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Zhang Z, Timmerman E, Impens F, Van Breusegem F. Characterization of RBPome in Oxidative Stress Conditions. Methods Mol Biol 2022; 2526:259-275. [PMID: 35657526 DOI: 10.1007/978-1-0716-2469-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cellular redox signaling is triggered by accumulation of various reactive oxygen species (ROS) that integrate with other signaling cascades to enable plants to ultimately respond to (a)biotic stresses. The identification of key regulators underlying redox signaling networks is therefore of high priority. This chapter describes an improved mRNA interactome capture method that allows to systematically detect oxidative stress responsive regulators in the post-transcriptional gene regulation (PTGR) pathway. The protocol includes PSB-D suspension cell culture preparation, setup of oxidative stress conditions, short-term exposure to UV irradiation, cell lysis, pull-down and purification of crosslinked messenger ribonucleoproteins, their mass spectrometric analyses, and identification of proteome by statistical analyses. As result, a comprehensive inventory of the functional oxidative stress responsive RBPome (OxRBPome) is generated, which paves the way toward new insights into PTGR processes in redox signaling.
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Affiliation(s)
- Zhicheng Zhang
- Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, Ghent, Belgium
- UGent Department of Biomolecular Medicine, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, Ghent, Belgium
- UGent Department of Biomolecular Medicine, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Frank Van Breusegem
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
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2
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Akter S, Khan MS, Smith EN, Flashman E. Measuring ROS and redox markers in plant cells. RSC Chem Biol 2021; 2:1384-1401. [PMID: 34704044 PMCID: PMC8495998 DOI: 10.1039/d1cb00071c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/28/2021] [Indexed: 01/05/2023] Open
Abstract
Reactive oxygen species (ROS) are produced throughout plant cells as a by-product of electron transfer processes. While highly oxidative and potentially damaging to a range of biomolecules, there exists a suite of ROS-scavenging antioxidant strategies that maintain a redox equilibrium. This balance can be disrupted in the event of cellular stress leading to increased ROS levels, which can act as a useful stress signal but, in excess, can result in cell damage and death. As crop plants become exposed to greater degrees of multiple stresses due to climate change, efforts are ongoing to engineer plants with greater stress tolerance. It is therefore important to understand the pathways underpinning ROS-mediated signalling and damage, both through measuring ROS themselves and other indicators of redox imbalance. The highly reactive and transient nature of ROS makes this challenging to achieve, particularly in a way that is specific to individual ROS species. In this review, we describe the range of chemical and biological tools and techniques currently available for ROS and redox marker measurement in plant cells and tissues. We discuss the limitations inherent in current methodology and opportunities for advancement.
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Affiliation(s)
- Salma Akter
- Department of Chemistry, University of Oxford Oxford UK
- Faculty of Biological Sciences, University of Dhaka Dhaka 1000 Bangladesh
| | - Mohammad Shahneawz Khan
- Department of Chemistry, University of Oxford Oxford UK
- Faculty of Biological Sciences, University of Dhaka Dhaka 1000 Bangladesh
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3
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Nikolić IP, Nešić SB, Samardžić JT, Timotijević GS. Intrinsically disordered protein AtDSS1(V) participates in plant defense response to oxidative stress. PROTOPLASMA 2021; 258:779-792. [PMID: 33404921 DOI: 10.1007/s00709-020-01598-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
DSS1 is a small protein, highly conserved across different species. As a member of the intrinsically disordered protein family, DSS1 interacts with different protein partners, thus forming complexes involved in diverse biological mechanisms: DNA repair, regulation of protein homeostasis, mRNA export, etc. Additionally, DSS1 has a novel intriguing role in the post-translational protein modification named DSSylation. Oxidatively damaged proteins are targeted for removal with DSS1 and then degraded by proteasome. Yet, DSS1 involvement in the maintenance of genome integrity through homologous recombination is the only function well studied in Arabidopsis research. The fact that animal DSS1 shows wide multifunctionality imposes a need to investigate the additional roles of two Arabidopsis thaliana DSS1 homologs. Having in mind the universality of various biological processes, we considered the possibility of plant DSS1 involvement in cellular homeostasis maintenance during stress exposure. Using real-time PCR and immunoblot analysis, we investigated the profiles of DSS1 gene and protein expression under oxidative stress. We grew and selected the homozygous Arabidopsis mutant line, carrying the T-DNA intron insertion in the DSS1(V) gene. The mutant line was phenotypically described during plant development, and its sensitivity to oxidative stress was characterized. This is the first report which indicates that plant DSS1 gene expression has an altered profile under the influence of oxidative stress. dss1(V)-/- plants showed an increased sensitivity to oxidative stress, germinated faster than WT, but generally showed developmental delay in further stages. Our results indicate that the DSS1 protein could be a crucial player in the molecular mechanisms underlying plant abiotic stress responses.
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Affiliation(s)
- Ivana P Nikolić
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Plant Molecular Biology, University of Belgrade, Vojvode Stepe 444a, Belgrade 152, 11042, Serbia
| | - Sofija B Nešić
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Plant Molecular Biology, University of Belgrade, Vojvode Stepe 444a, Belgrade 152, 11042, Serbia
| | - Jelena T Samardžić
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Plant Molecular Biology, University of Belgrade, Vojvode Stepe 444a, Belgrade 152, 11042, Serbia
| | - Gordana S Timotijević
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Plant Molecular Biology, University of Belgrade, Vojvode Stepe 444a, Belgrade 152, 11042, Serbia.
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4
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Vo TN, Malo Pueyo J, Wahni K, Ezeriņa D, Bolduc J, Messens J. Prdx1 Interacts with ASK1 upon Exposure to H 2O 2 and Independently of a Scaffolding Protein. Antioxidants (Basel) 2021; 10:antiox10071060. [PMID: 34209102 PMCID: PMC8300624 DOI: 10.3390/antiox10071060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 01/02/2023] Open
Abstract
Hydrogen peroxide (H2O2) is a key redox signaling molecule that selectively oxidizes cysteines on proteins. It can accomplish this even in the presence of highly efficient and abundant H2O2 scavengers, peroxiredoxins (Prdxs), as it is the Prdxs themselves that transfer oxidative equivalents to specific protein thiols on target proteins via their redox-relay functionality. The first evidence of a mammalian cytosolic Prdx-mediated redox-relay—Prdx1 with the kinase ASK1—was presented a decade ago based on the outcome of a co-immunoprecipitation experiment. A second such redox-relay—Prdx2:STAT3—soon followed, for which further studies provided insights into its specificity, organization, and mechanism. The Prdx1:ASK1 redox-relay, however, has never undergone such a characterization. Here, we combine cellular and in vitro protein–protein interaction methods to investigate the Prdx1:ASK1 interaction more thoroughly. We show that, contrary to the Prdx2:STAT3 redox-relay, Prdx1 interacts with ASK1 at elevated H2O2 concentrations, and that this interaction can happen independently of a scaffolding protein. We also provide evidence of a Prdx2:ASK1 interaction, and demonstrate that it requires a facilitator that, however, is not annexin A2. Our results reveal that cytosolic Prdx redox-relays can be organized in different ways and yet again highlight the differentiated roles of Prdx1 and Prdx2.
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Affiliation(s)
- Trung Nghia Vo
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Julia Malo Pueyo
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Daria Ezeriņa
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Jesalyn Bolduc
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut Voor Biotechnologie, B-1050 Brussels, Belgium; (T.N.V.); (J.M.P.); (K.W.); (D.E.); (J.B.)
- Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Correspondence:
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5
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Smythers AL, Hicks LM. Mapping the plant proteome: tools for surveying coordinating pathways. Emerg Top Life Sci 2021; 5:203-220. [PMID: 33620075 PMCID: PMC8166341 DOI: 10.1042/etls20200270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein-protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
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6
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Sonego G, Le TTM, Crettaz D, Abonnenc M, Tissot JD, Prudent M. Sulfenylome analysis of pathogen-inactivated platelets reveals the presence of cysteine oxidation in integrin signaling pathway and cytoskeleton regulation. J Thromb Haemost 2021; 19:233-247. [PMID: 33047470 DOI: 10.1111/jth.15121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/17/2020] [Accepted: 10/01/2020] [Indexed: 12/16/2022]
Abstract
Essentials Cysteine oxidation to sulfenic acid plays a key role in redox regulation and signal transduction. Platelet sulfenylome was studied by quantitative proteomics in pathogen inactivated platelets. One hundred and seventy-four sulfenylated proteins were identified in resting platelets. Pathogen inactivation oxidized integrin βIII, which could activate the mitogen-activated protein kinases pathway. ABSTRACT: Background Cysteine-containing protein modifications are involved in numerous biological processes such redox regulation or signal transduction. During the preparation and storage of platelet concentrates, cell functions and protein regulations are impacted. In spite of several proteomic investigations, the platelet sulfenylome, ie, the proteins containing cysteine residues (R-SH) oxidized to sulfenic acid (R-SOH), has not been characterized. Methods A dimedone-based sulfenic acid tagging and enrichment coupled to a mass spectrometry identification workflow was developed to identify and quantify the sulfenic acid-containing proteins in platelet concentrates treated or not with an amotosalen/ultraviolet A (UVA) pathogen inactivation technique. Results One hundred and seventy-four sulfenylated proteins were identified belonging mainly to the integrin signal pathway and cytoskeletal regulation by Rho GTPase. The impact on pathogen inactivated platelet concentrates was weak compared to untreated ones where three sulfenylated proteins (myosin heavy chain 9, integrin βIII, and transgelin 2) were significantly affected by amotosalen/UVA treatment. Of particular interest, the reported oxidation of cysteine residues in integrin βIII is known to activate the receptor αIIbβIII. Following the pathogen inactivation, it might trigger the phosphorylation of p38MAPK and explain the lesions reported in the literature. Moreover, procaspase activating compound-1 (PAC-1) binding assays on platelet activation showed an increased response to adenosine diphosphate exacerbated by the tagging of proteins with dimedone. This result corroborates the hypothesis of an oxidation-triggered activation of αIIbβIII by the pathogen inactivation treatment. Conclusions The present work completes missing information on the platelet proteome and provides new insights on the effect of pathogen inactivation linked to integrin signaling and cytoskeleton regulation.
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Affiliation(s)
- Giona Sonego
- Laboratoire de Recherche sur les Produits Sanguins, Recherche et Développement Produits, Transfusion Interrégionale CRS, Epalinges, Switzerland
| | - Truong-Thien Melvin Le
- Laboratoire de Recherche sur les Produits Sanguins, Recherche et Développement Produits, Transfusion Interrégionale CRS, Epalinges, Switzerland
| | - David Crettaz
- Laboratoire de Recherche sur les Produits Sanguins, Recherche et Développement Produits, Transfusion Interrégionale CRS, Epalinges, Switzerland
| | - Mélanie Abonnenc
- Laboratoire de Recherche sur les Produits Sanguins, Recherche et Développement Produits, Transfusion Interrégionale CRS, Epalinges, Switzerland
| | - Jean-Daniel Tissot
- Laboratoire de Recherche sur les Produits Sanguins, Recherche et Développement Produits, Transfusion Interrégionale CRS, Epalinges, Switzerland
- Centre de Transfusion Sanguine, Faculté de Biologie et de Médecine, University of Lausanne, Lausanne, Switzerland
| | - Michel Prudent
- Laboratoire de Recherche sur les Produits Sanguins, Recherche et Développement Produits, Transfusion Interrégionale CRS, Epalinges, Switzerland
- Centre de Transfusion Sanguine, Faculté de Biologie et de Médecine, University of Lausanne, Lausanne, Switzerland
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7
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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8
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Corpas FJ, González-Gordo S, Palma JM. Plant Peroxisomes: A Factory of Reactive Species. FRONTIERS IN PLANT SCIENCE 2020; 11:853. [PMID: 32719691 PMCID: PMC7348659 DOI: 10.3389/fpls.2020.00853] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/27/2020] [Indexed: 05/19/2023]
Abstract
Plant peroxisomes are organelles enclosed by a single membrane whose biochemical composition has the capacity to adapt depending on the plant tissue, developmental stage, as well as internal and external cellular stimuli. Apart from the peroxisomal metabolism of reactive oxygen species (ROS), discovered several decades ago, new molecules with signaling potential, including nitric oxide (NO) and hydrogen sulfide (H2S), have been detected in these organelles in recent years. These molecules generate a family of derived molecules, called reactive nitrogen species (RNS) and reactive sulfur species (RSS), whose peroxisomal metabolism is autoregulated through posttranslational modifications (PTMs) such as S-nitrosation, nitration and persulfidation. The peroxisomal metabolism of these reactive species, which can be weaponized against pathogens, is susceptible to modification in response to external stimuli. This review aims to provide up-to-date information on crosstalk between these reactive species families and peroxisomes, as well as on their cellular environment in light of the well-recognized signaling properties of H2O2, NO and H2S.
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Affiliation(s)
- Francisco J. Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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9
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Yu J, Li Y, Qin Z, Guo S, Li Y, Miao Y, Song C, Chen S, Dai S. Plant Chloroplast Stress Response: Insights from Thiol Redox Proteomics. Antioxid Redox Signal 2020; 33:35-57. [PMID: 31989831 DOI: 10.1089/ars.2019.7823] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significance: Plant chloroplasts generate reactive oxygen species (ROS) during photosynthesis, especially under stresses. The sulfhydryl groups of protein cysteine residues are susceptible to redox modifications, which regulate protein structure and function, and thus different signaling and metabolic processes. The ROS-governed protein thiol redox switches play important roles in chloroplasts. Recent Advances: Various high-throughput thiol redox proteomic approaches have been developed, and they have enabled the improved understanding of redox regulatory mechanisms in chloroplasts. For example, the thioredoxin-modulated antioxidant enzymes help to maintain cellular ROS homeostasis. The light- and dark-dependent redox regulation of photosynthetic electron transport, the Calvin/Benson cycle, and starch biosynthesis ensures metabolic coordination and efficient energy utilization. In addition, redox cascades link the light with the dynamic changes of metabolites in nitrate and sulfur assimilation, shikimate pathway, and biosynthesis of fatty acid hormone as well as purine, pyrimidine, and thiamine. Importantly, redox regulation of tetrapyrrole and chlorophyll biosynthesis is critical to balance the photodynamic tetrapyrrole intermediates and prevent oxidative damage. Moreover, redox regulation of diverse elongation factors, chaperones, and kinases plays an important role in the modulation of gene expression, protein conformation, and posttranslational modification that contribute to photosystem II (PSII) repair, state transition, and signaling in chloroplasts. Critical Issues: This review focuses on recent advances in plant thiol redox proteomics and redox protein networks toward understanding plant chloroplast signaling, metabolism, and stress responses. Future Directions: Using redox proteomics integrated with biochemical and molecular genetic approaches, detailed studies of cysteine residues, their redox states, cross talk with other modifications, and the functional implications will yield a holistic understanding of chloroplast stress responses.
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Affiliation(s)
- Juanjuan Yu
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China.,College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Zhi Qin
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Yongfang Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Chunpeng Song
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
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10
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Foyer CH, Baker A, Wright M, Sparkes IA, Mhamdi A, Schippers JHM, Van Breusegem F. On the move: redox-dependent protein relocation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:620-631. [PMID: 31421053 DOI: 10.1093/jxb/erz330] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/01/2019] [Indexed: 05/04/2023]
Abstract
Compartmentation of proteins and processes is a defining feature of eukaryotic cells. The growth and development of organisms is critically dependent on the accurate sorting of proteins within cells. The mechanisms by which cytosol-synthesized proteins are delivered to the membranes and membrane compartments have been extensively characterized. However, the protein complement of any given compartment is not precisely fixed and some proteins can move between compartments in response to metabolic or environmental triggers. The mechanisms and processes that mediate such relocation events are largely uncharacterized. Many proteins can in addition perform multiple functions, catalysing alternative reactions or performing structural, non-enzymatic functions. These alternative functions can be equally important functions in each cellular compartment. Such proteins are generally not dual-targeted proteins in the classic sense of having targeting sequences that direct de novo synthesized proteins to specific cellular locations. We propose that redox post-translational modifications (PTMs) can control the compartmentation of many such proteins, including antioxidant and/or redox-associated enzymes.
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Affiliation(s)
- Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Alison Baker
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Centre for Plant Sciences, University of Leeds, Leeds, UK
| | - Megan Wright
- The Astbury Centre for Structural Biology, University of Leeds, Leeds, UK
- School of Chemistry, University of Leeds, Leeds, UK
| | - Imogen A Sparkes
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Amna Mhamdi
- VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jos H M Schippers
- Institute of Biology I, RWTH Aachen University, Aachen, Germany
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Frank Van Breusegem
- VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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11
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Sandalio LM, Gotor C, Romero LC, Romero-Puertas MC. Multilevel Regulation of Peroxisomal Proteome by Post-Translational Modifications. Int J Mol Sci 2019; 20:E4881. [PMID: 31581473 PMCID: PMC6801620 DOI: 10.3390/ijms20194881] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
Peroxisomes, which are ubiquitous organelles in all eukaryotes, are highly dynamic organelles that are essential for development and stress responses. Plant peroxisomes are involved in major metabolic pathways, such as fatty acid β-oxidation, photorespiration, ureide and polyamine metabolism, in the biosynthesis of jasmonic, indolacetic, and salicylic acid hormones, as well as in signaling molecules such as reactive oxygen and nitrogen species (ROS/RNS). Peroxisomes are involved in the perception of environmental changes, which is a complex process involving the regulation of gene expression and protein functionality by protein post-translational modifications (PTMs). Although there has been a growing interest in individual PTMs in peroxisomes over the last ten years, their role and cross-talk in the whole peroxisomal proteome remain unclear. This review provides up-to-date information on the function and crosstalk of the main peroxisomal PTMs. Analysis of whole peroxisomal proteomes shows that a very large number of peroxisomal proteins are targeted by multiple PTMs, which affect redox balance, photorespiration, the glyoxylate cycle, and lipid metabolism. This multilevel PTM regulation could boost the plasticity of peroxisomes and their capacity to regulate metabolism in response to environmental changes.
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Affiliation(s)
- Luisa M Sandalio
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain.
| | - Cecilia Gotor
- Institute of Plant Biochemistry and Photosynthesis, CSIC and the University of Seville, 41092 Seville, Spain.
| | - Luis C Romero
- Institute of Plant Biochemistry and Photosynthesis, CSIC and the University of Seville, 41092 Seville, Spain.
| | - Maria C Romero-Puertas
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain.
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12
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Berg P, McConnell EW, Hicks LM, Popescu SC, Popescu GV. Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics. BMC Bioinformatics 2019; 20:102. [PMID: 30871482 PMCID: PMC6419331 DOI: 10.1186/s12859-019-2619-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM) analysis like reversible cysteine oxidation are evaluated. The paper proposes a pipeline based on the R programming language to analyze PTMs from peptide-centric label-free quantitative proteomics data. RESULTS Our methodology includes variance stabilization, normalization, and missing data imputation to account for the large dynamic range of PTM measurements. It also corrects biases from an enrichment protocol and reduces the random and systematic errors associated with label-free quantification. The performance of the methodology is tested by performing proteome-wide differential PTM quantitation using linear models analysis (limma). We objectively compare two imputation methods along with significance testing when using multiple-imputation for missing data. CONCLUSION Identifying PTMs in large-scale datasets is a problem with distinct characteristics that require new methods for handling missing data imputation and differential proteome analysis. Linear models in combination with multiple-imputation could significantly outperform a t-test-based decision method.
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Affiliation(s)
- Philip Berg
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA
| | - Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - George V Popescu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA. .,The National Institute for Laser, Plasma & Radiation Physics, Bucharest, Romania.
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13
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De Smet B, Willems P, Fernandez-Fernandez AD, Alseekh S, Fernie AR, Messens J, Van Breusegem F. In vivo detection of protein cysteine sulfenylation in plastids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:765-778. [PMID: 30394608 DOI: 10.1111/tpj.14146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 05/04/2023]
Abstract
Protein cysteine thiols are post-translationally modified under oxidative stress conditions. Illuminated chloroplasts are one of the important sources of hydrogen peroxide (H2 O2 ) and are highly sensitive to environmental stimuli, yet a comprehensive view of the oxidation-sensitive chloroplast proteome is still missing. By targeting the sulfenic acid YAP1C-trapping technology to the plastids of light-grown Arabidopsis cells, we identified 132 putatively sulfenylated plastid proteins upon H2 O2 pulse treatment. Almost half of the sulfenylated proteins are enzymes of the amino acid metabolism. Using metabolomics, we observed a reversible decrease in the levels of the amino acids Ala, Asn, Cys, Gln, Glu, His, Ile, Leu, Lys, Phe, Ser, Thr and Val after H2 O2 treatment, which is in line with an anticipated decrease in the levels of the glycolysis and tricarboxylic acid metabolites. Through the identification of an organelle-tailored proteome, we demonstrated that the subcellular targeting of the YAP1C probe enables us to study in vivo cysteine sulfenylation at the organellar level. All in all, the identification of these oxidation events in plastids revealed that several enzymes of the amino acid metabolism rapidly undergo cysteine oxidation upon oxidative stress.
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Affiliation(s)
- Barbara De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- VIB-VUB Center for Structural Biology, VIB, 1050, Brussels, Belgium
- Brussels Center for Redox Biology, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000, Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
| | - Alvaro D Fernandez-Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Joris Messens
- VIB-VUB Center for Structural Biology, VIB, 1050, Brussels, Belgium
- Brussels Center for Redox Biology, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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14
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Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1435934. [PMID: 30533169 PMCID: PMC6250043 DOI: 10.1155/2018/1435934] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Mitochondria are highly dynamic and regulated organelles that historically have been defined based on their crucial role in cell metabolism. However, they are implicated in a variety of other important functions, making mitochondrial dysfunction an important axis in several pathological contexts. Despite that conventional biochemical and molecular biology approaches have provided significant insight into mitochondrial functionality, innovative techniques that provide a global view of the mitochondrion are still necessary. Proteomics fulfils this need by enabling accurate, systems-wide quantitative analysis of protein abundance. More importantly, redox proteomics approaches offer unique opportunities to tackle oxidative stress, a phenomenon that is intimately linked to aging, cardiovascular disease, and cancer. In addition, cutting-edge proteomics approaches reveal how proteins exert their functions in complex interaction networks where even subtle alterations stemming from early pathological states can be monitored. Here, we describe the proteomics approaches that will help to deepen the role of mitochondria in health and disease by assessing not only changes to mitochondrial protein composition but also alterations to their redox state and how protein interaction networks regulate mitochondrial function and dynamics. This review is aimed at showing the reader how the application of proteomics approaches during the last 20 years has revealed crucial mitochondrial roles in the context of aging, neurodegenerative disorders, metabolic disease, and cancer.
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15
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Roos G, Miranda-Quintana RA, Martínez González M. How Biochemical Environments Fine-Tune a Redox Process: From Theoretical Models to Practical Applications. J Phys Chem B 2018; 122:8157-8165. [PMID: 30040409 DOI: 10.1021/acs.jpcb.8b04736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this study, we give a new physical insight into how enzymatic environments influence a redox process. This is particularly important in a biochemical context, in which oxidoreductase enzymes and low-molecular-weight cofactors create a microenvironment, fine-tuning their specific redox potential. We present a new theoretical model, quantitatively backed up by quantum chemically calculated data obtained for key biological sulfur-based model reactions involved in preserving the cellular redox homeostasis during oxidative stress. We show that environmental effects can be quantitatively predicted from the thermodynamic cycle linking ΔΔ G(OX/RED)ref-ligand values to the differential interaction energy ΔΔ Gint of the reduced and oxidized species with the environment. Our obtained data can be linked to hydrogen-bond patterns found in protein active sites. The thermodynamic model is further understood in the framework of molecular orbital theory. The key insight of this work is that the intrinsic properties of neither a redox couple nor the interacting environment (e.g., ligand) are enough by themselves to uniquely predict reduction potentials. Instead, system-environment interactions need to be considered. This study is of general interest as redox processes are pivotal to empower, protect, or damage organisms. Our presented thermodynamic model allows a pragmatically evaluation on the expected influence of a particular environment on a redox process, necessary to fully understand how redox processes take place in living organisms.
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Affiliation(s)
- Goedele Roos
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) , Université de Lille , 1 Sciences et Technologies 50 Avenue de Halley BP 70478, 59658 Villeneuve d'Ascq Cedex, France
| | | | - Marco Martínez González
- Laboratory of Computational and Theoretical Chemistry, Faculty of Chemistry , University of Havana , 10400 Havana , Cuba.,Departamento de Química, y Centro de Química , Universidade de Coimbra , 3004-535 Coimbra , Portugal
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16
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Foyer CH, Wilson MH, Wright MH. Redox regulation of cell proliferation: Bioinformatics and redox proteomics approaches to identify redox-sensitive cell cycle regulators. Free Radic Biol Med 2018; 122:137-149. [PMID: 29605447 PMCID: PMC6146653 DOI: 10.1016/j.freeradbiomed.2018.03.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/16/2018] [Accepted: 03/27/2018] [Indexed: 01/16/2023]
Abstract
Plant stem cells are the foundation of plant growth and development. The balance of quiescence and division is highly regulated, while ensuring that proliferating cells are protected from the adverse effects of environment fluctuations that may damage the genome. Redox regulation is important in both the activation of proliferation and arrest of the cell cycle upon perception of environmental stress. Within this context, reactive oxygen species serve as 'pro-life' signals with positive roles in the regulation of the cell cycle and survival. However, very little is known about the metabolic mechanisms and redox-sensitive proteins that influence cell cycle progression. We have identified cysteine residues on known cell cycle regulators in Arabidopsis that are potentially accessible, and could play a role in redox regulation, based on secondary structure and solvent accessibility likelihoods for each protein. We propose that redox regulation may function alongside other known posttranslational modifications to control the functions of core cell cycle regulators such as the retinoblastoma protein. Since our current understanding of how redox regulation is involved in cell cycle control is hindered by a lack of knowledge regarding both which residues are important and how modification of those residues alters protein function, we discuss how critical redox modifications can be mapped at the molecular level.
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Affiliation(s)
- Christine H Foyer
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Michael H Wilson
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Megan H Wright
- The Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
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17
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Wurzinger B, Mair A, Fischer-Schrader K, Nukarinen E, Roustan V, Weckwerth W, Teige M. Redox state-dependent modulation of plant SnRK1 kinase activity differs from AMPK regulation in animals. FEBS Lett 2017; 591:3625-3636. [PMID: 28940407 PMCID: PMC5698759 DOI: 10.1002/1873-3468.12852] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 01/30/2023]
Abstract
The evolutionarily highly conserved SNF1‐related protein kinase (SnRK1) protein kinase is a metabolic master regulator in plants, balancing the critical energy consumption between growth‐ and stress response‐related metabolic pathways. While the regulation of the mammalian [AMP‐activated protein kinase (AMPK)] and yeast (SNF1) orthologues of SnRK1 is well‐characterised, the regulation of SnRK1 kinase activity in plants is still an open question. Here we report that the activity and T‐loop phosphorylation of AKIN10, the kinase subunit of the SnRK1 complex, is regulated by the redox status. Although this regulation is dependent on a conserved cysteine residue, the underlying mechanism is different to the redox regulation of animal AMPK and has functional implications for the regulation of the kinase complex in plants under stress conditions.
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Affiliation(s)
- Bernhard Wurzinger
- Department of Ecogenomics and Systems Biology, University of Vienna, Austria
| | - Andrea Mair
- Department of Ecogenomics and Systems Biology, University of Vienna, Austria
| | - Katrin Fischer-Schrader
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Germany
| | - Ella Nukarinen
- Department of Ecogenomics and Systems Biology, University of Vienna, Austria
| | - Valentin Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Austria
| | - Markus Teige
- Department of Ecogenomics and Systems Biology, University of Vienna, Austria
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