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Graska J, Fidler J, Gietler M, Prabucka B, Nykiel M, Labudda M. Nitric Oxide in Plant Functioning: Metabolism, Signaling, and Responses to Infestation with Ecdysozoa Parasites. BIOLOGY 2023; 12:927. [PMID: 37508359 PMCID: PMC10376146 DOI: 10.3390/biology12070927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological processes in plants, including responses to biotic and abiotic stresses. Changes in endogenous NO concentration lead to activation/deactivation of NO signaling and NO-related processes. This paper presents the current state of knowledge on NO biosynthesis and scavenging pathways in plant cells and highlights the role of NO in post-translational modifications of proteins (S-nitrosylation, nitration, and phosphorylation) in plants under optimal and stressful environmental conditions. Particular attention was paid to the interactions of NO with other signaling molecules: reactive oxygen species, abscisic acid, auxins (e.g., indole-3-acetic acid), salicylic acid, and jasmonic acid. In addition, potential common patterns of NO-dependent defense responses against attack and feeding by parasitic and molting Ecdysozoa species such as nematodes, insects, and arachnids were characterized. Our review definitely highlights the need for further research on the involvement of NO in interactions between host plants and Ecdysozoa parasites, especially arachnids.
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Affiliation(s)
- Jakub Graska
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland; (J.F.); (M.G.); (B.P.); (M.N.)
| | | | | | | | | | - Mateusz Labudda
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland; (J.F.); (M.G.); (B.P.); (M.N.)
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Wu J, Gao T, Guo H, Zhao L, Lv S, Lv J, Yao R, Yu Y, Ma F. Application of molecular dynamics simulation for exploring the roles of plant biomolecules in promoting environmental health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161871. [PMID: 36708839 DOI: 10.1016/j.scitotenv.2023.161871] [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: 11/19/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Understanding the dynamic changes of plant biomolecules is vital for exploring their mechanisms in the environment. Molecular dynamics (MD) simulation has been widely used to study structural evolution and corresponding properties of plant biomolecules at the microscopic scale. Here, this review (i) outlines structural properties of plant biomolecules, and the crucial role of MD simulation in advancing studies of the biomolecules; (ii) describes the development of MD simulation in plant biomolecules, determinants of simulation, and analysis parameters; (iii) introduces the applications of MD simulation in plant biomolecules, including the response of the biomolecules to multiple stresses, their roles in corrosive environments, and their contributions in improving environmental health; (iv) reviews techniques integrated with MD simulation, such as molecular biology, quantum mechanics, molecular docking, and machine learning modeling, which bridge gaps in MD simulation. Finally, we make suggestions on determination of force field types, investigation of plant biomolecule mechanisms, and use of MD simulation in combination with other techniques. This review provides comprehensive summaries of the mechanisms of plant biomolecules in the environment revealed by MD simulation and validates it as an applicable tool for bridging gaps between macroscopic and microscopic behavior, providing insights into the wide application of MD simulation in plant biomolecules.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China.
| | - Tian Gao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Haijuan Guo
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Sidi Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Ruyi Yao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Yanyi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
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Yan J, Zhu J, Zhou J, Xing C, Song H, Wu K, Cai M. Using brefeldin A to disrupt cell wall polysaccharide components in rice and nitric oxide to modify cell wall structure to change aluminum tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:948212. [PMID: 35991413 PMCID: PMC9390061 DOI: 10.3389/fpls.2022.948212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
The components and structure of cell wall are closely correlated with aluminum (Al) toxicity and tolerance for plants. However, the cell wall assembly and function construction in response to Al is not known. Brefeldin A (BFA), a macrolide, is used to disrupt cell wall polysaccharide components, and nitric oxide (NO), a signal molecule, is used to modify the cell wall structure. Pretreatment with BFA accelerated Al accumulation in root tips and Al-induced inhibition of root growth of two rice genotypes of Nipponbare and Zhefu 802, and significantly decreased the cell wall polysaccharide content including pectin, hemicellulose 1, and hemicellulose 2, indicating that BFA inhibits the biosynthesis of components in the cell wall and makes the root cell wall lose the ability to resist Al. The addition of NO donor (SNP) significantly alleviated the toxic effects of Al on root growth, Al accumulation, and oxidative damage, and decreased the content of pectin polysaccharide and functional groups of hydroxyl, carboxyl, and amino in the cell wall via FTIR analysis, while had no significant effect on hemicellulose 1 and hemicellulose 2 content compared with Al treatment. Furthermore, NO didn't change the inhibition effect of BFA-induced cell wall polysaccharide biosynthesis and root growth. Taken together, BFA disrupts the integrity of cell wall and NO modifies partial cell wall composition and their functional groups, which change the Al tolerance in rice.
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Affiliation(s)
- Jianchao Yan
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, China
| | - Jiandong Zhu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, China
| | - Jun Zhou
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, China
| | - Chenghua Xing
- College of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Hongming Song
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, China
| | - Kun Wu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, China
| | - Miaozhen Cai
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, China
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van Wijk KJ, Leppert T, Sun Q, Boguraev SS, Sun Z, Mendoza L, Deutsch EW. The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. THE PLANT CELL 2021; 33:3421-3453. [PMID: 34411258 PMCID: PMC8566204 DOI: 10.1093/plcell/koab211] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/13/2021] [Indexed: 05/02/2023]
Abstract
We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA
- Authors for correspondence: (K.J.V.W.), (E.W.D.)
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, USA
| | - Sascha S Boguraev
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
- Authors for correspondence: (K.J.V.W.), (E.W.D.)
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Dvořák P, Krasylenko Y, Zeiner A, Šamaj J, Takáč T. Signaling Toward Reactive Oxygen Species-Scavenging Enzymes in Plants. FRONTIERS IN PLANT SCIENCE 2021; 11:618835. [PMID: 33597960 PMCID: PMC7882706 DOI: 10.3389/fpls.2020.618835] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/11/2020] [Indexed: 05/26/2023]
Abstract
Reactive oxygen species (ROS) are signaling molecules essential for plant responses to abiotic and biotic stimuli as well as for multiple developmental processes. They are produced as byproducts of aerobic metabolism and are affected by adverse environmental conditions. The ROS content is controlled on the side of their production but also by scavenging machinery. Antioxidant enzymes represent a major ROS-scavenging force and are crucial for stress tolerance in plants. Enzymatic antioxidant defense occurs as a series of redox reactions for ROS elimination. Therefore, the deregulation of the antioxidant machinery may lead to the overaccumulation of ROS in plants, with negative consequences both in terms of plant development and resistance to environmental challenges. The transcriptional activation of antioxidant enzymes accompanies the long-term exposure of plants to unfavorable environmental conditions. Fast ROS production requires the immediate mobilization of the antioxidant defense system, which may occur via retrograde signaling, redox-based modifications, and the phosphorylation of ROS detoxifying enzymes. This review aimed to summarize the current knowledge on signaling processes regulating the enzymatic antioxidant capacity of plants.
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Lorenzen I, Eble JA, Hanschmann EM. Thiol switches in membrane proteins - Extracellular redox regulation in cell biology. Biol Chem 2020; 402:253-269. [PMID: 33108336 DOI: 10.1515/hsz-2020-0266] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022]
Abstract
Redox-mediated signal transduction depends on the enzymatic production of second messengers such as hydrogen peroxide, nitric oxide and hydrogen sulfite, as well as specific, reversible redox modifications of cysteine-residues in proteins. So-called thiol switches induce for instance conformational changes in specific proteins that regulate cellular pathways e.g., cell metabolism, proliferation, migration, gene expression and inflammation. Reduction, oxidation and disulfide isomerization are controlled by oxidoreductases of the thioredoxin family, including thioredoxins, glutaredoxins, peroxiredoxins and protein dsisulfide isomerases. These proteins are located in different cellular compartments, interact with substrates and catalyze specific reactions. Interestingly, some of these proteins are released by cells. Their extracellular functions and generally extracellular redox control have been widely underestimated. Here, we give an insight into extracellular redox signaling, extracellular thiol switches and their regulation by secreted oxidoreductases and thiol-isomerases, a topic whose importance has been scarcely studied so far, likely due to methodological limitations. We focus on the secreted redox proteins and characterized thiol switches in the ectodomains of membrane proteins, such as integrins and the metalloprotease ADAM17, which are among the best-characterized proteins and discuss their underlying mechanisms and biological implications.
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Affiliation(s)
- Inken Lorenzen
- Centre of Biochemistry and Molecular Biology, Structural Biology, Christian-Albrecht University of Kiel, Am Botanischen Garten 1-9, D-24118Kiel, Germany
| | - Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, D-48149Münster, Germany
| | - Eva-Maria Hanschmann
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Life Science Center, Merowingerplatz 1a, D-40225Düsseldorf, Germany
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Jedelská T, Luhová L, Petřivalský M. Thioredoxins: Emerging Players in the Regulation of Protein S-Nitrosation in Plants. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1426. [PMID: 33114295 PMCID: PMC7690881 DOI: 10.3390/plants9111426] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/22/2020] [Accepted: 10/22/2020] [Indexed: 02/01/2023]
Abstract
S-nitrosation has been recognized as an important mechanism of ubiquitous posttranslational modification of proteins on the basis of the attachment of the nitroso group to cysteine thiols. Reversible S-nitrosation, similarly to other redox-based modifications of protein thiols, has a profound effect on protein structure and activity and is considered as a convergence of signaling pathways of reactive nitrogen and oxygen species. This review summarizes the current knowledge on the emerging role of the thioredoxin-thioredoxin reductase (TRXR-TRX) system in protein denitrosation. Important advances have been recently achieved on plant thioredoxins (TRXs) and their properties, regulation, and functions in the control of protein S-nitrosation in plant root development, translation of photosynthetic light harvesting proteins, and immune responses. Future studies of plants with down- and upregulated TRXs together with the application of genomics and proteomics approaches will contribute to obtain new insights into plant S-nitrosothiol metabolism and its regulation.
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Affiliation(s)
| | | | - Marek Petřivalský
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic; (T.J.); (L.L.)
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O'Leary B, Plaxton WC. Multifaceted functions of post-translational enzyme modifications in the control of plant glycolysis. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:28-37. [PMID: 32200227 DOI: 10.1016/j.pbi.2020.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/24/2020] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Glycolysis is a central feature of metabolism and its regulation plays important roles during plant developmental and stress responses. Recent advances in proteomics and mass spectrometry have documented extensive and dynamic post-translational modifications (PTMs) of most glycolytic enzymes in diverse plant tissues. Protein PTMs represent fundamental regulatory events that integrate signalling and gene expression with cellular metabolic networks, and can regulate glycolytic enzyme activity, localization, protein:protein interactions, moonlighting functions, and turnover. Serine/threonine phosphorylation and redox PTMs of cysteine thiol groups appear to be the most prevalent forms of reversible covalent modification involved in plant glycolytic control. Additional PTMs including monoubiquitination also have important functions. However, the molecular functions and mechanisms of most glycolytic enzyme PTMs remain unknown, and represent important objectives for future studies.
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Affiliation(s)
- Brendan O'Leary
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Australia
| | - William C Plaxton
- Department of Biology, Queen's University, Kingston, Ontario K7L3N6, Canada.
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Freire JEC, Moreno FBMB, Monteiro-Júnior JE, Sousa AJS, Vasconcelos IM, Oliveira JTA, Monteiro-Moreira ACO, Rocha BAM, Grangeiro TB. Mo-CBP 3, a 2S albumin from Moringa oleifera, is a complex mixture of isoforms that arise from different post-translational modifications. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 140:68-77. [PMID: 31085448 DOI: 10.1016/j.plaphy.2019.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Mo-CBP3 is a chitin-binding 2S albumin from Moringa oleifera. This seed storage protein is resistant to thermal denaturation and shows biological activities that might be of practical use, such as antifungal properties against Candida sp., a pathogen that causes candidiasis, and against Fusarium solani, a soil fungus that can cause diseases in plants and humans. Previous work has demonstrated that Mo-CBP3 is a mixture of isoforms encoded by members of a small multigene family. Mature Mo-CBP3 is a small protein (∼14 kDa), constituted by a small chain of approximately 4 kDa and a large chain of 8 kDa, which are held together by disulfide bridges. However, a more comprehensive picture on the spectrum of Mo-CBP3 isoforms which are found in mature seeds, is still lacking. In this work, genomic DNA fragments were obtained from M. oleifera leaves, cloned and completely sequenced, thus revealing new genes encoding Mo-CBP3. Moreover, mass spectrometry analysis showed that the mature protein is a complex mixture of isoforms with a remarkable number of molecular mass variants. Using computational predictions and calculations, most (∼86%) of the experimentally determined masses were assigned to amino acid sequences deduced from DNA fragments. The results suggested that the complex mixture of Mo-CBP3 isoforms originates from proteins encoded by closely related genes, whose products undergo different combinations of distinct post-translational modifications, including cleavage at the N- and C-terminal ends of both subunits, cyclization of N-terminal Gln, as well as Pro hydroxylation, Ser/Thr phosphorylation, and Met oxidation.
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Affiliation(s)
- José E C Freire
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, Brazil
| | - Frederico B M B Moreno
- Núcleo de Biologia Experimental, Centro de Ciências da Saúde, Universidade de Fortaleza, Fortaleza, CE, 60810-431, Brazil
| | | | - Antônio J S Sousa
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, Brazil
| | - Ilka M Vasconcelos
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, Brazil
| | - José T A Oliveira
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, Brazil
| | - Ana C O Monteiro-Moreira
- Núcleo de Biologia Experimental, Centro de Ciências da Saúde, Universidade de Fortaleza, Fortaleza, CE, 60810-431, Brazil
| | - Bruno A M Rocha
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, Brazil
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