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Meloni M, Rossi J, Fanti S, Carloni G, Tedesco D, Treffon P, Piccinini L, Falini G, Trost P, Vierling E, Licausi F, Giuntoli B, Musiani F, Fermani S, Zaffagnini M. Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1054-1070. [PMID: 38308388 DOI: 10.1111/tpj.16651] [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: 10/20/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
Alcohol dehydrogenases (ADHs) are a group of zinc-binding enzymes belonging to the medium-length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH-ADH1 and apo-GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo- and holo-forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long-chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol-oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.
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Affiliation(s)
- Maria Meloni
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Giacomo Carloni
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Daniele Tedesco
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), 40129, Bologna, Italy
| | - Patrick Treffon
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Luca Piccinini
- Department of Biology, University of Pisa, Pisa, 56127, Italy
- Center for Plant Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Giuseppe Falini
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | | | - Beatrice Giuntoli
- Department of Biology, University of Pisa, Pisa, 56127, Italy
- Center for Plant Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy
- Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, 40064, Bologna, Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
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Lambert L, de Carpentier F, André P, Marchand CH, Danon A. Type II metacaspase mediates light-dependent programmed cell death in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2024; 194:2648-2662. [PMID: 37971939 PMCID: PMC10980519 DOI: 10.1093/plphys/kiad618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/12/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023]
Abstract
Among the crucial processes that preside over the destiny of cells from any type of organism are those involving their self-destruction. This process is well characterized and conceptually logical to understand in multicellular organisms; however, the levels of knowledge and comprehension of its existence are still quite enigmatic in unicellular organisms. We use Chlamydomonas (Chlamydomonas reinhardtii) to lay the foundation for understanding the mechanisms of programmed cell death (PCD) in a unicellular photosynthetic organism. In this paper, we show that while PCD induces the death of a proportion of cells, it allows the survival of the remaining population. A quantitative proteomic analysis aiming at unveiling the proteome of PCD in Chlamydomonas allowed us to identify key proteins that led to the discovery of essential mechanisms. We show that in Chlamydomonas, PCD relies on the light dependence of a photosynthetic organism to generate reactive oxygen species and induce cell death. Finally, we obtained and characterized mutants for the 2 metacaspase genes in Chlamydomonas and showed that a type II metacaspase is essential for PCD execution.
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Affiliation(s)
- Lou Lambert
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
| | - Félix de Carpentier
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
- Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin 91190, France
| | - Phuc André
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
| | - Christophe H Marchand
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
- Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique (CNRS), Paris F-75005, France
| | - Antoine Danon
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
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Babuta P, Deswal R. Differential S-nitrosylation and characterization of purified S-nitrosoglutathione reductase (GSNOR) from Brassica juncea shows multiple forms of the enzyme. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108404. [PMID: 38330777 DOI: 10.1016/j.plaphy.2024.108404] [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: 10/31/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Abstract
S-nitrosoglutathione reductase (GSNOR). a master regulator of NO homeostasis, is a single-copy gene in most plants. In Lotus japonicus, two GSNOR isoforms were identified exhibiting similar kinetic properties but differential tissue-specific expressions. Previously, a genome-wide identification in Brassica juncea revealed four copies of GSNOR, each encoding proteins that vary in subunit molecular weights and pI. Here, we report multiple forms of GSNOR using 2D immunoblot which showed 4 immunopositive spots of 41.5 kDa (pl 5.79 and 6.78) and 43 kDa (pl 6.16 and 6.23). To confirm, purification of GSNOR using anion-exchange chromatography yielded 2 distinct pools (GSNOR-A & GSNOR-B) with GSNOR activities. Subsequently, affinity-based purification resulted in 1 polypeptide from GSNOR-A and 2 polypeptides from GSNOR-B. Size exclusion-HPLC confirmed 3 GSNORs with molecular weight of 87.48 ± 2.74 KDa (GSNOR-A); 87.36 ± 3.25 and 82.74 ± 2.75 kDa (GSNOR-B). Kinetic analysis showed Km of 118 ± 11 μM and Vmax of 287 ± 22 nkat/mg for GSNOR-A, whereas Km of 96.4 ± 8 μM and Vmax of 349 ± 15 nkat/mg for GSNOR-B. S-nitrosylation and inhibition by NO showed redox regulation of all BjGSNORs. Both purified GSNORs exhibited variable denitrosylation efficiency as depicted by Biotin Switch assay. To the best of our knowledge, this is the first report confirming multiple isoforms of GSNOR in B. juncea.
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Affiliation(s)
- Priyanka Babuta
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
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de Carpentier F, Maes A, Marchand CH, Chung C, Durand C, Crozet P, Lemaire SD, Danon A. How abiotic stress-induced socialization leads to the formation of massive aggregates in Chlamydomonas. PLANT PHYSIOLOGY 2022; 190:1927-1940. [PMID: 35775951 PMCID: PMC9614484 DOI: 10.1093/plphys/kiac321] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/16/2022] [Indexed: 05/05/2023]
Abstract
Multicellular organisms implement a set of reactions involving signaling and cooperation between different types of cells. Unicellular organisms, on the other hand, activate defense systems that involve collective behaviors between individual organisms. In the unicellular model alga Chlamydomonas (Chlamydomonas reinhardtii), the existence and the function of collective behaviors mechanisms in response to stress remain mostly at the level of the formation of small structures called palmelloids. Here, we report the characterization of a mechanism of abiotic stress response that Chlamydomonas can trigger to form massive multicellular structures. We showed that these aggregates constitute an effective bulwark within which the cells are efficiently protected from the toxic environment. We generated a family of mutants that aggregate spontaneously, the socializer (saz) mutants, of which saz1 is described here in detail. We took advantage of the saz mutants to implement a large-scale multiomics approach that allowed us to show that aggregation is not the result of passive agglutination, but rather genetic reprogramming and substantial modification of the secretome. The reverse genetic analysis we conducted allowed us to identify positive and negative regulators of aggregation and to make hypotheses on how this process is controlled in Chlamydomonas.
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Affiliation(s)
- Félix de Carpentier
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 75005 Paris, France
- Université Paris-Saclay, 91190 Saint-Aubin, France
| | - Alexandre Maes
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 75005 Paris, France
| | - Christophe H Marchand
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 75005 Paris, France
| | - Céline Chung
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 75005 Paris, France
| | - Cyrielle Durand
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 75005 Paris, France
| | - Pierre Crozet
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 75005 Paris, France
- Polytech-Sorbonne, Sorbonne Université, 75005 Paris, France
| | - Stéphane D Lemaire
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 75005 Paris, France
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Mattioli EJ, Rossi J, Meloni M, De Mia M, Marchand CH, Tagliani A, Fanti S, Falini G, Trost P, Lemaire SD, Fermani S, Calvaresi M, Zaffagnini M. Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH. Redox Biol 2022; 54:102387. [PMID: 35793584 PMCID: PMC9287727 DOI: 10.1016/j.redox.2022.102387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 06/25/2022] [Indexed: 10/30/2022] Open
Abstract
S-nitrosylation is a redox post-translational modification widely recognized to play an important role in cellular signaling as it can modulate protein function and conformation. At the physiological level, nitrosoglutathione (GSNO) is considered the major physiological NO-releasing compound due to its ability to transfer the NO moiety to protein thiols but the structural determinants regulating its redox specificity are not fully elucidated. In this study, we employed photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) to investigate the molecular mechanisms underlying GSNO-dependent thiol oxidation. We first observed that GSNO causes reversible enzyme inhibition by inducing S-nitrosylation. While the cofactor NADP+ partially protects the enzyme from GSNO-mediated S-nitrosylation, protein inhibition is not observed in the presence of the substrate 1,3-bisphosphoglycerate, indicating that the S-nitrosylation of the catalytic Cys149 is responsible for CrGAPA inactivation. The crystal structures of CrGAPA in complex with NADP+ and NAD+ reveal a general structural similarity with other photosynthetic GAPDH. Starting from the 3D structure, we carried out molecular dynamics simulations to identify the protein residues involved in GSNO binding. The reaction mechanism of GSNO with CrGAPA Cys149 was investigated by quantum mechanical/molecular mechanical calculations, which permitted to disclose the relative contribution of protein residues in modulating the activation barrier of the trans-nitrosylation reaction. Based on our findings, we provide functional and structural insights into the response of CrGAPA to GSNO-dependent regulation, possibly expanding the mechanistic features to other protein cysteines susceptible to be oxidatively modified by GSNO.
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Affiliation(s)
- Edoardo Jun Mattioli
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126, Bologna, Italy
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnologies, University of Bologna, I-40126, Bologna, Italy
| | - Maria Meloni
- Department of Pharmacy and Biotechnologies, University of Bologna, I-40126, Bologna, Italy
| | - Marcello De Mia
- CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, UMR8226, F-75005, Paris, France
| | - Christophe H Marchand
- CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, UMR8226, F-75005, Paris, France; CNRS, Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FR550, F-75005, Paris, France
| | - Andrea Tagliani
- Department of Pharmacy and Biotechnologies, University of Bologna, I-40126, Bologna, Italy; CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, UMR8226, F-75005, Paris, France
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126, Bologna, Italy
| | - Giuseppe Falini
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnologies, University of Bologna, I-40126, Bologna, Italy
| | - Stéphane D Lemaire
- CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, UMR8226, F-75005, Paris, France; Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238, F-75005, Paris, France
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126, Bologna, Italy; CIRI Health Sciences & Technologies (HST), University of Bologna, I-40064, Bologna, Italy.
| | - Matteo Calvaresi
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126, Bologna, Italy; CIRI Health Sciences & Technologies (HST), University of Bologna, I-40064, Bologna, Italy.
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnologies, University of Bologna, I-40126, Bologna, Italy.
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Treffon P, Rossi J, Gabellini G, Trost P, Zaffagnini M, Vierling E. Quantitative Proteome Profiling of a S-Nitrosoglutathione Reductase (GSNOR) Null Mutant Reveals a New Class of Enzymes Involved in Nitric Oxide Homeostasis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:787435. [PMID: 34956283 PMCID: PMC8695856 DOI: 10.3389/fpls.2021.787435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Nitric oxide (NO) is a short-lived radical gas that acts as a signaling molecule in all higher organisms, and that is involved in multiple plant processes, including germination, root growth, and fertility. Regulation of NO-levels is predominantly achieved by reaction of oxidation products of NO with glutathione to form S-nitrosoglutathione (GSNO), the principal bioactive form of NO. The enzyme S-nitrosoglutathione reductase (GSNOR) is a major route of NADH-dependent GSNO catabolism and is critical to NO homeostasis. Here, we performed a proteomic analysis examining changes in the total leaf proteome of an Arabidopsis thaliana GSNOR null mutant (hot5-2/gsnor1-3). Significant increases or decreases in proteins associated with chlorophyll metabolism and with redox and stress metabolism provide insight into phenotypes observed in hot5-2/gsnor1-3 plants. Importantly, we identified a significant increase in proteins that belong to the aldo-keto reductase (AKR) protein superfamily, AKR4C8 and 9. Because specific AKRs have been linked to NO metabolism in mammals, we expressed and purified A. thaliana AKR4C8 and 9 and close homologs AKR4C10 and 11 and determined that they have NADPH-dependent activity in GSNO and S-nitroso-coenzyme A (SNO-CoA) reduction. Further, we found an increase of NADPH-dependent GSNO reduction activity in hot5-2/gsnor1-3 mutant plants. These data uncover a new, NADPH-dependent component of NO metabolism that may be integrated with NADH-dependent GSNOR activity to control NO homeostasis in plants.
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Affiliation(s)
- Patrick Treffon
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Giuseppe Gabellini
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, United States
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Tedesco D, Maj M, Malarczyk P, Cingolani A, Zaffagnini M, Wnorowski A, Czapiński J, Benelli T, Mazzoni R, Bartolini M, Jóźwiak K. Application of the SMALP technology to the isolation of GPCRs from low-yielding cell lines. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183641. [PMID: 33984320 DOI: 10.1016/j.bbamem.2021.183641] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 12/21/2022]
Abstract
The ability of styrene-maleic acid (SMAc) co-polymers to spontaneously insert into biological membranes can be exploited to extract G protein-coupled receptors (GPCRs) embedded in styrene-maleic acid lipid particles (SMALPs), preserving the native environment around the protein and thus enhancing the feasibility of functional studies. So far, the SMALP technology has been primarily employed on non-mammalian cells and protocols are not optimized for adherent human cell lines, which cannot be harvested in large amounts. In this work, a fine investigation of key parameters affecting the formation of SMALPs was undertaken with the purpose of maximizing the yield of extraction of a recombinant form of human β2-adrenergic receptor (rhβ2AR) from HEK293T cells. The study highlighted an important influence of ionic strength on the membrane solubilization efficiency and GPCR purification yield of SMAc co-polymers: by lowering the salt concentration of all buffers used in previously published SMALP protocols, the water solubility and extraction efficiency of the selected SMAc co-polymer (commercially supplied as a potassium salt) were enhanced. In-line combination of size-exclusion chromatography (SEC) with immobilized metal affinity chromatography (IMAC) allowed further improvement of the final rhβ2AR yield by reducing the loss of SMALP-embedded GPCRs during the fractionation and purification of SMALPs. The overall findings of this study show that the available SMALP protocols can be significantly optimized in several aspects in order to increase the efficiency of GPCR solubilization and isolation from low-yielding expression systems.
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Affiliation(s)
- Daniele Tedesco
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, Bologna, Italy; Institute for Organic Synthesis and Photoreactivity, National Research Center (ISOF-CNR), via P. Gobetti 101, Bologna, Italy
| | - Maciej Maj
- Department of Biopharmacy, Medical University of Lublin, ulica W. Chodźki 4a, Lublin, Poland
| | - Paulina Malarczyk
- Department of Biopharmacy, Medical University of Lublin, ulica W. Chodźki 4a, Lublin, Poland
| | - Andrea Cingolani
- Department of Industrial Chemistry, University of Bologna, viale del Risorgimento 4, Bologna, Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 42, Bologna, Italy
| | - Artur Wnorowski
- Department of Biopharmacy, Medical University of Lublin, ulica W. Chodźki 4a, Lublin, Poland
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, ulica W. Chodźki 1, Lublin, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, ulica Żwirki i Wigury 61, Warsaw, Poland
| | - Tiziana Benelli
- Department of Industrial Chemistry, University of Bologna, viale del Risorgimento 4, Bologna, Italy
| | - Rita Mazzoni
- Department of Industrial Chemistry, University of Bologna, viale del Risorgimento 4, Bologna, Italy
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, Bologna, Italy.
| | - Krzysztof Jóźwiak
- Department of Biopharmacy, Medical University of Lublin, ulica W. Chodźki 4a, Lublin, Poland.
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