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Gomaa AE, El Mounadi K, Parperides E, Garcia-Ruiz H. Cell Fractionation and the Identification of Host Proteins Involved in Plant-Virus Interactions. Pathogens 2024; 13:53. [PMID: 38251360 PMCID: PMC10819628 DOI: 10.3390/pathogens13010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Plant viruses depend on host cellular factors for their replication and movement. There are cellular proteins that change their localization and/or expression and have a proviral role or antiviral activity and interact with or target viral proteins. Identification of those proteins and their roles during infection is crucial for understanding plant-virus interactions and to design antiviral resistance in crops. Important host proteins have been identified using approaches such as tag-dependent immunoprecipitation or yeast two hybridization that require cloning individual proteins or the entire virus. However, the number of possible interactions between host and viral proteins is immense. Therefore, an alternative method is needed for proteome-wide identification of host proteins involved in host-virus interactions. Here, we present cell fractionation coupled with mass spectrometry as an option to identify protein-protein interactions between viruses and their hosts. This approach involves separating subcellular organelles using differential and/or gradient centrifugation from virus-free and virus-infected cells (1) followed by comparative analysis of the proteomic profiles obtained for each subcellular organelle via mass spectrometry (2). After biological validation, prospect host proteins with proviral or antiviral roles can be subject to fundamental studies in the context of basic biology to shed light on both virus replication and cellular processes. They can also be targeted via gene editing to develop virus-resistant crops.
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Affiliation(s)
- Amany E. Gomaa
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
- Department of Botany, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Kaoutar El Mounadi
- Department of Biology, Kutztown University of Pennsylvania, Kutztown, PA 19530, USA
| | - Eric Parperides
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
| | - Hernan Garcia-Ruiz
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
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2
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Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024; 21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~ 25 nt from predominantly NOR4 ribosomal DNA copies, obtaining mosaic mutational events on ~ 5% of all rDNA copies. The excised region consists of P-loop and Helix-82 segments of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves, all previously observed for defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies by elevated expression of VAR1 in mutants and further associated single-nucleotide variants, thus, resulting in altered rRNA sub-population. Furthermore, the mutants exhibited rRNA maturation defects specifically in the minor pathway typified by 32S pre-rRNA accumulation. Density-gradient fractionation and subsequent RT-PCR of rRNA analyses revealed that mutated copies were not incorporated into the translating ribosomes. The mutants in addition displayed an elevated autophagic flux as shown by the autophagic marker GFP-ATG8e, likely related to ribophagy.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Deniz Streit
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thorsten Bergelt
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Simm
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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Ding G, Mugume Y, Dueñas ME, Lee YJ, Liu M, Nettleton DS, Zhao X, Li L, Bassham DC, Nikolau BJ. Biological insights from multi-omics analysis strategies: Complex pleotropic effects associated with autophagy. FRONTIERS IN PLANT SCIENCE 2023; 14:1093358. [PMID: 36875559 PMCID: PMC9978356 DOI: 10.3389/fpls.2023.1093358] [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: 11/08/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Research strategies that combine molecular data from multiple levels of genome expression (i.e., multi-omics data), often referred to as a systems biology strategy, has been advocated as a route to discovering gene functions. In this study we conducted an evaluation of this strategy by combining lipidomics, metabolite mass-spectral imaging and transcriptomics data from leaves and roots in response to mutations in two AuTophaGy-related (ATG) genes of Arabidopsis. Autophagy is an essential cellular process that degrades and recycles macromolecules and organelles, and this process is blocked in the atg7 and atg9 mutants that were the focus of this study. Specifically, we quantified abundances of ~100 lipids and imaged the cellular locations of ~15 lipid molecular species and the relative abundance of ~26,000 transcripts from leaf and root tissues of WT, atg7 and atg9 mutant plants, grown either in normal (nitrogen-replete) and autophagy-inducing conditions (nitrogen-deficient). The multi-omics data enabled detailed molecular depiction of the effect of each mutation, and a comprehensive physiological model to explain the consequence of these genetic and environmental changes in autophagy is greatly facilitated by the a priori knowledge of the exact biochemical function of the ATG7 and ATG9 proteins.
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Affiliation(s)
- Geng Ding
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Yosia Mugume
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | | | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Meiling Liu
- Department of Statistics, Iowa State University, Ames, IA, United States
| | | | - Xuefeng Zhao
- Research Information Technology, College of Liberal Arts & Sciences, Iowa State University, Ames, IA, United States
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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Sánchez-Sevilla JF, Botella MA, Valpuesta V, Sanchez-Vera V. Autophagy Is Required for Strawberry Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2021; 12:688481. [PMID: 34512686 PMCID: PMC8429490 DOI: 10.3389/fpls.2021.688481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Autophagy is a catabolic and recycling pathway that maintains cellular homeostasis under normal growth and stress conditions. Two major types of autophagy, microautophagy and macroautophagy, have been described in plants. During macroautophagy, cellular content is engulfed by a double-membrane vesicle called autophagosome. This vesicle fuses its outer membrane with the tonoplast and releases the content into the vacuole for degradation. During certain developmental processes, autophagy is enhanced by induction of several autophagy-related genes (ATG genes). Autophagy in crop development has been studied in relation to leaf senescence, seed and reproductive development, and vascular formation. However, its role in fruit ripening has only been partially addressed. Strawberry is an important berry crop, representative of non-climacteric fruit. We have analyzed the occurrence of autophagy in developing and ripening fruits of the cultivated strawberry. Our data show that most ATG genes are conserved in the genome of the cultivated strawberry Fragaria x ananassa and they are differentially expressed along the ripening of the fruit receptacle. ATG8-lipidation analysis proves the presence of two autophagic waves during ripening. In addition, we have confirmed the presence of autophagy at the cellular level by the identification of autophagy-related structures at different stages of the strawberry ripening. Finally, we show that blocking autophagy either biochemically or genetically dramatically affects strawberry growth and ripening. Our data support that autophagy is an active and essential process with different implications during strawberry fruit ripening.
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Affiliation(s)
- José F Sánchez-Sevilla
- Unidad Asociada al CSIC de I+D+i Biotecnología y Mejora en Fresa, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA Málaga, Junta de Andalucía, Málaga, Spain
| | - Miguel A Botella
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - Victoriano Valpuesta
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - Victoria Sanchez-Vera
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
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Abstract
Autophagy is a widely shared pathway among different eukaryotes, which helps to maintain cellular homeostasis via recycling unwanted cytoplasmic components. Autophagy plays an important role in plant growth, also assists plants in confronting various environmental stresses. Drought stress can activate autophagy pathway in plants to favor their environmental adaptations, however, a direct link to wire drought and autophagy is still missing. We have recently identified a plant-unique COST1 (Constitutively Stressed 1) protein that can negatively regulate plant drought tolerance through direct interaction with an autophagy receptor protein ATG8e (autophagy-related 8e). COST1 thus represents an innovation of plant-specific autophagy regulation, extending our understating of this conserved but complex pathway, as well as underlying its potential in agricultural usage.
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Affiliation(s)
- Yan Bao
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- CONTACT Yan Bao Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI48864, USAThis article has been republished with minor changes. These changes do not impact the academic content of the article
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Abstract
Plants balance their competing requirements for growth and stress tolerance via a sophisticated regulatory circuitry that controls responses to the external environments. We have identified a plant-specific gene, COST1 (constitutively stressed 1), that is required for normal plant growth but negatively regulates drought resistance by influencing the autophagy pathway. An Arabidopsis thaliana cost1 mutant has decreased growth and increased drought tolerance, together with constitutive autophagy and increased expression of drought-response genes, while overexpression of COST1 confers drought hypersensitivity and reduced autophagy. The COST1 protein is degraded upon plant dehydration, and this degradation is reduced upon treatment with inhibitors of the 26S proteasome or autophagy pathways. The drought resistance of a cost1 mutant is dependent on an active autophagy pathway, but independent of other known drought signaling pathways, indicating that COST1 acts through regulation of autophagy. In addition, COST1 colocalizes to autophagosomes with the autophagosome marker ATG8e and the autophagy adaptor NBR1, and affects the level of ATG8e protein through physical interaction with ATG8e, indicating a pivotal role in direct regulation of autophagy. We propose a model in which COST1 represses autophagy under optimal conditions, thus allowing plant growth. Under drought, COST1 is degraded, enabling activation of autophagy and suppression of growth to enhance drought tolerance. Our research places COST1 as an important regulator controlling the balance between growth and stress responses via the direct regulation of autophagy.
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Bao Y, Bassham DC. Using Arabidopsis Mesophyll Protoplasts to Study Unfolded Protein Response Signaling. Bio Protoc 2018; 8:e3101. [PMID: 34532547 DOI: 10.21769/bioprotoc.3101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 01/23/2023] Open
Abstract
Various environmental stresses or artificial reagents can trigger unfolded protein accumulation in the endoplasmic reticulum (ER) due to the folding capacity of the ER being exceeded. This is termed ER stress, and triggers the unfolded protein response (UPR). Assays for activation of the UPR in plants include Tunicamycin (Tm)- or dithiothreitol (DTT)-mediated root growth inhibition, analysis of splicing of the UPR-responsive transcription factor bZIP60 (basic Leucine Zipper Domain 60), and upregulation of relevant UPR genes. We provide here a quick and robust method to detect UPR signaling in Arabidopsis thaliana protoplasts. This assay can also be applied to other plant species for which protoplasts can be isolated.
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Affiliation(s)
- Yan Bao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
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Marion J, Le Bars R, Besse L, Batoko H, Satiat-Jeunemaitre B. Multiscale and Multimodal Approaches to Study Autophagy in Model Plants. Cells 2018; 7:E5. [PMID: 29315263 PMCID: PMC5789278 DOI: 10.3390/cells7010005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/05/2018] [Accepted: 01/05/2018] [Indexed: 12/31/2022] Open
Abstract
Autophagy is a catabolic process used by eukaryotic cells to maintain or restore cellular and organismal homeostasis. A better understanding of autophagy in plant biology could lead to an improvement of the recycling processes of plant cells and thus contribute, for example, towards reducing the negative ecological consequences of nitrogen-based fertilizers in agriculture. It may also help to optimize plant adaptation to adverse biotic and abiotic conditions through appropriate plant breeding or genetic engineering to incorporate useful traits in relation to this catabolic pathway. In this review, we describe useful protocols for studying autophagy in the plant cell, taking into account some specificities of the plant model.
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Affiliation(s)
- Jessica Marion
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91 198 Gif-sur-Yvette, France; (J.M.); (R.L.B.); (L.B.); (B.S.-J.)
| | - Romain Le Bars
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91 198 Gif-sur-Yvette, France; (J.M.); (R.L.B.); (L.B.); (B.S.-J.)
| | - Laetitia Besse
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91 198 Gif-sur-Yvette, France; (J.M.); (R.L.B.); (L.B.); (B.S.-J.)
| | - Henri Batoko
- Institute of Life Sciences, UCL/ISV, University of Louvain, Croix du Sud 4, L7.07.14, 1348 Louvain-la-Neuve, Belgium
| | - Béatrice Satiat-Jeunemaitre
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91 198 Gif-sur-Yvette, France; (J.M.); (R.L.B.); (L.B.); (B.S.-J.)
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Batoko H, Dagdas Y, Baluska F, Sirko A. Understanding and exploiting autophagy signaling in plants. Essays Biochem 2017; 61:675-685. [PMID: 29233877 PMCID: PMC5869243 DOI: 10.1042/ebc20170034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/11/2017] [Accepted: 10/19/2017] [Indexed: 12/20/2022]
Abstract
Autophagy is an essential catabolic pathway and is activated by various endogenous and exogenous stimuli. In particular, autophagy is required to allow sessile organisms such as plants to cope with biotic or abiotic stress conditions. It is thought that these various environmental signaling pathways are somehow integrated with autophagy signaling. However, the molecular mechanisms of plant autophagy signaling are not well understood, leaving a big gap of knowledge as a barrier to being able to manipulate this important pathway to improve plant growth and development. In this review, we discuss possible regulatory mechanisms at the core of plant autophagy signaling.
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Affiliation(s)
- Henri Batoko
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 4, L7.07.14, 1348 Louvain-la-Neuve, Belgium
| | - Yasin Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | | | - Agnieszka Sirko
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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Luo L, Zhang P, Zhu R, Fu J, Su J, Zheng J, Wang Z, Wang D, Gong Q. Autophagy Is Rapidly Induced by Salt Stress and Is Required for Salt Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:1459. [PMID: 28878796 PMCID: PMC5572379 DOI: 10.3389/fpls.2017.01459] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 08/04/2017] [Indexed: 05/18/2023]
Abstract
Salinity stress challenges agriculture and food security globally. Upon salt stress, plant growth slows down, nutrients are recycled, osmolytes are produced, and reallocation of Na+ takes place. Since autophagy is a high-throughput degradation pathway that contributes to nutrient remobilization in plants, we explored the involvement of autophagic flux in salt stress response of Arabidopsis with various approaches. Confocal microscopy of GFP-ATG8a in transgenic Arabidopsis showed that autophagosome formation is induced shortly after salt treatment. Immunoblotting of ATG8s and the autophagy receptor NBR1 confirmed that the level of autophagy peaks within 30 min of salt stress, and then settles to a new homeostasis in Arabidopsis. Such an induction is absent in mutants defective in autophagy. Within 3 h of salt treatment, accumulation of oxidized proteins is alleviated in the wild-type; however, such a reduction is not seen in atg2 or atg7. Consistently, the Arabidopsis atg mutants are hypersensitive to both salt and osmotic stresses, and plants overexpressing ATG8 perform better than the wild-type in germination assays. Quantification of compatible osmolytes further confirmed that the autophagic flux contributes to salt stress adaptation. Imaging of intracellular Na+ revealed that autophagy is required for Na+ sequestration in the central vacuole of root cortex cells following salt treatment. These data suggest that rapid protein turnover through autophagy is a prerequisite for salt stress tolerance in Arabidopsis.
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Affiliation(s)
| | | | | | | | | | | | | | - Dan Wang
- *Correspondence: Dan Wang, Qingqiu Gong,
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