1
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Ľuptáková E, Vigouroux A, Končitíková R, Kopečná M, Zalabák D, Novák O, Salcedo Sarmiento S, Ćavar Zeljković S, Kopečný DJ, von Schwartzenberg K, Strnad M, Spíchal L, De Diego N, Kopečný D, Moréra S. Plant nucleoside N-ribohydrolases: riboside binding and role in nitrogen storage mobilization. Plant J 2024; 117:1432-1452. [PMID: 38044809 DOI: 10.1111/tpj.16572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Cells save their energy during nitrogen starvation by selective autophagy of ribosomes and degradation of RNA to ribonucleotides and nucleosides. Nucleosides are hydrolyzed by nucleoside N-ribohydrolases (nucleosidases, NRHs). Subclass I of NRHs preferentially hydrolyzes the purine ribosides while subclass II is more active towards uridine and xanthosine. Here, we performed a crystallographic and kinetic study to shed light on nucleoside preferences among plant NRHs followed by in vivo metabolomic and phenotyping analyses to reveal the consequences of enhanced nucleoside breakdown. We report the crystal structure of Zea mays NRH2b (subclass II) and NRH3 (subclass I) in complexes with the substrate analog forodesine. Purine and pyrimidine catabolism are inseparable because nucleobase binding in the active site of ZmNRH is mediated via a water network and is thus unspecific. Dexamethasone-inducible ZmNRH overexpressor lines of Arabidopsis thaliana, as well as double nrh knockout lines of moss Physcomitrium patents, reveal a fine control of adenosine in contrast to other ribosides. ZmNRH overexpressor lines display an accelerated early vegetative phase including faster root and rosette growth upon nitrogen starvation or osmotic stress. Moreover, the lines enter the bolting and flowering phase much earlier. We observe changes in the pathways related to nitrogen-containing compounds such as β-alanine and several polyamines, which allow plants to reprogram their metabolism to escape stress. Taken together, crop plant breeding targeting enhanced NRH-mediated nitrogen recycling could therefore be a strategy to enhance plant growth tolerance and productivity under adverse growth conditions.
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Affiliation(s)
- Eva Ľuptáková
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Armelle Vigouroux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, F-91198, France
| | - Radka Končitíková
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Martina Kopečná
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - David Zalabák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 11, Olomouc, CZ-78371, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 11, Olomouc, CZ-78371, Czech Republic
| | - Sara Salcedo Sarmiento
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Sanja Ćavar Zeljković
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, 78371, Olomouc, Czech Republic
| | - David Jaroslav Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Klaus von Schwartzenberg
- Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 11, Olomouc, CZ-78371, Czech Republic
| | - Lukáš Spíchal
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Nuria De Diego
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Solange Moréra
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, F-91198, France
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Brunoni F, Pěnčík A, Žukauskaitė A, Ament A, Kopečná M, Collani S, Kopečný D, Novák O. Amino acid conjugation of oxIAA is a secondary metabolic regulation involved in auxin homeostasis. New Phytol 2023; 238:2264-2270. [PMID: 36941219 DOI: 10.1111/nph.18887] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 03/11/2023] [Indexed: 05/19/2023]
Affiliation(s)
- Federica Brunoni
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Asta Žukauskaitė
- Department of Chemical Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Anita Ament
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Martina Kopečná
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Silvio Collani
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, SE-90736, Sweden
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, Olomouc, CZ-78371, Czech Republic
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3
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Ondrová K, Zůvalová I, Vyhlídalová B, Krasulová K, Miková E, Vrzal R, Nádvorník P, Nepal B, Kortagere S, Kopečná M, Kopečný D, Šebela M, Rastinejad F, Pu H, Soural M, Rolfes KM, Haarmann-Stemmann T, Li H, Mani S, Dvořák Z. Monoterpenoid aryl hydrocarbon receptor allosteric antagonists protect against ultraviolet skin damage in female mice. Nat Commun 2023; 14:2728. [PMID: 37169746 PMCID: PMC10174618 DOI: 10.1038/s41467-023-38478-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
The human aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that is a pivotal regulator of human physiology and pathophysiology. Allosteric inhibition of AhR was previously thought to be untenable. Here, we identify carvones as noncompetitive, insurmountable antagonists of AhR and characterize the structural and functional consequences of their binding. Carvones do not displace radiolabeled ligands from binding to AhR but instead bind allosterically within the bHLH/PAS-A region of AhR. Carvones do not influence the translocation of ligand-activated AhR into the nucleus but inhibit the heterodimerization of AhR with its canonical partner ARNT and subsequent binding of AhR to the promoter of CYP1A1. As a proof of concept, we demonstrate physiologically relevant Ahr-antagonism by carvones in vivo in female mice. These substances establish the molecular basis for selective targeting of AhR regardless of the type of ligand(s) present and provide opportunities for the treatment of disease processes modified by AhR.
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Affiliation(s)
- Karolína Ondrová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Iveta Zůvalová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Barbora Vyhlídalová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Kristýna Krasulová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Eva Miková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Radim Vrzal
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Petr Nádvorník
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Binod Nepal
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Sandhya Kortagere
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Martina Kopečná
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Marek Šebela
- Department of Biochemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Fraydoon Rastinejad
- Target Discovery Institute Nuffield Department of Medicine Research Building Brasenose College University of Oxford, Oxford, UK
| | - Hua Pu
- Target Discovery Institute Nuffield Department of Medicine Research Building Brasenose College University of Oxford, Oxford, UK
| | - Miroslav Soural
- Department of Organic Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | | | | | - Hao Li
- Department of Medicine, Oncology, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sridhar Mani
- Department of Medicine, Oncology, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Zdeněk Dvořák
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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4
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Bělíček J, Ľuptáková E, Kopečný D, Frömmel J, Vigouroux A, Ćavar Zeljković S, Jagic F, Briozzo P, Kopečný DJ, Tarkowski P, Nisler J, De Diego N, Moréra S, Kopečná M. Biochemical and structural basis of polyamine, lysine and ornithine acetylation catalyzed by spermine/spermidine N-acetyl transferase in moss and maize. Plant J 2023; 114:482-498. [PMID: 36786691 DOI: 10.1111/tpj.16148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/08/2023] [Indexed: 05/10/2023]
Abstract
Polyamines such as spermidine and spermine are essential regulators of cell growth, differentiation, maintenance of ion balance and abiotic stress tolerance. Their levels are controlled by the spermidine/spermine N1 -acetyltransferase (SSAT) via acetylation to promote either their degradation or export outside the cell as shown in mammals. Plant genomes contain at least one gene coding for SSAT (also named NATA for N-AcetylTransferase Activity). Combining kinetics, HPLC-MS and crystallography, we show that three plant SSATs, one from the lower plant moss Physcomitrium patens and two from the higher plant Zea mays, acetylate various aliphatic polyamines and two amino acids lysine (Lys) and ornithine (Orn). Thus, plant SSATs exhibit a broad substrate specificity, unlike more specific human SSATs (hSSATs) as hSSAT1 targets polyamines, whereas hSSAT2 acetylates Lys and thiaLys. The crystal structures of two PpSSAT ternary complexes, one with Lys and CoA, the other with acetyl-CoA and polyethylene glycol (mimicking spermine), reveal a different binding mode for polyamine versus amino acid substrates accompanied by structural rearrangements of both the coenzyme and the enzyme. Two arginine residues, unique among plant SSATs, hold the carboxyl group of amino acid substrates. The most abundant acetylated compound accumulated in moss was N6 -acetyl-Lys, whereas N5 -acetyl-Orn, known to be toxic for aphids, was found in maize. Both plant species contain very low levels of acetylated polyamines. The present study provides a detailed biochemical and structural basis of plant SSAT enzymes that can acetylate a wide range of substrates and likely play various roles in planta.
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Affiliation(s)
- Jakub Bělíček
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic
| | - Eva Ľuptáková
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic
| | - Jan Frömmel
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Armelle Vigouroux
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), F-91198, Gif-sur-Yvette, France
| | - Sanja Ćavar Zeljković
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Šlechtitelů 29, CZ-78371, Olomouc, Czech Republic
| | - Franjo Jagic
- INRAE, AgroParisTech, Université Paris-Saclay, Institut Jean-Pierre Bourgin (IJPB), Route de Saint Cyr, F-78026, Versailles, France
| | - Pierre Briozzo
- INRAE, AgroParisTech, Université Paris-Saclay, Institut Jean-Pierre Bourgin (IJPB), Route de Saint Cyr, F-78026, Versailles, France
| | - David Jaroslav Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic
| | - Petr Tarkowski
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Šlechtitelů 29, CZ-78371, Olomouc, Czech Republic
| | - Jaroslav Nisler
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
- Isotope Laboratory, Institute of Experimental Botany, The Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague, Czech Republic
| | - Nuria De Diego
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Solange Moréra
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), F-91198, Gif-sur-Yvette, France
| | - Martina Kopečná
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic
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5
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Nisler J, Kopečný D, Pěkná Z, Končitíková R, Koprna R, Murvanidze N, Werbrouck SPO, Havlíček L, De Diego N, Kopečná M, Wimmer Z, Briozzo P, Moréra S, Zalabák D, Spíchal L, Strnad M. Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture. J Exp Bot 2021; 72:355-370. [PMID: 32945834 DOI: 10.1093/jxb/eraa437] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/17/2020] [Indexed: 05/11/2023]
Abstract
Increasing crop productivity is our major challenge if we are to meet global needs for food, fodder and fuel. Controlling the content of the plant hormone cytokinin is a method of improving plant productivity. Cytokinin oxidase/dehydrogenase (CKO/CKX) is a major target in this regard because it degrades cytokinins. Here, we describe the synthesis and biological activities of new CKX inhibitors derived mainly from diphenylurea. They were tested on four CKX isoforms from maize and Arabidopsis, where the best compounds showed IC50 values in the 10-8 M concentration range. The binding mode of the most efficient inhibitors was characterized from high-resolution crystal complexed structures. Although these compounds do not possess intrinsic cytokinin activity, we have demonstrated their tremendous potential for use in the plant tissue culture industry as well as in agriculture. We have identified a key substance, compound 19, which not only increases stress resistance and seed yield in Arabidopsis, but also improves the yield of wheat, barley and rapeseed grains under field conditions. Our findings reveal that modulation of cytokinin levels via CKX inhibition can positively affect plant growth, development and yield, and prove that CKX inhibitors can be an attractive target in plant biotechnology and agriculture.
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Affiliation(s)
- Jaroslav Nisler
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
- Department of Chemistry of Natural Compounds, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Technická 5, Prague, Czech Republic
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - Zuzana Pěkná
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - Radoslav Koprna
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - Nino Murvanidze
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Stefaan P O Werbrouck
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Libor Havlíček
- Isotope Laboratory, Institute of Experimental Botany, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Nuria De Diego
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - Martina Kopečná
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - Zdeněk Wimmer
- Department of Chemistry of Natural Compounds, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Technická 5, Prague, Czech Republic
- Isotope Laboratory, Institute of Experimental Botany, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Pierre Briozzo
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Route de Saint-Cyr, Versailles, France
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - David Zalabák
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - Lukáš Spíchal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 27, Olomouc, Czech Republic
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6
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Jacques F, Zhao Y, Kopečná M, Končitíková R, Kopečný D, Rippa S, Perrin Y. Roles for ALDH10 enzymes in γ-butyrobetaine synthesis, seed development, germination, and salt tolerance in Arabidopsis. J Exp Bot 2020; 71:7088-7102. [PMID: 32845293 DOI: 10.1093/jxb/eraa394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Plant genomes generally contain two aldehyde dehydrogenase 10 (ALDH10) genes, which encode NAD+-dependent enzymes. These oxidize various aminoaldehydes that are produced by the catabolism of amino acids and polyamines. ALDH10s are closely related to the animal and fungal trimethylaminobutyraldehyde dehydrogenases (TMABADHs) that are involved in the synthesis of γ-butyrobetaine, the precursor of carnitine. Here, we explore the ability of the Arabidopsis thaliana proteins AtALDH10A8 and AtALDH10A9 to oxidize aminoaldehydes. We demonstrate that these enzymes display high TMABADH activities in vitro. Moreover, they can complement the Candida albicans tmabadhΔ/Δ null mutant. These findings illustrate the link between AtALDH10A8 and AtALDH10A9 and γ-butyrobetaine synthesis. An analysis of single and double knockout Arabidopsis mutant lines revealed that the double mutants had reduced γ-butyrobetaine levels. However, there were no changes in the carnitine contents of these mutants. The double mutants were more sensitive to salt stress. In addition, the siliques of the double mutants had a significant proportion of seeds that failed to mature. The mature seeds contained higher amounts of triacylglycerol, facilitating accelerated germination. Taken together, these results show that ALDH10 enzymes are involved in γ-butyrobetaine synthesis. Furthermore, γ-butyrobetaine fulfils a range of physiological roles in addition to those related to carnitine biosynthesis.
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Affiliation(s)
- Florian Jacques
- Université de Technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de Recherche Royallieu - CS, Compiègne Cedex, France
| | - Yingjuan Zhao
- Université de Technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de Recherche Royallieu - CS, Compiègne Cedex, France
- Department of Applied Chemistry, School of Science, Xi'an University of Technology, Xi'an, China
| | - Martina Kopečná
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc CZ, Czech Republic
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc CZ, Czech Republic
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc CZ, Czech Republic
| | - Sonia Rippa
- Université de Technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de Recherche Royallieu - CS, Compiègne Cedex, France
| | - Yolande Perrin
- Université de Technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de Recherche Royallieu - CS, Compiègne Cedex, France
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7
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Magro M, Baratella D, Miotto G, Frömmel J, Šebela M, Kopečná M, Agostinelli E, Vianello F. Enzyme self-assembly on naked iron oxide nanoparticles for aminoaldehyde biosensing. Amino Acids 2019; 51:679-690. [PMID: 30725223 DOI: 10.1007/s00726-019-02704-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/16/2019] [Indexed: 11/28/2022]
Abstract
The preservation of enzymatic activity is a fundamental requirement for exploiting hybrid nano-bio-conjugates, and the control over protein-nanoparticle interactions, leading to stable and catalytically active hybrids, represents the key for designing new biosensing platforms. In this scenario, surface active maghemite nanoparticles (SAMNs) represent a new class of naked magnetic nanoparticles, displaying peculiar electrocatalytic features and the ability to selectively bind proteins. Recombinant aminoaldehyde dehydrogenase from tomato (SlAMADH1) was used as a model protein, and successfully immobilized by self-assembly on the surface of naked SAMNs, where its enzymatic activity resulted preserved for more than 6 months. The hybrid nanomaterial (SAMN@SlAMADH1) was characterized by UV-Vis spectroscopy, mass spectrometry, and TEM microscopy, and applied for the development of a biosensor for the determination of aminoaldehydes in alcoholic beverages. Measurements were carried out in a low volume electrochemical flow cell comprising a SAMN modified carbon paste electrode for the coulometric determination of the NADH produced during the enzymatic catalysis. The present findings, besides representing the first example of an electrochemical biosensor for aminoaldehydes in an alcoholic matrix, open the door to the use of immobilized enzymes on naked metal oxides nanomaterials for biosensing.
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Affiliation(s)
- Massimiliano Magro
- Department of Comparative Biomedicine and Food Science, University of Padua, Agripolis-Viale dell'Università 16, 35020, Legnaro, PD, Italy.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University in Olomouc, 17 Listopadu 12, 771 46, Olomouc, Czech Republic
| | - Davide Baratella
- Department of Comparative Biomedicine and Food Science, University of Padua, Agripolis-Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Giovanni Miotto
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121, Padua, Italy.,Proteomic Center of Padua University, VIMM and Padua University Hospital, Via G. Orus 2b, 35129, Padua, Italy
| | - Jan Frömmel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University in Olomouc, Šlechtitelu 11, 78371, Olomouc, Czech Republic
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University in Olomouc, Šlechtitelu 11, 78371, Olomouc, Czech Republic
| | - Martina Kopečná
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University in Olomouc, Šlechtitelu 11, 78371, Olomouc, Czech Republic
| | - Enzo Agostinelli
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome La Sapienza and CNR, Institute of Biology and Molecular Pathology, 00185, Rome, Italy.,International Polyamines Foundation-ONLUS, Via del Forte Tiburtino, 98, 00159, Rome, Italy
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padua, Agripolis-Viale dell'Università 16, 35020, Legnaro, PD, Italy. .,International Polyamines Foundation-ONLUS, Via del Forte Tiburtino, 98, 00159, Rome, Italy.
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8
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Kopečná M, Vigouroux A, Vilím J, Končitíková R, Briozzo P, Hájková E, Jašková L, von Schwartzenberg K, Šebela M, Moréra S, Kopečný D. The ALDH21 gene found in lower plants and some vascular plants codes for a NADP + -dependent succinic semialdehyde dehydrogenase. Plant J 2017; 92:229-243. [PMID: 28749584 DOI: 10.1111/tpj.13648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
Lower plant species including some green algae, non-vascular plants (bryophytes) as well as the oldest vascular plants (lycopods) and ferns (monilophytes) possess a unique aldehyde dehydrogenase (ALDH) gene named ALDH21, which is upregulated during dehydration. However, the gene is absent in flowering plants. Here, we show that ALDH21 from the moss Physcomitrella patens codes for a tetrameric NADP+ -dependent succinic semialdehyde dehydrogenase (SSALDH), which converts succinic semialdehyde, an intermediate of the γ-aminobutyric acid (GABA) shunt pathway, into succinate in the cytosol. NAD+ is a very poor coenzyme for ALDH21 unlike for mitochondrial SSALDHs (ALDH5), which are the closest related ALDH members. Structural comparison between the apoform and the coenzyme complex reveal that NADP+ binding induces a conformational change of the loop carrying Arg-228, which seals the NADP+ in the coenzyme cavity via its 2'-phosphate and α-phosphate groups. The crystal structure with the bound product succinate shows that its carboxylate group establishes salt bridges with both Arg-121 and Arg-457, and a hydrogen bond with Tyr-296. While both arginine residues are pre-formed for substrate/product binding, Tyr-296 moves by more than 1 Å. Both R121A and R457A variants are almost inactive, demonstrating a key role of each arginine in catalysis. Our study implies that bryophytes but presumably also some green algae, lycopods and ferns, which carry both ALDH21 and ALDH5 genes, can oxidize SSAL to succinate in both cytosol and mitochondria, indicating a more diverse GABA shunt pathway compared with higher plants carrying only the mitochondrial ALDH5.
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Affiliation(s)
- Martina Kopečná
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Armelle Vigouroux
- Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, F-91198, Gif-sur-Yvette, France
| | - Jan Vilím
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Pierre Briozzo
- Institut Jean-Pierre Bourgin, INRA-AgroParisTech, Université Paris-Saclay, Route de Saint-Cyr, F-78026, Versailles, France
| | - Eva Hájková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Lenka Jašková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | | | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, F-91198, Gif-sur-Yvette, France
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
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9
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Tichá T, Činčalová L, Kopečný D, Sedlářová M, Kopečná M, Luhová L, Petřivalský M. Characterization of S-nitrosoglutathione reductase from Brassica and Lactuca spp. and its modulation during plant development. Nitric Oxide 2017; 68:68-76. [PMID: 27940345 DOI: 10.1016/j.niox.2016.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 11/21/2022]
Abstract
Cellular homeostasis of S-nitrosoglutathione (GSNO), a major cache of nitric oxide bioactivity in plants, is controlled by the NADH-dependent S-nitrosoglutathione reductase (GSNOR) belonging to the family of class III alcohol dehydrogenases (EC 1.1.1.1). GSNOR is a key regulator of S-nitrosothiol metabolism and is involved in plant responses to abiotic and biotic stresses. This study was focused on GSNOR from two important crop plants, cauliflower (Brassica oleracea var. botrytis, BoGSNOR) and lettuce (Lactuca sativa, LsGSNOR). Both purified recombinant GSNORs were characterized in vitro and found to exists as dimers, exhibit high thermal stability and substrate preference towards GSNO, although both enzymes have dehydrogenase activity with a broad range of long-chain alcohols and ω-hydroxy fatty acids in presence of NAD+. Data on enzyme affinities to their cofactors NADH and NAD+ obtained by isothermal titration calorimetry suggest the high affinity to NADH might underline the GSNOR capacity to function in the intracellular environment. GSNOR activity and gene expression peak during early developmental stages of lettuce and cauliflower at 20 and 30 days after germination, respectively. GSNOR activity was also measured in four other Lactuca spp. genotypes with different degree of resistance to biotrophic pathogen Bremia lactucae. Higher GSNOR activities were found in non-infected plants of susceptible genotypes L. sativa UCDM2 and L. serriola as compared to resistant genotypes. GSNOR and GSNO were localized by confocal laser scanning microscopy in vascular bundles and in epidermal and parenchymal cells of leaf cross-sections. The presented results bring new insight in the role of GSNOR in the regulation of S-nitrosothiol levels in plant growth and development.
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Affiliation(s)
- Tereza Tichá
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Lucie Činčalová
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Michaela Sedlářová
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Martina Kopečná
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Lenka Luhová
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
| | - Marek Petřivalský
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
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Kopečný D, Končitíková R, Popelka H, Briozzo P, Vigouroux A, Kopečná M, Zalabák D, Šebela M, Skopalová J, Frébort I, Moréra S. Kinetic and structural investigation of the cytokinin oxidase/dehydrogenase active site. FEBS J 2015; 283:361-77. [PMID: 26519657 DOI: 10.1111/febs.13581] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/24/2022]
Abstract
Cytokinins are hormones that regulate plant development and their environmental responses. Their levels are mainly controlled by the cytokinin oxidase/dehydrogenase (CKO), which oxidatively cleaves cytokinins using redox-active electron acceptors. CKO belongs to the group of flavoproteins with an 8α-N1-histidyl FAD covalent linkage. Here, we investigated the role of seven active site residues, H105, D169, E288, V378, E381, P427 and L492, in substrate binding and catalysis of the CKO1 from maize (Zea mays, ZmCKO1) combining site-directed mutagenesis with kinetics and X-ray crystallography. We identify E381 as a key residue for enzyme specificity that restricts substrate binding as well as quinone electron acceptor binding. We show that D169 is important for catalysis and that H105 covalently linked to FAD maintains the enzyme's structural integrity, stability and high rates with electron acceptors. The L492A mutation significantly modulates the cleavage of aromatic cytokinins and zeatin isomers. The high resolution X-ray structures of ZmCKO1 and the E381S variant in complex with N6-(2-isopentenyl)adenosine reveal the binding mode of cytokinin ribosides. Those of ZmCKO2 and ZmCKO4a contain a mobile domain, which might contribute to binding of the N9 substituted cytokinins.
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Affiliation(s)
- David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Hana Popelka
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Pierre Briozzo
- Institut Jean-Pierre Bourgin, UMR1318 INRA, AgroParisTech, Versailles, France
| | - Armelle Vigouroux
- Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Martina Kopečná
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - David Zalabák
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Jana Skopalová
- Department of Analytical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Ivo Frébort
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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11
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Končitíková R, Vigouroux A, Kopečná M, Andree T, Bartoš J, Šebela M, Moréra S, Kopečný D. Role and structural characterization of plant aldehyde dehydrogenases from family 2 and family 7. Biochem J 2015; 468:109-23. [PMID: 25734422 DOI: 10.1042/bj20150009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aldehyde dehydrogenases (ALDHs) are responsible for oxidation of biogenic aldehyde intermediates as well as for cell detoxification of aldehydes generated during lipid peroxidation. So far, 13 ALDH families have been described in plants. In the present study, we provide a detailed biochemical characterization of plant ALDH2 and ALDH7 families by analysing maize and pea ALDH7 (ZmALDH7 and PsALDH7) and four maize cytosolic ALDH(cALDH)2 isoforms RF2C, RF2D, RF2E and RF2F [the first maize ALDH2 was discovered as a fertility restorer (RF2A)]. We report the crystal structures of ZmALDH7, RF2C and RF2F at high resolution. The ZmALDH7 structure shows that the three conserved residues Glu(120), Arg(300) and Thr(302) in the ALDH7 family are located in the substrate-binding site and are specific to this family. Our kinetic analysis demonstrates that α-aminoadipic semialdehyde, a lysine catabolism intermediate, is the preferred substrate for plant ALDH7. In contrast, aromatic aldehydes including benzaldehyde, anisaldehyde, cinnamaldehyde, coniferaldehyde and sinapaldehyde are the best substrates for cALDH2. In line with these results, the crystal structures of RF2C and RF2F reveal that their substrate-binding sites are similar and are formed by an aromatic cluster mainly composed of phenylalanine residues and several nonpolar residues. Gene expression studies indicate that the RF2C gene, which is strongly expressed in all organs, appears essential, suggesting that the crucial role of the enzyme would certainly be linked to the cell wall formation using aldehydes from phenylpropanoid pathway as substrates. Finally, plant ALDH7 may significantly contribute to osmoprotection because it oxidizes several aminoaldehydes leading to products known as osmolytes.
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Affiliation(s)
- Radka Končitíková
- *Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
| | - Armelle Vigouroux
- ‡Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - Martina Kopečná
- *Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
| | - Tomáš Andree
- †Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
| | - Jan Bartoš
- §Centre of Plant Structural and Functional Genomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic
| | - Marek Šebela
- *Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
| | - Solange Moréra
- ‡Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - David Kopečný
- *Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc CZ-783 71, Czech Republic
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12
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Kopečná M, Blaschke H, Kopečný D, Vigouroux A, Končitíková R, Novák O, Kotland O, Strnad M, Moréra S, von Schwartzenberg K. Structure and function of nucleoside hydrolases from Physcomitrella patens and maize catalyzing the hydrolysis of purine, pyrimidine, and cytokinin ribosides. Plant Physiol 2013; 163:1568-83. [PMID: 24170203 PMCID: PMC3850210 DOI: 10.1104/pp.113.228775] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We present a comprehensive characterization of the nucleoside N-ribohydrolase (NRH) family in two model plants, Physcomitrella patens (PpNRH) and maize (Zea mays; ZmNRH), using in vitro and in planta approaches. We identified two NRH subclasses in the plant kingdom; one preferentially targets the purine ribosides inosine and xanthosine, while the other is more active toward uridine and xanthosine. Both subclasses can hydrolyze plant hormones such as cytokinin ribosides. We also solved the crystal structures of two purine NRHs, PpNRH1 and ZmNRH3. Structural analyses, site-directed mutagenesis experiments, and phylogenetic studies were conducted to identify the residues responsible for the observed differences in substrate specificity between the NRH isoforms. The presence of a tyrosine at position 249 (PpNRH1 numbering) confers high hydrolase activity for purine ribosides, while an aspartate residue in this position confers high activity for uridine. Bud formation is delayed by knocking out single NRH genes in P. patens, and under conditions of nitrogen shortage, PpNRH1-deficient plants cannot salvage adenosine-bound nitrogen. All PpNRH knockout plants display elevated levels of certain purine and pyrimidine ribosides and cytokinins that reflect the substrate preferences of the knocked out enzymes. NRH enzymes thus have functions in cytokinin conversion and activation as well as in purine and pyrimidine metabolism.
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