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Fuchs H, Staszak AM, Vargas PA, Sahrawy M, Serrato AJ, Dyderski MK, Klupczyńska EA, Głodowicz P, Rolle K, Ratajczak E. Redox dynamics in seeds of Acer spp: unraveling adaptation strategies of different seed categories. FRONTIERS IN PLANT SCIENCE 2024; 15:1430695. [PMID: 39114470 PMCID: PMC11303208 DOI: 10.3389/fpls.2024.1430695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024]
Abstract
Background Seeds of woody plant species, such as those in the Acer genus like Norway maple (Acer platanoides L.) and sycamore (Acer pseudoplatanus L.), exhibit unique physiological traits and responses to environmental stress. Thioredoxins (Trxs) play a central role in the redox regulation of cells, interacting with other redox-active proteins such as peroxiredoxins (Prxs), and contributing to plant growth, development, and responses to biotic and abiotic stresses. However, there is limited understanding of potential variations in this system between seeds categorized as recalcitrant and orthodox, which could provide insights into adaptive strategies. Methods Using proteomic analysis and DDA methods we investigated the Trx-h1 target proteins in seed axes. We complemented the results of the proteomic analysis with gene expression analysis of the Trx-h1, 1-Cys-Prx, and TrxR NTRA genes in the embryonic axes of maturing, mature, and stored seeds from two Acer species. Results and discussion The expression of Trx-h1 and TrxR NTRA throughout seed maturation in both species was low. The expression of 1-Cys-Prx remained relatively stable throughout seed maturation. In stored seeds, the expression levels were minimal, with slightly higher levels in sycamore seeds, which may confirm that recalcitrant seeds remain metabolically active during storage. A library of 289 proteins interacting with Trx-h1 was constructed, comprising 68 from Norway maple and 221 from sycamore, with distinct profiles in each seed category. Recalcitrant seed axes displayed a wide array of metabolic, stress response, and signaling proteins, suggesting sustained metabolic activity during storage and the need to address oxidative stress. Conversely, the orthodox seed axes presented a protein profile, reflecting efficient metabolic shutdown, which contributes to their extended viability. The results of the study provide new insights into seed viability and storage longevity mechanisms. They enhance the understanding of seed biology and lay the foundation for further evolutionary research on seeds of different categories.
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Affiliation(s)
- Hanna Fuchs
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - Aleksandra M. Staszak
- Laboratory of Plant Physiology, Department of Plant Biology and Ecology Faculty of Biology, University of Białystok, Białystok, Poland
| | - Paola A. Vargas
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Mariam Sahrawy
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio J. Serrato
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | | | - Paweł Głodowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Katarzyna Rolle
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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Sougrakpam Y, Babuta P, Deswal R. Nitric oxide (NO) modulates low temperature-stress signaling via S-nitrosation, a NO PTM, inducing ethylene biosynthesis inhibition leading to enhanced post-harvest shelf-life of agricultural produce. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:2051-2065. [PMID: 38222283 PMCID: PMC10784255 DOI: 10.1007/s12298-023-01371-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 01/16/2024]
Abstract
Low temperature (cold) stress is one of the major abiotic stress conditions affecting crop productivity worldwide. Nitric oxide (NO) is a dynamic signaling molecule that interacts with various stress regulators and provides abiotic stress tolerance. Stress enhanced NO contributes to S-nitrosothiol accumulation which causes oxidation of the -SH group in proteins leading to S-nitrosation, a post-translational modification. Cold stress induced in vivo S-nitrosation of > 240 proteins majorly belonging to stress/signaling/redox (myrosinase, SOD, GST, CS, DHAR), photosynthesis (RuBisCO, PRK), metabolism (FBA, GAPDH, TPI, SBPase), and cell wall modification (Beta-xylosidases, alpha-l-arabinogalactan) in different crop plants indicated role of NO in these important cellular and metabolic pathways. NO mediated regulation of a transcription factor CBF (C-repeat Binding Factor, a transcription factor) at transcriptional and post-translational level was shown in Solanum lycopersicum seedlings. NO donor priming enhances seed germination, breaks dormancy and provides tolerance to stress in crops. Its role in averting stress, promoting seed germination, and delaying senescence paved the way for use of NO and NO releasing compounds to prevent crop loss and increase the shelf-life of fruits and vegetables. An alternative to energy consuming and expensive cold storage led to development of a storage device called "shelf-life enhancer" that delays senescence and increases shelf-life at ambient temperature (25-27 °C) using NO donor. The present review summarizes NO research in plants and exploration of NO for its translational potential to improve agricultural yield and post-harvest crop loss. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01371-z.
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Affiliation(s)
- Yaiphabi Sougrakpam
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, Delhi 110007 India
| | - Priyanka Babuta
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, Delhi 110007 India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, Delhi 110007 India
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Melicher P, Dvořák P, Šamaj J, Takáč T. Protein-protein interactions in plant antioxidant defense. FRONTIERS IN PLANT SCIENCE 2022; 13:1035573. [PMID: 36589041 PMCID: PMC9795235 DOI: 10.3389/fpls.2022.1035573] [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: 09/02/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The regulation of reactive oxygen species (ROS) levels in plants is ensured by mechanisms preventing their over accumulation, and by diverse antioxidants, including enzymes and nonenzymatic compounds. These are affected by redox conditions, posttranslational modifications, transcriptional and posttranscriptional modifications, Ca2+, nitric oxide (NO) and mitogen-activated protein kinase signaling pathways. Recent knowledge about protein-protein interactions (PPIs) of antioxidant enzymes advanced during last decade. The best-known examples are interactions mediated by redox buffering proteins such as thioredoxins and glutaredoxins. This review summarizes interactions of major antioxidant enzymes with regulatory and signaling proteins and their diverse functions. Such interactions are important for stability, degradation and activation of interacting partners. Moreover, PPIs of antioxidant enzymes may connect diverse metabolic processes with ROS scavenging. Proteins like receptor for activated C kinase 1 may ensure coordination of antioxidant enzymes to ensure efficient ROS regulation. Nevertheless, PPIs in antioxidant defense are understudied, and intensive research is required to define their role in complex regulation of ROS scavenging.
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Holušová K, Čmejlová J, Suran P, Čmejla R, Sedlák J, Zelený L, Bartoš J. High-resolution genome-wide association study of a large Czech collection of sweet cherry ( Prunus avium L.) on fruit maturity and quality traits. HORTICULTURE RESEARCH 2022; 10:uhac233. [PMID: 36643756 PMCID: PMC9832837 DOI: 10.1093/hr/uhac233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/10/2022] [Indexed: 06/17/2023]
Abstract
In sweet cherry (Prunus avium L.), quantitative trait loci have been identified for fruit maturity, colour, firmness, and size to develop markers for marker-assisted selection. However, resolution is usually too low in those analyses to directly target candidate genes, and some associations are missed. In contrast, genome-wide association studies are performed on broad collections of accessions, and assemblies of reference sequences from Tieton and Satonishiki cultivars enable identification of single nucleotide polymorphisms after whole-genome sequencing, providing high marker density. Two hundred and thirty-five sweet cherry accessions were sequenced and phenotyped for harvest time and fruit colour, firmness, and size. Genome-wide association studies were used to identify single nucleotide polymorphisms associated with each trait, which were verified in breeding material consisting of 64 additional accessions. A total of 1 767 106 single nucleotide polymorphisms were identified. At that density, significant single nucleotide polymorphisms could be linked to co-inherited haplotype blocks (median size ~10 kb). Thus, markers were tightly associated with respective phenotypes, and individual allelic combinations of particular single nucleotide polymorphisms provided links to distinct phenotypes. In addition, yellow-fruit accessions were sequenced, and a ~ 90-kb-deletion on chromosome 3 that included five MYB10 transcription factors was associated with the phenotype. Overall, the study confirmed numerous quantitative trait loci from bi-parental populations using high-diversity accession populations, identified novel associations, and genome-wide association studies reduced the size of trait-associated loci from megabases to kilobases and to a few candidate genes per locus. Thus, a framework is provided to develop molecular markers and evaluate and characterize genes underlying important agronomic traits.
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Affiliation(s)
- Kateřina Holušová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 779 00, Czech Republic
| | - Jana Čmejlová
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
| | - Pavol Suran
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
| | - Radek Čmejla
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
| | - Jiří Sedlák
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
| | - Lubor Zelený
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
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Gomez Barroso JA, Miranda MR, Pereira CA, Garratt RC, Aguilar CF. X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure. Acta Crystallogr D Struct Biol 2022; 78:30-42. [PMID: 34981759 DOI: 10.1107/s2059798321011219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
Trypanosoma cruzi is a flagellated protozoan parasite that causes Chagas disease, which represents a serious health problem in the Americas. Nucleoside diphosphate kinases (NDPKs) are key enzymes that are implicated in cellular energy management. TcNDPK1 is the canonical isoform in the T. cruzi parasite. TcNDPK1 has a cytosolic, perinuclear and nuclear distribution. It is also found in non-membrane-bound filaments adjacent to the nucleus. In the present work, X-ray diffraction and in vivo studies of TcNDPK1 are described. The structure reveals a novel, multi-hexameric, left-handed helical oligomer structure. The results of directed mutagenesis studies led to the conclusion that the microscopic TcNDPK1 granules observed in vivo in T. cruzi parasites are made up by the association of TcNDPK1 oligomers. In the absence of experimental data, analysis of the interactions in the X-ray structure of the TcNDPK1 oligomer suggests the probable assembly and disassembly steps: dimerization, assembly of the hexamer as a trimer of dimers, hexamer association to generate the left-handed helical oligomer structure and finally oligomer association in a parallel manner to form the microscopic TcNDPK1 filaments that are observed in vivo in T. cruzi parasites. Oligomer disassembly takes place on the binding of substrate in the active site of TcNDPK1, leading to dissociation of the hexamers. This study constitutes the first report of such a protein arrangement, which has never previously been seen for any protein or NDPK. Further studies are needed to determine its physiological role. However, it may suggest a paradigm for protein storage reflecting the complex mechanism of action of TcNDPK1.
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Affiliation(s)
- Juan Arturo Gomez Barroso
- Laboratorio de Biología Molecular Estructural, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Mariana Reneé Miranda
- Laboratorio de Parasitología Molecular, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Claudio Alejandro Pereira
- Laboratorio de Parasitología Molecular, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Richard Charles Garratt
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense No. 400, São Carlos, São Paulo 13566-590, Brazil
| | - Carlos Fernando Aguilar
- Laboratorio de Biología Molecular Estructural, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina
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Woyda-Ploszczyca AM, Rybak AS. How can the commercial potential of microalgae from the Dunaliella genus be improved? The importance of nucleotide metabolism with a focus on nucleoside diphosphate kinase (NDPK). ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Liang W, Chen Y, Li X, Guo F, Sun J, Zhang X, Xu B, Gao W. Label-Free Proteomic Analysis of Smoke-Drying and Shade-Drying Processes of Postharvest Rhubarb: A Comparative Study. FRONTIERS IN PLANT SCIENCE 2021; 12:663180. [PMID: 34140961 PMCID: PMC8205111 DOI: 10.3389/fpls.2021.663180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Postharvest processing plays a very important role in improving the quality of traditional Chinese medicine. According to previous studies, smoke-drying could significantly promote the accumulation of the bioactive components and pharmacological activities of rhubarb, but so far, the molecular mechanism has not been studied yet. In this research, to study the molecular mechanisms of postharvest processing for rhubarb during shade-drying and smoke-drying, label-free proteomic analyses were conducted. In total, 1,927 differentially abundant proteins (DAPs) were identified from rhubarb samples treated by different drying methods. These DAPs were mainly involved in response and defense, signal transduction, starch, carbohydrate and energy metabolism, and anthraquinone and phenolic acid biosynthesis. Smoke-drying significantly enhanced the expression of proteins involved in these metabolic pathways. Accordingly, the molecular mechanism of the accumulation of effective ingredients of rhubarb was clarified, which provided a novel insight into the biosynthesis of active ingredients that occur during the rhubarb dry process.
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Affiliation(s)
- Wei Liang
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Chen
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xia Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Fengxia Guo
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiachen Sun
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Xuemin Zhang
- Key Laboratory of Modern Chinese Medicine Resources Research Enterprises, Tianjin, China
| | - Bo Xu
- Key Laboratory of Modern Chinese Medicine Resources Research Enterprises, Tianjin, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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Structure, Folding and Stability of Nucleoside Diphosphate Kinases. Int J Mol Sci 2020; 21:ijms21186779. [PMID: 32947863 PMCID: PMC7554756 DOI: 10.3390/ijms21186779] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/29/2022] Open
Abstract
Nucleoside diphosphate kinases (NDPK) are oligomeric proteins involved in the synthesis of nucleoside triphosphates. Their tridimensional structure has been solved by X-ray crystallography and shows that individual subunits present a conserved ferredoxin fold of about 140 residues in prokaryotes, archaea, eukaryotes and viruses. Monomers are functionally independent from each other inside NDPK complexes and the nucleoside kinase catalytic mechanism involves transient phosphorylation of the conserved catalytic histidine. To be active, monomers must assemble into conserved head to tail dimers, which further assemble into hexamers or tetramers. The interfaces between these oligomeric states are very different but, surprisingly, the assembly structure barely affects the catalytic efficiency of the enzyme. While it has been shown that assembly into hexamers induces full formation of the catalytic site and stabilizes the complex, it is unclear why assembly into tetramers is required for function. Several additional activities have been revealed for NDPK, especially in metastasis spreading, cytoskeleton dynamics, DNA binding and membrane remodeling. However, we still lack the high resolution structural data of NDPK in complex with different partners, which is necessary for deciphering the mechanism of these diverse functions. In this review we discuss advances in the structure, folding and stability of NDPKs.
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Igamberdiev AU. Citrate valve integrates mitochondria into photosynthetic metabolism. Mitochondrion 2020; 52:218-230. [PMID: 32278088 DOI: 10.1016/j.mito.2020.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/21/2020] [Accepted: 04/07/2020] [Indexed: 12/31/2022]
Abstract
While in heterotrophic cells and in darkness mitochondria serve as main producers of energy, during photosynthesis this function is transferred to chloroplasts and the main role of mitochondria in bioenergetics turns to be the balance of the level of phosphorylation of adenylates and of reduction of pyridine nucleotides to avoid over-energization of the cell and optimize major metabolic fluxes. This is achieved via the establishment and regulation of local equilibria of the tricarboxylic acid (TCA) cycle enzymes malate dehydrogenase and fumarase in one branch and aconitase and isocitrate dehydrogenase in another branch. In the conditions of elevation of redox level, the TCA cycle is transformed into a non-cyclic open structure (hemicycle) leading to the export of the tricarboxylic acid (citrate) to the cytosol and to the accumulation of the dicarboxylic acids (malate and fumarate). While the buildup of NADPH in chloroplasts provides operation of the malate valve leading to establishment of NADH/NAD+ ratios in different cell compartments, the production of NADH by mitochondria drives citrate export by establishing conditions for the operation of the citrate valve. The latter regulates the intercompartmental NADPH/NADP+ ratio and contributes to the biosynthesis of amino acids and other metabolic products during photosynthesis.
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Affiliation(s)
- Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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Kapoor I, Varshney U. Diverse roles of nucleoside diphosphate kinase in genome stability and growth fitness. Curr Genet 2020; 66:671-682. [PMID: 32249353 DOI: 10.1007/s00294-020-01073-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Nucleoside diphosphate kinase (NDK), a ubiquitous enzyme, catalyses reversible transfer of the γ phosphate from nucleoside triphosphates to nucleoside diphosphates and functions to maintain the pools of ribonucleotides and deoxyribonucleotides in the cell. As even a minor imbalance in the nucleotide pools can be mutagenic, NDK plays an antimutator role in maintaining genome integrity. However, the mechanism of the antimutator roles of NDK is not completely understood. In addition, NDKs play important roles in the host-pathogen interactions, metastasis, gene regulation, and various cellular metabolic processes. To add to these diverse roles of NDK in cells, a recent study now reveals that NDK may even confer mutator phenotypes to the cell by acting on the damaged deoxyribonucleoside diphosphates that may be formed during the oxidative stress. In this review, we discuss the roles of NDK in homeostasis of the nucleotide pools and genome integrity, and its possible implications in conferring growth/survival fitness to the organisms in the changing environmental niches.
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Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India. .,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
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Witte CP, Herde M. Nucleotide Metabolism in Plants. PLANT PHYSIOLOGY 2020; 182:63-78. [PMID: 31641078 PMCID: PMC6945853 DOI: 10.1104/pp.19.00955] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/15/2019] [Indexed: 05/14/2023]
Abstract
Nucleotide metabolism is an essential function in plants.
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Affiliation(s)
- Claus-Peter Witte
- Leibniz Universität Hannover, Department of Molecular Nutrition and Biochemistry of Plants, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Marco Herde
- Leibniz Universität Hannover, Department of Molecular Nutrition and Biochemistry of Plants, Herrenhäuser Strasse 2, 30419 Hannover, Germany
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