Staphylococcus on Carcinogenesis. Microorganisms 2022; 10:microorganisms10122353. [PMID: 36557606 PMCID: PMC9783839 DOI: 10.3390/microorganisms10122353] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
As a Gram-positive cocci existing in nature, Staphylococcus has a variety of species, such as Staphylococcus aureus and Staphylococcus epidermidis, etc. Growing evidence reveals that Staphylococcus is closely related to the occurrence and development of various cancers. On the one hand, cancer patients are more likely to suffer from bacterial infection and antibiotic-resistant strain infection compared to healthy controls. On the other hand, there exists an association between staphylococcal infection and carcinogenesis. Staphylococcus often plays a pathogenic role and evades the host immune system through surface adhesion molecules, α-hemolysin, PVL (Panton-Valentine leukocidin), SEs (staphylococcal enterotoxins), SpA (staphylococcal protein A), TSST-1 (Toxic shock syndrom toxin-1) and other factors. Staphylococcal nucleases (SNases) are extracellular nucleases that serve as genomic markers for Staphylococcus aureus. Interestingly, a human homologue of SNases, SND1 (staphylococcal nuclease and Tudor domain-containing 1), has been recognized as an oncoprotein. This review is the first to summarize the reported basic and clinical evidence on staphylococci and neoplasms. Investigations on the correlation between Staphylococcus and the occurrence, development, diagnosis and treatment of breast, skin, oral, colon and other cancers, are made from the perspectives of various virulence factors and SND1.
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Affiliation(s)
- Yuannan Wei
- Faculty of Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Esha Sandhu
- Faculty of Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Xi Yang
- Department of Immunology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
- Department of Immunology, School of Basic Medical Science, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
| | - Yuanyuan Ren
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
- Department of Immunology, School of Basic Medical Science, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
- Correspondence: (Y.R.); (X.G.); Tel./Fax: +86-022-83336806 (X.G.)
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
- Department of Immunology, School of Basic Medical Science, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Qixiangtai Road No. 22, Heping District, Tianjin 300070, China
- Correspondence: (Y.R.); (X.G.); Tel./Fax: +86-022-83336806 (X.G.)
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Zhou X, Li X, Zhang X, Yin D, Wang J, Zhao Y. Construction of a high-density genetic map and localization of grazing-tolerant QTLs in Medicago falcata L. FRONTIERS IN PLANT SCIENCE 2022; 13:985603. [PMID: 36262664 PMCID: PMC9574245 DOI: 10.3389/fpls.2022.985603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Using genomic DNA from 79 F1 plants resulted from a crossing between parents with strong and weak grazing tolerance in Medicago falcata L., we generated an EcoRI restriction site-associated DNA (RAD) sequencing library. After sequencing and assembly, a high-density genetic map with high-quality SNP markers was constructed, with a total length of 1312.238 cM and an average density of 0.844 SNP/cM. METHODS The phenotypic traits of 79 F1 families were observed and the QTLS of 6 traits were analyzed by interval mapping. RESULTS Sixty three QTLs were identified for seven traits with LOD values from 3 to 6 and the contribution rates from 15% to 30%. Among the 63 QTLs, 17 were for natural shoot height, 12 for rhizome Length, 10 for Shoot canopy diameter, 9 for Basal plant diameter, 6 for stem number, 5 for absolute shoot height, and 4 for rhizome width. These QTLs were concentrated on LG2, LG4, LG5, LG7, and LG8. LG6 had only 6 QTLs. According to the results of QTL mapping, comparison of reference genomes, and functional annotation, 10 candidate genes that may be related to grazing tolerance were screened. qRT-PCR analysis showed that two candidate genes (LOC11412291 and LOC11440209) may be the key genes related to grazing tolerance of M. falcata. CONCLUSION The identified trait-associated QTLs and candidate genes in this study will provide a solid foundation for future molecular breeding for enhanced grazing-tolerance in M. falcata.
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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: 19] [Impact Index Per Article: 9.5] [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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10
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Ahmad I, Zhu G, Zhou G, Song X, Hussein Ibrahim ME, Ibrahim Salih EG, Hussain S, Younas MU. Pivotal Role of Phytohormones and Their Responsive Genes in Plant Growth and Their Signaling and Transduction Pathway under Salt Stress in Cotton. Int J Mol Sci 2022; 23:ijms23137339. [PMID: 35806344 PMCID: PMC9266544 DOI: 10.3390/ijms23137339] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
The presence of phyto-hormones in plants at relatively low concentrations plays an indispensable role in regulating crop growth and yield. Salt stress is one of the major abiotic stresses limiting cotton production. It has been reported that exogenous phyto-hormones are involved in various plant defense systems against salt stress. Recently, different studies revealed the pivotal performance of hormones in regulating cotton growth and yield. However, a comprehensive understanding of these exogenous hormones, which regulate cotton growth and yield under salt stress, is lacking. In this review, we focused on new advances in elucidating the roles of exogenous hormones (gibberellin (GA) and salicylic acid (SA)) and their signaling and transduction pathways and the cross-talk between GA and SA in regulating crop growth and development under salt stress. In this review, we not only focused on the role of phyto-hormones but also identified the roles of GA and SA responsive genes to salt stress. Our aim is to provide a comprehensive review of the performance of GA and SA and their responsive genes under salt stress, assisting in the further elucidation of the mechanism that plant hormones use to regulate growth and yield under salt stress.
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Affiliation(s)
- Irshad Ahmad
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (I.A.); (M.E.H.I.); (E.G.I.S.)
| | - Guanglong Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (I.A.); (M.E.H.I.); (E.G.I.S.)
- Correspondence: (G.Z.); (G.Z.)
| | - Guisheng Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (I.A.); (M.E.H.I.); (E.G.I.S.)
- Key Lab of Crop Genetics & Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
- Correspondence: (G.Z.); (G.Z.)
| | - Xudong Song
- Jiangsu Yanjiang Area Institute of Agricultural Sciences, Nantong 226541, China;
| | - Muhi Eldeen Hussein Ibrahim
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (I.A.); (M.E.H.I.); (E.G.I.S.)
- Department of Agronomy, College of Agricultural Studies, Sudan University of Science and Technology, Khartoum 13311, Sudan
| | - Ebtehal Gabralla Ibrahim Salih
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (I.A.); (M.E.H.I.); (E.G.I.S.)
| | - Shahid Hussain
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China;
| | - Muhammad Usama Younas
- Department of Crop Genetics and Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China;
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11
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Baudouin E, Puyaubert J, Meimoun P, Blein-Nicolas M, Davanture M, Zivy M, Bailly C. Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination. Int J Mol Sci 2022; 23:ijms23137059. [PMID: 35806063 PMCID: PMC9266807 DOI: 10.3390/ijms23137059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Seed germination is critical for early plantlet development and is tightly controlled by environmental factors. Nevertheless, the signaling networks underlying germination control remain elusive. In this study, the remodeling of Arabidopsis seed phosphoproteome during imbibition was investigated using stable isotope dimethyl labeling and nanoLC-MS/MS analysis. Freshly harvested seeds were imbibed under dark or constant light to restrict or promote germination, respectively. For each light regime, phosphoproteins were extracted and identified from dry and imbibed (6 h, 16 h, and 24 h) seeds. A large repertoire of 10,244 phosphopeptides from 2546 phosphoproteins, including 110 protein kinases and key regulators of seed germination such as Delay Of Germination 1 (DOG1), was established. Most phosphoproteins were only identified in dry seeds. Early imbibition led to a similar massive downregulation in dormant and non-dormant seeds. After 24 h, 411 phosphoproteins were specifically identified in non-dormant seeds. Gene ontology analyses revealed their involvement in RNA and protein metabolism, transport, and signaling. In addition, 489 phosphopeptides were quantified, and 234 exhibited up or downregulation during imbibition. Interaction networks and motif analyses revealed their association with potential signaling modules involved in germination control. Our study provides evidence of a major role of phosphosignaling in the regulation of Arabidopsis seed germination.
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Affiliation(s)
- Emmanuel Baudouin
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
- Correspondence: ; Tel.: +33-1-44-27-59-87
| | - Juliette Puyaubert
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Patrice Meimoun
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Mélisande Blein-Nicolas
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Marlène Davanture
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Michel Zivy
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
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12
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Guo H, Cui Y, Huang L, Ge L, Xu X, Xue D, Tang M, Zheng J, Yi Y, Chen L. The RNA binding protein OsLa influences grain and anther development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1397-1414. [PMID: 35322500 DOI: 10.1111/tpj.15746] [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: 12/30/2021] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
La proteins are found widely in eukaryotes and play a variety of vital roles. AtLa1 has been identified as an La protein that is necessary for embryogenesis in Arabidopsis; however, the existence and biological functions of La proteins in rice (Oryza sativa L.) remain unclear. In this study, we identified and characterized two La proteins in rice that are homologous to AtLa1 and named them OsLa1 and OsLa2. Both the OsLa1 and OsLa2 genes encode RNA-binding proteins with an La domain and two RNA-binding domains. Mutant OsLa1 reduced grain length and pollen fertility, whereas OsLa1 overexpression caused the opposite phenotypes. Further experiments indicated that OsLa1 modulates grain size by influencing cell expansion. Interestingly, mutant OsLa2 resulted in thin grains with decreased weight and a low seed-setting rate. We also found that OsLa1 interacted with OsLa2 and that both OsLa1 and OsLa2 interacted with OseIF6.1, a eukaryotic translation initiation factor involved in ribosome biogenesis. In addition, OsLa1 was able to bind to OseIF6.1 mRNA to modulate its expression. Complete OseIF6.1 knockout caused lethality and OseIF6.1/oseif6.1 heterozygous plants displayed low fertility and low seed setting. Together, our results enrich our knowledge of the role of La proteins in rice growth and development, as well as the relationship between La and eIF6 in rice.
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Affiliation(s)
- Hongming Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Linjuan Huang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Li Ge
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaorong Xu
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Danyang Xue
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ming Tang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Jingsheng Zheng
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
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13
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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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14
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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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15
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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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16
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Rodriguez MC, Mehta D, Tan M, Uhrig RG. Quantitative Proteome and PTMome Analysis of Arabidopsis thaliana Root Responses to Persistent Osmotic and Salinity Stress. PLANT & CELL PHYSIOLOGY 2021; 62:1012-1029. [PMID: 34059891 DOI: 10.1093/pcp/pcab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h to d) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while post-translational modifications (PTMs) do not. Further, we find significant changes in PTMs, and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulfur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.
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Affiliation(s)
- Maria C Rodriguez
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Richard G Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
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17
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Bhattarai S, Fu YB, Coulman B, Tanino K, Karunakaran C, Biligetu B. Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance. BMC PLANT BIOLOGY 2021; 21:446. [PMID: 34610811 PMCID: PMC8491396 DOI: 10.1186/s12870-021-03201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Alfalfa (Medicago sativa L.) production decreases under salt stress. Identification of genes associated with salt tolerance in alfalfa is essential for the development of molecular markers used for breeding and genetic improvement. RESULT An RNA-Seq technique was applied to identify the differentially expressed genes (DEGs) associated with salt stress in two alfalfa cultivars: salt tolerant 'Halo' and salt intolerant 'Vernal'. Leaf and root tissues were sampled for RNA extraction at 0 h, 3 h, and 27 h under 12 dS m- 1 salt stress maintained by NaCl. The sequencing generated a total of 381 million clean sequence reads and 84.8% were mapped on to the alfalfa reference genome. A total of 237 DEGs were identified in leaves and 295 DEGs in roots of the two alfalfa cultivars. In leaf tissue, the two cultivars had a similar number of DEGs at 3 h and 27 h of salt stress, with 31 and 49 DEGs for 'Halo', 34 and 50 for 'Vernal', respectively. In root tissue, 'Halo' maintained 55 and 56 DEGs at 3 h and 27 h, respectively, while the number of DEGs decreased from 42 to 10 for 'Vernal'. This differential expression pattern highlights different genetic responses of the two cultivars to salt stress at different time points. Interestingly, 28 (leaf) and 31 (root) salt responsive candidate genes were highly expressed in 'Halo' compared to 'Vernal' under salt stress, of which 13 candidate genes were common for leaf and root tissues. About 60% of DEGs were assigned to known gene ontology (GO) categories. The genes were involved in transmembrane protein function, photosynthesis, carbohydrate metabolism, defense against oxidative damage, cell wall modification and protection against lipid peroxidation. Ion binding was found to be a key molecular activity for salt tolerance in alfalfa under salt stress. CONCLUSION The identified DEGs are significant for understanding the genetic basis of salt tolerance in alfalfa. The generated genomic information is useful for molecular marker development for alfalfa genetic improvement for salt tolerance.
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Affiliation(s)
- Surendra Bhattarai
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Bruce Coulman
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Karen Tanino
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Chithra Karunakaran
- Canadian Light Source, 44 Innovation Boulevard, Saskatoon, SK, S7N 2V3, Canada
| | - Bill Biligetu
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.
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18
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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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19
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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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20
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Zhang C, van Leeuwen W, Blotenburg M, Aguilera-Gomez A, Brussee S, Grond R, Kampinga HH, Rabouille C. Activation of salt Inducible Kinases, IRE1 and PERK leads to Sec bodies formation in Drosophila S2 cells. J Cell Sci 2021; 134:272062. [PMID: 34350957 PMCID: PMC8445602 DOI: 10.1242/jcs.258685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
The phase separation of the non-membrane bound Sec bodies occurs in Drosophila S2 cells by coalescence of components of the endoplasmic reticulum (ER) exit sites under the stress of amino acid starvation. Here, we address which signaling pathways cause Sec body formation and find that two pathways are critical. The first is the activation of the salt-inducible kinases (SIKs; SIK2 and SIK3) by Na+ stress, which, when it is strong, is sufficient. The second is activation of IRE1 and PERK (also known as PEK in flies) downstream of ER stress induced by the absence of amino acids, which needs to be combined with moderate salt stress to induce Sec body formation. SIK, and IRE1 and PERK activation appear to potentiate each other through the stimulation of the unfolded protein response, a key parameter in Sec body formation. This work shows the role of SIKs in phase transition and re-enforces the role of IRE1 and PERK as a metabolic sensor for the level of circulating amino acids and salt. This article has an associated First Person interview with the first author of the paper. Summary: In S2 cells, the phase-separated Sec bodies form upon the combined activation of salt-inducible kinases, IRE1 and PERK.
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Affiliation(s)
- Chujun Zhang
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | | | | | | | - Sem Brussee
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | - Rianne Grond
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | - Harm H Kampinga
- Department of Biomedical Sciences in Cells and Systems, UMC Groningen, The Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands.,Department of Biomedical Sciences in Cells and Systems, UMC Groningen, The Netherlands.,Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
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21
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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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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: 31] [Impact Index Per Article: 7.8] [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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23
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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: 67] [Impact Index Per Article: 16.8] [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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24
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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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25
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Shamloo-Dashtpagerdi R, Lindlöf A, Aliakbari M, Pirasteh-Anosheh H. Plausible association between drought stress tolerance of barley (Hordeum vulgare L.) and programmed cell death via MC1 and TSN1 genes. PHYSIOLOGIA PLANTARUM 2020; 170:46-59. [PMID: 32246464 DOI: 10.1111/ppl.13102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/17/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Studying the drought-responsive transcriptome is of high interest as it can serve as a blueprint for stress adaptation strategies. Despite extensive studies in this area, there are still many details to be uncovered, such as the importance of each gene involved in the stress response as well as the relationship between these genes and the physiochemical processes governing stress tolerance. This study was designed to address such important details and to gain insights into molecular responses of barley (Hordeum vulgare L.) to drought stress. To that, we combined RNA-seq data analysis with field and greenhouse drought experiments in a systems biology approach. RNA-sequence analysis identified a total of 665 differentially expressed genes (DEGs) belonging to diverse functional categories. A gene network was derived from the DEGs, which comprised of a total of 131 nodes and 257 edges. Gene network topology analysis highlighted two programmed cell death (PCD) modulating genes, MC1 (metacaspase 1) and TSN1 (Tudor-SN 1), as important (hub) genes in the predicted network. Based on the field trial, a drought-tolerant and a drought-susceptible barley genotype was identified from eight tested cultivars. Identified genotypes exhibited different physiochemical characteristics, including proline content, chlorophyll concentration, percentage of electrolyte leakage and malondialdehyde content as well as expression profiles of MC1 and TSN1 genes. Machine learning and correspondence analysis revealed a significant relationship between drought tolerance and measured characteristics in the context of PCD. Our study provides new insights which bridge barley drought tolerance to PCD through MC1 and TSN1 pathway.
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Affiliation(s)
| | | | - Massume Aliakbari
- Department of Crop Production and Plant Breeding, Shiraz University, Shiraz, Iran
| | - Hadi Pirasteh-Anosheh
- National Salinity Research Center, Agricultural Research, Education and Extension Organization, Yazd, Iran
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26
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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: 23] [Impact Index Per Article: 5.8] [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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27
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Hu SF, Wei WL, Hong SF, Fang RY, Wu HY, Lin PC, Sanobar N, Wang HP, Sulistio M, Wu CT, Lo HF, Lin SS. Investigation of the effects of P1 on HC-pro-mediated gene silencing suppression through genetics and omics approaches. BOTANICAL STUDIES 2020; 61:22. [PMID: 32748085 PMCID: PMC7399735 DOI: 10.1186/s40529-020-00299-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/16/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Posttranscriptional gene silencing (PTGS) is one of the most important mechanisms for plants during viral infection. However, viruses have also developed viral suppressors to negatively control PTGS by inhibiting microRNA (miRNA) and short-interfering RNA (siRNA) regulation in plants. The first identified viral suppressor, P1/HC-Pro, is a fusion protein that was translated from potyviral RNA. Upon infecting plants, the P1 protein itself is released from HC-Pro by the self-cleaving activity of P1. P1 has an unknown function in enhancing HC-Pro-mediated PTGS suppression. We performed proteomics to identify P1-interacting proteins. We also performed transcriptomics that were generated from Col-0 and various P1/HC-Pro-related transgenic plants to identify novel genes. The results showed several novel genes were identified through the comparative network analysis that might be involved in P1/HC-Pro-mediated PTGS suppression. RESULTS First, we demonstrated that P1 enhances HC-Pro function and that the mechanism might work through P1 binding to VERNALIZATION INDEPENDENCE 3/SUPERKILLER 8 (VIP3/SKI8), a subunit of the exosome, to interfere with the 5'-fragment of the PTGS-cleaved RNA degradation product. Second, the AGO1 was specifically posttranslationally degraded in transgenic Arabidopsis expressing P1/HC-Pro of turnip mosaic virus (TuMV) (P1/HCTu plant). Third, the comparative network highlighted potentially critical genes in PTGS, including miRNA targets, calcium signaling, hormone (JA, ET, and ABA) signaling, and defense response. CONCLUSION Through these genetic and omics approaches, we revealed an overall perspective to identify many critical genes involved in PTGS. These new findings significantly impact in our understanding of P1/HC-Pro-mediated PTGS suppression.
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Affiliation(s)
- Sin-Fen Hu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Wei-Lun Wei
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Ru-Ying Fang
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei, 106, Taiwan
| | - Pin-Chun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Neda Sanobar
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hsin-Ping Wang
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan
| | - Margo Sulistio
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan
| | - Chun-Ta Wu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan
| | - Hsiao-Feng Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Center of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
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28
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Navarro-Imaz H, Ochoa B, García-Arcos I, Martínez MJ, Chico Y, Fresnedo O, Rueda Y. Molecular and cellular insights into the role of SND1 in lipid metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158589. [DOI: 10.1016/j.bbalip.2019.158589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/20/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
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29
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Cao X, Jin X, Liu B. The involvement of stress granules in aging and aging-associated diseases. Aging Cell 2020; 19:e13136. [PMID: 32170904 PMCID: PMC7189987 DOI: 10.1111/acel.13136] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are nonmembrane assemblies formed in cells in response to stress conditions. SGs mainly contain untranslated mRNA and a variety of proteins. RNAs and scaffold proteins with intrinsically disordered regions or RNA-binding domains are essential for the assembly of SGs, and multivalent macromolecular interactions among these components are thought to be the driving forces for SG assembly. The SG assembly process includes regulation through post-translational modification and involvement of the cytoskeletal system. During aging, many intracellular bioprocesses become disrupted by factors such as cellular environmental changes, mitochondrial dysfunction, and decline in the protein quality control system. Such changes could lead to the formation of aberrant SGs, as well as alterations in their maintenance, disassembly, and clearance. These aberrant SGs might in turn promote aging and aging-associated diseases. In this paper, we first review the latest progress on the molecular mechanisms underlying SG assembly and SG functioning under stress conditions. Then, we provide a detailed discussion of the relevance of SGs to aging and aging-associated diseases.
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Affiliation(s)
- Xiuling Cao
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
- Department of Chemistry and Molecular Biology University of Gothenburg Goteborg Sweden
- Center for Large‐scale Cell‐based Screening Faculty of Science University of Gothenburg Goteborg Sweden
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30
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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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31
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Chou HL, Tian L, Washida H, Fukuda M, Kumamaru T, Okita TW. The rice storage protein mRNAs as a model system for RNA localization in higher plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 284:203-211. [PMID: 31084873 DOI: 10.1016/j.plantsci.2019.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
The transport and targeting of mRNAs to specific intracellular locations is a ubiquitous process in prokaryotic and eukaryotic organisms. Despite the prevalent nature of RNA localization in guiding development, differentiation, cellular movement and intracellular organization of biochemical activities, only a few examples exist in higher plants. Here, we summarize past studies on mRNA-based protein targeting to specific subdomains of the cortical endoplasmic reticulum (ER) using the rice storage protein mRNAs as a model. Such studies have demonstrated that there are multiple pathways of RNA localization to the cortical ER that are controlled by cis-determinants (zipcodes) on the mRNA. These zipcode sequences are recognized by specific RNA binding proteins organized into multi-protein complexes. The available evidence suggests mRNAs are transported to their destination sites by co-opting membrane trafficking factors. Lastly, we discuss the major gaps in our knowledge on RNA localization and how information on the targeting of storage protein mRNAs can be used to further our understanding on how plant mRNAs are organized into regulons to facilitate protein localization and formation of multi-protein complexes.
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Affiliation(s)
- Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Haruhiko Washida
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States
| | - Masako Fukuda
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States; Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395, Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395, Japan
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, United States.
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32
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Tian L, Chou HL, Zhang L, Okita TW. Targeted Endoplasmic Reticulum Localization of Storage Protein mRNAs Requires the RNA-Binding Protein RBP-L. PLANT PHYSIOLOGY 2019; 179:1111-1131. [PMID: 30659066 PMCID: PMC6393789 DOI: 10.1104/pp.18.01434] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/11/2019] [Indexed: 05/18/2023]
Abstract
The transport and targeting of glutelin and prolamine mRNAs to distinct subdomains of the cortical endoplasmic reticulum is a model for mRNA localization in plants. This process requires a number of RNA-binding proteins (RBPs) that recognize and bind to mRNA cis-localization (zipcode) elements to form messenger ribonucleoprotein complexes, which then transport the RNAs to their destination sites at the cortical endoplasmic reticulum. Here, we present evidence that the rice (Oryza sativa) RNA-binding protein, RBP-L, like its interacting RBP-P partner, specifically binds to glutelin and prolamine zipcode RNA sequences and is required for proper mRNA localization in rice endosperm cells. A transfer DNA insertion in the 3' untranslated region resulted in reduced expression of the RBP-L gene to 10% to 25% of that in the wild-type. Reduced amounts of RBP-L caused partial mislocalization of glutelin and prolamine RNAs and conferred other general growth defects, including dwarfism, late flowering, and smaller seeds. Transcriptome analysis showed that RBP-L knockdown greatly affected the expression of prolamine family genes and several classes of transcription factors. Collectively, these results indicate that RBP-L, like RBP-P, is a key RBP involved in mRNA localization in rice endosperm cells. Moreover, distinct from RBP-P, RBP-L exhibits additional regulatory roles in development, either directly through its binding to corresponding RNAs or indirectly through its effect on transcription factors.
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Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Laining Zhang
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
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33
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Hamada T, Yako M, Minegishi M, Sato M, Kamei Y, Yanagawa Y, Toyooka K, Watanabe Y, Hara-Nishimura I. Stress granule formation is induced by a threshold temperature rather than a temperature difference in Arabidopsis. J Cell Sci 2018; 131:jcs.216051. [PMID: 30030372 DOI: 10.1242/jcs.216051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/12/2018] [Indexed: 12/12/2022] Open
Abstract
Stress granules, a type of cytoplasmic RNA granule in eukaryotic cells, are induced in response to various environmental stresses, including high temperature. However, how high temperatures induce the formation of these stress granules in plant cells is largely unknown. Here, we characterized the process of stress granule formation in Arabidopsis thaliana by combining live imaging and electron microscopy analysis. In seedlings grown at 22°C, stress granule formation was induced at temperatures above a critical threshold level of 34°C in the absence of transpiration. The threshold temperature was the same, regardless of whether the seedlings were grown at 22°C or 4°C. High-resolution live imaging microscopy revealed that stress granule formation is not correlated with the sizes of pre-existing RNA processing bodies (P-bodies) but that the two structures often associated rapidly. Immunoelectron microscopy revealed a previously unidentified characteristic of the fine structures of Arabidopsis stress granules and P-bodies: the lack of ribosomes and the presence of characteristic electron-dense globular and filamentous structures. These results provide new insights into the universal nature of stress granules in eukaryotic cells.
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Affiliation(s)
- Takahiro Hamada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Mako Yako
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Marina Minegishi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Yasuhiro Kamei
- National Institute for Basic Biology, Aichi 444-8585, Japan
| | - Yuki Yanagawa
- Institute of Agrobiological Sciences, NARO, Tsukuba 305-8602, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
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Kosmacz M, Luzarowski M, Kerber O, Leniak E, Gutiérrez-Beltrán E, Moreno JC, Gorka M, Szlachetko J, Veyel D, Graf A, Skirycz A. Interaction of 2',3'-cAMP with Rbp47b Plays a Role in Stress Granule Formation. PLANT PHYSIOLOGY 2018; 177:411-421. [PMID: 29618637 PMCID: PMC5933139 DOI: 10.1104/pp.18.00285] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/26/2018] [Indexed: 05/14/2023]
Abstract
2',3'-cAMP is an intriguing small molecule that is conserved among different kingdoms. 2',3'-cAMP is presumably produced during RNA degradation, with increased cellular levels observed especially under stress conditions. Previously, we observed the presence of 2',3'-cAMP in Arabidopsis (Arabidopsis thaliana) protein complexes isolated from native lysate, suggesting that 2',3'-cAMP has potential protein partners in plants. Here, affinity purification experiments revealed that 2',3'-cAMP associates with the stress granule (SG) proteome. SGs are aggregates composed of protein and mRNA, which enable cells to selectively store mRNA for use in response to stress such as heat whereby translation initiation is impaired. Using size-exclusion chromatography and affinity purification analyses, we identified Rbp47b, the key component of SGs, as a potential interacting partner of 2',3'-cAMP. Furthermore, SG formation was promoted in 2',3'-cAMP-treated Arabidopsis seedlings, and interactions between 2',3'-cAMP and RNA-binding domains of Rbp47b, RRM2 and RRM3, were confirmed in vitro using microscale thermophoresis. Taken together, these results (1) describe novel small-molecule regulation of SG formation, (2) provide evidence for the biological role of 2',3'-cAMP, and (3) demonstrate an original biochemical pipeline for the identification of protein-metabolite interactors.
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Affiliation(s)
- Monika Kosmacz
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Olga Kerber
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Ewa Leniak
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Emilio Gutiérrez-Beltrán
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla/Consejo Superior de Investigaciones Científicas, 41092 Seville, Spain
| | - Juan Camilo Moreno
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Michał Gorka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Jagoda Szlachetko
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Daniel Veyel
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Alexander Graf
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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Bollhöner B, Jokipii-Lukkari S, Bygdell J, Stael S, Adriasola M, Muñiz L, Van Breusegem F, Ezcurra I, Wingsle G, Tuominen H. The function of two type II metacaspases in woody tissues of Populus trees. THE NEW PHYTOLOGIST 2018; 217:1551-1565. [PMID: 29243818 DOI: 10.1111/nph.14945] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 11/07/2017] [Indexed: 05/03/2023]
Abstract
Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populus tremula × tremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.
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Affiliation(s)
- Benjamin Bollhöner
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Soile Jokipii-Lukkari
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Joakim Bygdell
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - Simon Stael
- VIB-Ugent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Mathilda Adriasola
- School of Biotechnology, Royal Institute of Technology (KTH), 10691, Stockholm, Sweden
| | - Luis Muñiz
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Frank Van Breusegem
- VIB-Ugent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Inés Ezcurra
- School of Biotechnology, Royal Institute of Technology (KTH), 10691, Stockholm, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Hannele Tuominen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
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Chantarachot T, Bailey-Serres J. Polysomes, Stress Granules, and Processing Bodies: A Dynamic Triumvirate Controlling Cytoplasmic mRNA Fate and Function. PLANT PHYSIOLOGY 2018; 176:254-269. [PMID: 29158329 PMCID: PMC5761823 DOI: 10.1104/pp.17.01468] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/17/2017] [Indexed: 05/05/2023]
Abstract
Discoveries illuminate highly regulated dynamics of mRNA translation, sequestration, and degradation within the cytoplasm of plants.
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Affiliation(s)
- Thanin Chantarachot
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
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Chou HL, Tian L, Kumamaru T, Hamada S, Okita TW. Multifunctional RNA Binding Protein OsTudor-SN in Storage Protein mRNA Transport and Localization. PLANT PHYSIOLOGY 2017; 175:1608-1623. [PMID: 29084903 PMCID: PMC5717745 DOI: 10.1104/pp.17.01388] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/26/2017] [Indexed: 05/04/2023]
Abstract
The multifunctional RNA-binding protein Tudor-SN plays multiple roles in transcriptional and posttranscriptional processes due to its modular domain structure, consisting of four tandem Staphylococcus nuclease (SN)-like domains (4SN), followed by a carboxyl-terminal Tudor domain, followed by a fifth partial SN sequence (Tsn). In plants, it confers stress tolerance, is a component of stress granules and P-bodies, and may participate in stabilizing and localizing RNAs to specific subdomains of the cortical-endoplasmic reticulum in developing rice (Oryza sativa) endosperm. Here, we show that, in addition to the intact rice OsTudor-SN protein, the 4SN and Tsn modules exist as independent polypeptides, which collectively may coassemble to form a complex population of homodimer and heteroduplex species. The 4SN and Tsn modules exhibit different roles in RNA binding and as a protein scaffold for stress-associated proteins and RNA-binding proteins. Despite their distinct individual properties, mutations in both the 4SN and Tsn modules mislocalize storage protein mRNAs to the cortical endoplasmic reticulum. These results indicate that the two modular peptide regions of OsTudor-SN confer different cellular properties but cooperate in mRNA localization, a process linking its multiple functions in the nucleus and cytoplasm.
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Affiliation(s)
- Hong-Li Chou
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
| | - Toshihiro Kumamaru
- Plant Genetics Laboratory, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Shigeki Hamada
- Institute of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340
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38
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Shang M, Wang X, Zhang J, Qi X, Ping A, Hou L, Xing G, Li G, Li M. Genetic Regulation of GA Metabolism during Vernalization, Floral Bud Initiation and Development in Pak Choi ( Brassica rapa ssp. chinensis Makino). FRONTIERS IN PLANT SCIENCE 2017; 8:1533. [PMID: 29038660 PMCID: PMC5628244 DOI: 10.3389/fpls.2017.01533] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 08/22/2017] [Indexed: 05/31/2023]
Abstract
Pak choi (Brassica rapa ssp. chinensis Makino) is a representative seed vernalization vegetable and premature bolting in spring can cause significant economic loss. Thus, it is critical to elucidate the mechanism of molecular regulation of vernalization and floral bud initiation to prevent premature bolting. Gibberellin (GA) is the key plant hormone involved in regulating plant development. To gain a better understanding of GA metabolism in pak choi, the content of GA in pak choi was measured at different stages of plant development using enzyme-linked immunosorbent assay. The results showed that the GA content increased significantly after low-temperature treatment (4°C) and then decreased rapidly with vegetative growth. During floral bud initiation, the GA content increased rapidly until it peaked upon floral bud differentiation. To elucidate these changes in GA content, the expression of homologous genes encoding enzymes directly involved in GA metabolism were analyzed. The results showed that the changes in the expression of four genes involved in GA synthesis (Bra035120 encoding ent-kaurene synthase, Bra009868 encoding ent-kaurene oxidase, Bra015394 encoding ent-kaurenoic acid oxidase, and Bra013890 encoding GA20-oxidase) were correlated with the changes in GA content. In addition, by comparing the expression of genes involved in GA metabolism at different growth stages, seven differentially expressed genes (Bra005596, Bra009285, Bra022565, Bra008362, Bra033324, Bra010802, and Bra030500) were identified. The differential expression of these genes were directly correlated with changes in GA content, suggesting that these genes were directly related to vernalization, floral bud initiation and development. These results contribute to the understanding of the molecular mechanism of changes in GA content during different developmental phases in pak choi.
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Affiliation(s)
- Mengya Shang
- College of Horticulture, Shanxi Agricultural UniversityTaigu, China
| | - Xueting Wang
- College of Horticulture, Shanxi Agricultural UniversityTaigu, China
| | - Jing Zhang
- College of Horticulture, Shanxi Agricultural UniversityTaigu, China
| | - Xianhui Qi
- Vegetables Research Institute, Shanxi Academy of Agriculture SciencesTaiyuan, China
| | - Amin Ping
- College of Horticulture, Shanxi Agricultural UniversityTaigu, China
| | - Leiping Hou
- College of Horticulture, Shanxi Agricultural UniversityTaigu, China
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural UniversityTaigu, China
| | - Gaizhen Li
- Vegetables Research Institute, Shanxi Academy of Agriculture SciencesTaiyuan, China
| | - Meilan Li
- College of Horticulture, Shanxi Agricultural UniversityTaigu, China
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Shao J, Gao F, Zhang B, Zhao M, Zhou Y, He J, Ren L, Yao Z, Yang J, Su C, Gao X. Aggregation of SND1 in Stress Granules is Associated with the Microtubule Cytoskeleton During Heat Shock Stimulus. Anat Rec (Hoboken) 2017; 300:2192-2199. [PMID: 28758359 PMCID: PMC5697672 DOI: 10.1002/ar.23642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/19/2017] [Accepted: 05/30/2017] [Indexed: 12/19/2022]
Abstract
Stress granules (SGs) are dynamic dense structures in the cytoplasm that form in response to a variety of environmental stress stimuli. Staphylococcal nuclease and Tudor domain containing 1 (SND1) is a type of RNA‐binding protein and has been identified as a transcriptional co‐activator. Our previous studies have shown that SND1 is a component of the stress granule, which forms under stress conditions. Here, we observed that SND1 granules were often surrounded by ɑ‐tubulin‐microtubules in 45°C‐treated HeLa cells at 15 min or colocalized with microtubules at 30 or 45 min. Furthermore, Nocodazole‐mediated microtubule depolymerization could significantly affect the efficient recruitment of SND1 proteins to the SGs during heat shock stress. In addition, the 45°C heat shock mediated the enhancement of eIF2α phosphorylation, which was not affected by treatment with Nocodazole, an agent that disrupts the cytoskeleton. The intact microtubule cytoskeletal tracks are important for the efficient assembly of SND1 granules under heat shock stress and may facilitate SND1 shuttling between cytoplasmic RNA foci. Anat Rec, 300:2192–2199, 2017. © 2017 The Authors The Anatomical Record published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.
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Affiliation(s)
- Jie Shao
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Fei Gao
- Department of Pediatric Cardiology, Tianjin Children's Hospital, Tianjin, 300070, People's Republic of China
| | - Bingbing Zhang
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Meng Zhao
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Yunli Zhou
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Jinyan He
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Department of Physiology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Li Ren
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Zhi Yao
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Jie Yang
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Chao Su
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Xingjie Gao
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, 300070, People's Republic of China
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40
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Takáč T, Šamajová O, Pechan T, Luptovčiak I, Šamaj J. Feedback Microtubule Control and Microtubule-Actin Cross-talk in Arabidopsis Revealed by Integrative Proteomic and Cell Biology Analysis of KATANIN 1 Mutants. Mol Cell Proteomics 2017; 16:1591-1609. [PMID: 28706004 DOI: 10.1074/mcp.m117.068015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/06/2017] [Indexed: 12/20/2022] Open
Abstract
Microtubule organization and dynamics are critical for key developmental processes such as cell division, elongation, and morphogenesis. Microtubule severing is an essential regulator of microtubules and is exclusively executed by KATANIN 1 in Arabidopsis In this study, we comparatively studied the proteome-wide effects in two KATANIN 1 mutants. Thus, shotgun proteomic analysis of roots and aerial parts of single nucleotide mutant fra2 and T-DNA insertion mutant ktn1-2 was carried out. We have detected 42 proteins differentially abundant in both fra2 and ktn1-2 KATANIN 1 dysfunction altered the abundance of proteins involved in development, metabolism, and stress responses. The differential regulation of tubulins and microtubule-destabilizing protein MDP25 implied a feedback microtubule control in KATANIN 1 mutants. Furthermore, deregulation of profilin 1, actin-depolymerizing factor 3, and actin 7 was observed. These findings were confirmed by immunoblotting analysis of actin and by microscopic observation of actin filaments using fluorescently labeled phalloidin. Results obtained by quantitative RT-PCR analysis revealed that changed protein abundances were not a consequence of altered expression levels of corresponding genes in the mutants. In conclusion, we show that abundances of several cytoskeletal proteins as well as organization of microtubules and the actin cytoskeleton are amended in accordance with defective microtubule severing.
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Affiliation(s)
- Tomáš Takáč
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Tibor Pechan
- §Institute for Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Starkville, Mississippi 39759
| | - Ivan Luptovčiak
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- From the ‡Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic;
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Cázares-Apátiga J, Medina-Gómez C, Chávez-Munguía B, Calixto-Gálvez M, Orozco E, Vázquez-Calzada C, Martínez-Higuera A, Rodríguez MA. The Tudor Staphylococcal Nuclease Protein of Entamoeba histolytica Participates in Transcription Regulation and Stress Response. Front Cell Infect Microbiol 2017; 7:52. [PMID: 28293543 PMCID: PMC5328994 DOI: 10.3389/fcimb.2017.00052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/10/2017] [Indexed: 12/18/2022] Open
Abstract
Entamoeba histolytica is the protozoa parasite responsible of human amoebiasis, disease that causes from 40,000 to 100,000 deaths annually worldwide. However, few are known about the expression regulation of molecules involved in its pathogenicity. Transcription of some virulence-related genes is positively controlled by the cis-regulatory element named URE1. Previously we identified the transcription factor that binds to URE1, which displayed a nuclear and cytoplasmic localization. This protein belongs to the Tudor Staphyococcal nuclease (TSN) family, which in other systems participates in virtually all pathways of gene expression, suggesting that this amoebic transcription factor (EhTSN; former EhURE1BP) could also play multiple functions in E. histolytica. The aim of this study was to identify the possible cellular events where EhTSN is involved. Here, we found that EhTSN in nucleus is located in euchromatin and close to, but not into, heterochromatin. We also showed the association of EhTSN with proteins involved in transcription and that the knockdown of EhTSN provokes a diminishing in the mRNA level of the EhRabB gene, which in its promoter region contains the URE1 motif, confirming that EhTSN participates in transcription regulation. In cytoplasm, this protein was found linked to the membrane of small vesicles and to plasma membrane. Through pull-down assays and mass spectrometry we identity thirty two candidate proteins to interact with EhTSN. These proteins participate in transcription, metabolism, signaling, and stress response, among other cellular processes. Interaction of EhTSN with some candidate proteins involved in metabolism, and signaling was validated by co-immunoprecipitation or co-localization. Finally we showed the co-localization of EhTSN and HSP70 in putative stress granules during heat shock and that the knockdown of EhTSN increases the cell death during heat shock treatment, reinforcing the hypothesis that EhTSN has a role during stress response. All data support the proposal that EhTSN is a multifunctional protein of E. histolytica.
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Affiliation(s)
- Javier Cázares-Apátiga
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN Ciudad de México, Mexico
| | - Christian Medina-Gómez
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN Ciudad de México, Mexico
| | - Bibiana Chávez-Munguía
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN Ciudad de México, Mexico
| | | | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN Ciudad de México, Mexico
| | - Carlos Vázquez-Calzada
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN Ciudad de México, Mexico
| | - Aarón Martínez-Higuera
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN Ciudad de México, Mexico
| | - Mario A Rodríguez
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN Ciudad de México, Mexico
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Krapp S, Greiner E, Amin B, Sonnewald U, Krenz B. The stress granule component G3BP is a novel interaction partner for the nuclear shuttle proteins of the nanovirus pea necrotic yellow dwarf virus and geminivirus abutilon mosaic virus. Virus Res 2017; 227:6-14. [PMID: 27693920 DOI: 10.1016/j.virusres.2016.09.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/26/2016] [Accepted: 09/29/2016] [Indexed: 11/25/2022]
Abstract
Stress granules (SGs) are structures within cells that regulate gene expression during stress response, e.g. viral infection. In mammalian cells assembly of SGs is dependent on the Ras-GAP SH3-domain-binding protein (G3BP). The C-terminal domain of the viral nonstructural protein 3 (nsP3) of Semliki Forest virus (SFV) forms a complex with mammalian G3BP and sequesters it into viral RNA replication complexes in a manner that inhibits the formation of SGs. The binding domain of nsP3 to HsG3BP was mapped to two tandem 'FGDF' repeat motifs close to the C-terminus of the viral proteins. It was speculated that plant viruses employ a similar strategy to inhibit SG function. This study identifies an Arabidopsis thaliana NTF2-RRM domain-containing protein as a G3BP-like protein (AtG3BP), which localizes to plant SGs. Moreover, the nuclear shuttle protein (NSP) of the begomovirus abutilon mosaic virus (AbMV), which harbors a 'FVSF'-motif at its C-terminal end, interacts with the AtG3BP-like protein, as does the 'FNGSF'-motif containing NSP of pea necrotic yellow dwarf virus (PNYDV), a member of the Nanoviridae family. We therefore propose that SG formation upon stress is conserved between mammalian and plant cells and that plant viruses may follow a similar strategy to inhibit plant SG function as it has been shown for their mammalian counterparts.
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Affiliation(s)
- Susanna Krapp
- Universität Erlangen-Nürnberg, Lehrstuhl für Biochemie, Department Biologie, Staudtstr. 5, 91058 Erlangen, Germany
| | - Eva Greiner
- Universität Erlangen-Nürnberg, Lehrstuhl für Biochemie, Department Biologie, Staudtstr. 5, 91058 Erlangen, Germany
| | - Bushra Amin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Uwe Sonnewald
- Universität Erlangen-Nürnberg, Lehrstuhl für Biochemie, Department Biologie, Staudtstr. 5, 91058 Erlangen, Germany
| | - Björn Krenz
- Universität Erlangen-Nürnberg, Lehrstuhl für Biochemie, Department Biologie, Staudtstr. 5, 91058 Erlangen, Germany.
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Mäkinen K, Lõhmus A, Pollari M. Plant RNA Regulatory Network and RNA Granules in Virus Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:2093. [PMID: 29312371 PMCID: PMC5732267 DOI: 10.3389/fpls.2017.02093] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual components contribute to these processes. In this review we discuss the roles of cellular RNA regulatory mechanisms and RNA granules in plant virus infection in the light of current knowledge and compare the findings to those made in animal virus studies.
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Su C, Gao X, Yang W, Zhao Y, Fu X, Cui X, Zhang C, Xin L, Ren Y, Li L, Shui W, Yang X, Wei M, Yang J. Phosphorylation of Tudor-SN, a novel substrate of JNK, is involved in the efficient recruitment of Tudor-SN into stress granules. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:562-571. [PMID: 28011284 DOI: 10.1016/j.bbamcr.2016.12.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/12/2016] [Accepted: 12/18/2016] [Indexed: 12/24/2022]
Abstract
Posttranslational modifications of certain stress granule (SG) proteins are closely related to the assembly of SGs, a type of cytoplasmic foci structure. Our previous studies revealed that the Tudor staphylococcal nuclease (Tudor-SN) protein participates in the formation of SGs. However, the functional significance of potential Tudor-SN modifications during stress has not been reported. In this study, we demonstrated that the Tudor-SN protein was phosphorylated at threonine 103 (T103) upon stimulation with arsenite. In addition, c-Jun N-terminal kinase (JNK) was found to be responsible for Tudor-SN phosphorylation at the T103 site. We further illustrated that either a T103A mutation or the suppression of phosphorylation of T103 by the JNK inhibitor SP600125 inhibited the efficient recruitment of Tudor-SN into SGs. In addition, the T103A mutation could affect the physical binding of Tudor-SN with the G3BP (Ras-GAP SH3 domain-binding protein) protein but not with the HuR (Hu antigen R) protein and AGTR1-3'UTR (3'-untranslated region of angiotensin II receptor, type 1) mRNA cargo. These data suggested that JNK-enhanced Tudor-SN phosphorylation promotes the interaction between Tudor-SN and G3BP and facilitates the efficient recruitment of Tudor-SN into SGs under conditions of sodium arsenite-induced oxidative stress. This finding provides novel insights into the physiological function of Tudor-SN modification.
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Affiliation(s)
- Chao Su
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Wendong Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Yali Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xue Fu
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xiaoteng Cui
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Chunyan Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Lingbiao Xin
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Yuanyuan Ren
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Lixin Li
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Wenqing Shui
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Xi Yang
- Department of Immunology, University of Manitoba, 471 Apotex Centre, 750 McDermot Avenue, Winnipeg R3E 0T5, Canada
| | - Minxin Wei
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin 300070, China.
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China.
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Tudor staphylococcal nuclease: biochemistry and functions. Cell Death Differ 2016; 23:1739-1748. [PMID: 27612014 DOI: 10.1038/cdd.2016.93] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 08/01/2016] [Indexed: 12/17/2022] Open
Abstract
Tudor staphylococcal nuclease (TSN, also known as Tudor-SN, SND1 or p100) is an evolutionarily conserved protein with invariant domain composition, represented by tandem repeat of staphylococcal nuclease domains and a tudor domain. Conservation along significant evolutionary distance, from protozoa to plants and animals, suggests important physiological functions for TSN. It is known that TSN is critically involved in virtually all pathways of gene expression, ranging from transcription to RNA silencing. Owing to its high protein-protein binding affinity coexistent with enzymatic activity, TSN can exert its biochemical function by acting as both a scaffolding molecule of large multiprotein complexes and/or as a nuclease. TSN is indispensible for normal development and stress resistance, whereas its increased expression is closely associated with various types of cancer. Thus, TSN is an attractive target for anti-cancer therapy and a potent tumor marker. Considering ever increasing interest to further understand a multitude of TSN-mediated processes and a mechanistic role of TSN in these processes, here we took an attempt to summarize and update the available information about this intriguing multifunctional protein.
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Guo C, Luo C, Guo L, Li M, Guo X, Zhang Y, Wang L, Chen L. OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:492-502. [PMID: 26172270 DOI: 10.1111/jipb.12376] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/07/2015] [Indexed: 05/26/2023]
Abstract
Domain of unknown function 1644 (DUF1644) is a highly conserved amino acid sequence motif present only in plants. Analysis of expression data of the family of DUF1644-containing genes indicated that they may regulate responses to abiotic stress in rice. Here we present our discovery of the role of OsSIDP366, a member of the DUF1644 gene family, in response to drought and salinity stresses in rice. Transgenic rice plants overexpressing OsSIDP366 showed enhanced drought and salinity tolerance and reduced water loss as compared to that in the control, whereas plants with downregulated OsSIDP366 expression levels using RNA interference (RNAi) were more sensitive to salinity and drought treatments. The sensitivity to abscisic acid (ABA) treatment was not changed in OsSIDP366-overexpressing plants, and OsSIDP366 expression was not affected in ABA-deficient mutants. Subcellular localization analysis revealed that OsSIDP366 is presented in the cytoplasmic foci that colocalized with protein markers for both processing bodies (PBs) and stress granules (SGs) in rice protoplasts. Digital gene expression (DGE) profile analysis indicated that stress-related genes such as SNAC1, OsHAK5 and PRs were upregulated in OsSIDP366-overexpressing plants. These results suggest that OsSIDP366 may function as a regulator of the PBs/SGs and positively regulate salt and drought resistance in rice.
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Affiliation(s)
- Chiming Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Chengke Luo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Lijia Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Min Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaoling Guo
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Yuxia Zhang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, 29634, USA
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
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Niedojadło J, Dełeńko K, Niedojadło K. Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia. RNA Biol 2016; 13:531-43. [PMID: 27002417 DOI: 10.1080/15476286.2016.1166331] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Last finding indicates that post-transcriptional processes are significant in low-oxygen conditions, but their nature is poorly understood. Here, we localized poly(A) RNA and mRNA coding proteins involved and not involved with resistance to hypoxia in Lupinus luteus and Arabidopsis thaliana during submergence and after recovery of aerobic conditions. We showed a strong nuclear accumulation of poly(A) RNA and 6 of 7 studied mRNAs with a concurrent strong reduction in RNA polymerase II transcription during hypoxia. In this study, the nucleus did not accumulate mRNA of the ADH1 (alcohol dehydrogenase 1) gene, which is a core hypoxia gene. The RNA accumulation in the nucleus is among the mechanisms of post-transcriptional gene regulation that prevents translation. However re-aeration was accompanied by a strong increase in the amount of the mRNAs in the cytoplasm and a simultaneous decrease in nuclear mRNAs. This finding indicates that the nucleus is a storage site for those of mRNAs which are not involved in the response to hypoxia for use by the plants after the hypoxic stress. In this study, the highest intensity of RNA accumulation occurred in Cajal bodies (CBs); the intensity of accumulation was inversely correlated with transcription. Under hypoxia, ncb-1 mutants of Arabidopsis thaliana with a complete absence of CBs died sooner than wild type (WT), accompanied by a strong reduction in the level of poly(A) RNA in the nucleus. These results suggest that the CBs not only participate in the storage of the nuclear RNA, but they also could take part in its stabilization under low-oxygen conditions.
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Affiliation(s)
- Janusz Niedojadło
- a Department of Cell Biology, Faculty of Biology and Environment Protection , Nicolaus Copernicus University , Torun , Poland
| | - Konrad Dełeńko
- a Department of Cell Biology, Faculty of Biology and Environment Protection , Nicolaus Copernicus University , Torun , Poland
| | - Katarzyna Niedojadło
- a Department of Cell Biology, Faculty of Biology and Environment Protection , Nicolaus Copernicus University , Torun , Poland
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Lokdarshi A, Conner WC, McClintock C, Li T, Roberts DM. Arabidopsis CML38, a Calcium Sensor That Localizes to Ribonucleoprotein Complexes under Hypoxia Stress. PLANT PHYSIOLOGY 2016; 170:1046-59. [PMID: 26634999 PMCID: PMC4734562 DOI: 10.1104/pp.15.01407] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/30/2015] [Indexed: 05/18/2023]
Abstract
During waterlogging and the associated oxygen deprivation stress, plants respond by the induction of adaptive programs, including the redirected expression of gene networks toward the synthesis of core hypoxia-response proteins. Among these core response proteins in Arabidopsis (Arabidopsis thaliana) is the calcium sensor CML38, a protein related to regulator of gene silencing calmodulin-like proteins (rgsCaMs). CML38 transcripts are up-regulated more than 300-fold in roots within 6 h of hypoxia treatment. Transfer DNA insertional mutants of CML38 show an enhanced sensitivity to hypoxia stress, with lowered survival and more severe inhibition of root and shoot growth. By using yellow fluorescent protein (YFP) translational fusions, CML38 protein was found to be localized to cytosolic granule structures similar in morphology to hypoxia-induced stress granules. Immunoprecipitation of CML38 from the roots of hypoxia-challenged transgenic plants harboring CML38pro::CML38:YFP followed by liquid chromatography-tandem mass spectrometry analysis revealed the presence of protein targets associated with messenger RNA ribonucleoprotein (mRNP) complexes including stress granules, which are known to accumulate as messenger RNA storage and triage centers during hypoxia. This finding is further supported by the colocalization of CML38 with the mRNP stress granule marker RNA Binding Protein 47 (RBP47) upon cotransfection of Nicotiana benthamiana leaves. Ruthenium Red treatment results in the loss of CML38 signal in cytosolic granules, suggesting that calcium is necessary for stress granule association. These results confirm that CML38 is a core hypoxia response calcium sensor protein and suggest that it serves as a potential calcium signaling target within stress granules and other mRNPs that accumulate during flooding stress responses.
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Affiliation(s)
- Ansul Lokdarshi
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
| | - W Craig Conner
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
| | - Carlee McClintock
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
| | - Tian Li
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
| | - Daniel M Roberts
- Department of Biochemistry and Cellular and Molecular Biology (A.L., W.C.C., C.M., D.M.R.) and Program in Genome Science and Technology (T.L., D.M.R.), University of Tennessee, Knoxville, Tennessee 37996
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49
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Julkowska MM, Testerink C. Tuning plant signaling and growth to survive salt. TRENDS IN PLANT SCIENCE 2015; 20:586-594. [PMID: 26205171 DOI: 10.1016/j.tplants.2015.06.008] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/16/2015] [Accepted: 06/25/2015] [Indexed: 05/20/2023]
Abstract
Salinity is one of the major abiotic factors threatening food security worldwide. Recently, our understanding of early processes underlying salinity tolerance has expanded. In this review, early signaling events, such as phospholipid signaling, calcium ion (Ca(2+)) responses, and reactive oxygen species (ROS) production, together with salt stress-induced abscisic acid (ABA) accumulation, are brought into the context of long-term salt stress-specific responses and alteration of plant growth. Salt-induced quiescent and recovery growth phases rely on modification of cell cycle activity, cell expansion, and cell wall extensibility. The period of initial growth arrest varies among different organs, leading to altered plant morphology. Studying stress-induced changes in growth dynamics can be used for screening to discover novel genes contributing to salt stress tolerance in model species and crops.
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Affiliation(s)
- Magdalena M Julkowska
- Section of Plant Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Christa Testerink
- Section of Plant Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands.
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Gutierrez-Beltran E, Moschou PN, Smertenko AP, Bozhkov PV. Tudor staphylococcal nuclease links formation of stress granules and processing bodies with mRNA catabolism in Arabidopsis. THE PLANT CELL 2015; 27:926-43. [PMID: 25736060 PMCID: PMC4558657 DOI: 10.1105/tpc.114.134494] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/03/2015] [Accepted: 02/16/2015] [Indexed: 05/18/2023]
Abstract
Tudor Staphylococcal Nuclease (TSN or Tudor-SN; also known as SND1) is an evolutionarily conserved protein involved in the transcriptional and posttranscriptional regulation of gene expression in animals. Although TSN was found to be indispensable for normal plant development and stress tolerance, the molecular mechanisms underlying these functions remain elusive. Here, we show that Arabidopsis thaliana TSN is essential for the integrity and function of cytoplasmic messenger ribonucleoprotein (mRNP) complexes called stress granules (SGs) and processing bodies (PBs), sites of posttranscriptional gene regulation during stress. TSN associates with SGs following their microtubule-dependent assembly and plays a scaffolding role in both SGs and PBs. The enzymatically active tandem repeat of four SN domains is crucial for targeting TSN to the cytoplasmic mRNA complexes and is sufficient for the cytoprotective function of TSN during stress. Furthermore, our work connects the cytoprotective function of TSN with its positive role in stress-induced mRNA decapping. While stress led to a pronounced increase in the accumulation of uncapped mRNAs in wild-type plants, this increase was abrogated in TSN knockout plants. Taken together, our results establish TSN as a key enzymatic component of the catabolic machinery responsible for the processing of mRNAs in the cytoplasmic mRNP complexes during stress.
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Affiliation(s)
- Emilio Gutierrez-Beltran
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Andrei P Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 Institute for Global Food Security, Queen's University Belfast, Belfast BT9 5BN, United Kingdom
| | - Peter V Bozhkov
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
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