1
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Pillay CS, Rohwer JM. Computational models as catalysts for investigating redoxin systems. Essays Biochem 2024; 68:27-39. [PMID: 38356400 DOI: 10.1042/ebc20230036] [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: 10/23/2023] [Revised: 01/11/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Thioredoxin, glutaredoxin and peroxiredoxin systems play central roles in redox regulation, signaling and metabolism in cells. In these systems, reducing equivalents from NAD(P)H are transferred by coupled thiol-disulfide exchange reactions to redoxins which then reduce a wide array of targets. However, the characterization of redoxin activity has been unclear, with redoxins regarded as enzymes in some studies and redox metabolites in others. Consequently, redoxin activities have been quantified by enzyme kinetic parameters in vitro, and redox potentials or redox ratios within cells. By analyzing all the reactions within these systems, computational models showed that many kinetic properties attributed to redoxins were due to system-level effects. Models of cellular redoxin networks have also been used to estimate intracellular hydrogen peroxide levels, analyze redox signaling and couple omic and kinetic data to understand the regulation of these networks in disease. Computational modeling has emerged as a powerful complementary tool to traditional redoxin enzyme kinetic and cellular assays that integrates data from a number of sources into a single quantitative framework to accelerate the analysis of redoxin systems.
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Affiliation(s)
- Ché S Pillay
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Johann M Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
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2
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Griffith M, Araújo A, Travasso R, Salvador A. The architecture of redox microdomains: Cascading gradients and peroxiredoxins' redox-oligomeric coupling integrate redox signaling and antioxidant protection. Redox Biol 2024; 69:103000. [PMID: 38150990 PMCID: PMC10829873 DOI: 10.1016/j.redox.2023.103000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023] Open
Abstract
In the cytosol of human cells under low oxidative loads, hydrogen peroxide is confined to microdomains around its supply sites, due to its fast consumption by peroxiredoxins. So are the sulfenic and disulfide forms of the 2-Cys peroxiredoxins, according to a previous theoretical analysis [Travasso et al., Redox Biology 15 (2017) 297]. Here, an extended reaction-diffusion model that for the first time considers the differential properties of human peroxiredoxins 1 and 2 and the thioredoxin redox cycle predicts important new aspects of the dynamics of redox microdomains. The peroxiredoxin 1 sulfenates and disulfides are more localized than the corresponding peroxiredoxin 2 forms, due to the former peroxiredoxin's faster resolution step. The thioredoxin disulfides are also localized. As the H2O2 supply rate (vsup) approaches and then surpasses the maximal rate of the thioredoxin/thioredoxin reductase system (V), these concentration gradients become shallower, and then vanish. At low vsup the peroxiredoxin concentration determines the H2O2 concentrations and gradient length scale, but as vsup approaches V, the thioredoxin reductase activity gains influence. A differential mobility of peroxiredoxin disulfide dimers vs. reduced decamers enhances the redox polarity of the cytosol: as vsup approaches V, reduced decamers are preferentially retained far from H2O2 sources, attenuating the local H2O2 buildup. Substantial total protein concentration gradients of both peroxiredoxins emerge under these conditions, and the concentration of reduced peroxiredoxin 1 far from the H2O2 sources even increases with vsup. Altogether, the properties of 2-Cys peroxiredoxins and thioredoxin are such that localized H2O2 supply induces a redox and functional polarization between source-proximal regions (redox microdomains) that facilitate peroxiredoxin-mediated signaling and distal regions that maximize antioxidant protection.
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Affiliation(s)
- Matthew Griffith
- CNC - Centre for Neuroscience Cell Biology, University of Coimbra, UC-Biotech, Parque Tecnológico de Cantanhede, Núcleo 4, Lote 8, 3060-197, Cantanhede, Portugal; Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Adérito Araújo
- CMUC, Department of Mathematics, University of Coimbra, Largo D. Dinis, 3004-143, Coimbra, Portugal.
| | - Rui Travasso
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Rua Larga, 3004-516, Coimbra, Portugal.
| | - Armindo Salvador
- CNC - Centre for Neuroscience Cell Biology, University of Coimbra, UC-Biotech, Parque Tecnológico de Cantanhede, Núcleo 4, Lote 8, 3060-197, Cantanhede, Portugal; Coimbra Chemistry Center - Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535, Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra, Casa Costa Alemão, Rua Dom Francisco de Lemos, 3030-789, Coimbra, Portugal.
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3
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Barry CJ, Pillay CS, Rohwer JM. Modelling the Decamerisation Cycle of PRDX1 and the Inhibition-like Effect on Its Peroxidase Activity. Antioxidants (Basel) 2023; 12:1707. [PMID: 37760010 PMCID: PMC10525498 DOI: 10.3390/antiox12091707] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Peroxiredoxins play central roles in the detoxification of reactive oxygen species and have been modelled across multiple organisms using a variety of kinetic methods. However, the peroxiredoxin dimer-to-decamer transition has been underappreciated in these studies despite the 100-fold difference in activity between these forms. This is due to the lack of available kinetics and a theoretical framework for modelling this process. Using published isothermal titration calorimetry data, we obtained association and dissociation rate constants of 0.050 µM-4·s-1 and 0.055 s-1, respectively, for the dimer-decamer transition of human PRDX1. We developed an approach that greatly reduces the number of reactions and species needed to model the peroxiredoxin decamer oxidation cycle. Using these data, we simulated horse radish peroxidase competition and NADPH-oxidation linked assays and found that the dimer-decamer transition had an inhibition-like effect on peroxidase activity. Further, we incorporated this dimer-decamer topology and kinetics into a published and validated in vivo model of PRDX2 in the erythrocyte and found that it almost perfectly reconciled experimental and simulated responses of PRDX2 oxidation state to hydrogen peroxide insult. By accounting for the dimer-decamer transition of peroxiredoxins, we were able to resolve several discrepancies between experimental data and available kinetic models.
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Affiliation(s)
- Christopher J. Barry
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg 3201, South Africa;
| | - Johann M. Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
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4
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Villar SF, Möller MN, Denicola A. Biophysical tools to study the oligomerization dynamics of Prx1-class peroxiredoxins. Biophys Rev 2023; 15:601-609. [PMID: 37681093 PMCID: PMC10480382 DOI: 10.1007/s12551-023-01076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/04/2023] [Indexed: 09/09/2023] Open
Abstract
Peroxiredoxins (Prx) are ubiquitous, highly conserved peroxidases whose activity depends on catalytic cysteine residues. The Prx1-class of the peroxiredoxin family, also called typical 2-Cys Prx, organize as head-to-tail homodimers containing two active sites. The peroxidatic cysteine CP of one monomer reacts with the peroxide substrate to form sulfenic acid that reacts with the resolving cysteine (CR) of the adjacent subunit to form an intermolecular disulfide, that is reduced back by the thioredoxin/thioredoxin reductase/NADPH system. Although the minimal catalytic unit is the dimer, these Prx oligomerize into (do)decamers. In addition, these ring-shaped decamers can pile-up into high molecular weight structures. Prx not only display peroxidase activity reducing H2O2, peroxynitrous acid and lipid hydroperoxides (antioxidant enzymes), but also exhibit holdase activity protecting other proteins from unfolding (molecular chaperones). Highly relevant is their participation in redox cellular signaling that is currently under active investigation. The different activities attributed to Prx are strongly ligated to their quaternary structure. In this review, we will describe different biophysical approaches used to characterize the oligomerization dynamics of Prx that include the classical size-exclusion chromatography, analytical ultracentrifugation, calorimetry, and also fluorescence anisotropy and lifetime measurements, as well as mass photometry.
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Affiliation(s)
- Sebastián F. Villar
- Laboratorio Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Matías N. Möller
- Laboratorio Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ana Denicola
- Laboratorio Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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5
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Morita K, Sasaki R, Jindai M, Yamada Y, Konno H. Elucidation of the Binding Mechanism of Anionic Phospholipids to Antioxidant Protein Peroxiredoxin 2. Biochemistry 2023. [PMID: 37220271 DOI: 10.1021/acs.biochem.2c00698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Peroxiredoxins (Prxs) belong to a family of ubiquitously expressed peroxidases that detoxify reactive oxygen species. In addition to their enzymatic function, Prxs also function as molecular chaperones. This functional switch is related to their degree of oligomerization. We have previously revealed that Prx2 interacts with anionic phospholipids and that the anionic phospholipid-containing Prx2 oligomer forms a high molecular weight (HMW) complex in a nucleotide-dependent manner. However, the detailed mechanism of the oligomer and HMW complex formation remains unclear. In this study, we investigated the anionic phospholipid binding site in Prx2 using site-directed mutagenesis to understand the mechanism of the oligomer formation. Our findings demonstrated that six binding site residues in Prx2 are important for the binding of anionic phospholipids.
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Affiliation(s)
- Kouki Morita
- Graduate School of Natural Science & Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Rino Sasaki
- College of Science and Engineering, School of Natural System, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Mami Jindai
- College of Science and Engineering, School of Natural System, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yutaro Yamada
- Graduate School of Natural Science & Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hiroki Konno
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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6
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Sadowska-Bartosz I, Bartosz G. Peroxiredoxin 2: An Important Element of the Antioxidant Defense of the Erythrocyte. Antioxidants (Basel) 2023; 12:antiox12051012. [PMID: 37237878 DOI: 10.3390/antiox12051012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/14/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Peroxiredoxin 2 (Prdx2) is the third most abundant erythrocyte protein. It was known previously as calpromotin since its binding to the membrane stimulates the calcium-dependent potassium channel. Prdx2 is present mostly in cytosol in the form of non-covalent dimers but may associate into doughnut-like decamers and other oligomers. Prdx2 reacts rapidly with hydrogen peroxide (k > 107 M-1 s-1). It is the main erythrocyte antioxidant that removes hydrogen peroxide formed endogenously by hemoglobin autoxidation. Prdx2 also reduces other peroxides including lipid, urate, amino acid, and protein hydroperoxides and peroxynitrite. Oxidized Prdx2 can be reduced at the expense of thioredoxin but also of other thiols, especially glutathione. Further reactions of Prdx2 with oxidants lead to hyperoxidation (formation of sulfinyl or sulfonyl derivatives of the peroxidative cysteine). The sulfinyl derivative can be reduced by sulfiredoxin. Circadian oscillations in the level of hyperoxidation of erythrocyte Prdx2 were reported. The protein can be subject to post-translational modifications; some of them, such as phosphorylation, nitration, and acetylation, increase its activity. Prdx2 can also act as a chaperone for hemoglobin and erythrocyte membrane proteins, especially during the maturation of erythrocyte precursors. The extent of Prdx2 oxidation is increased in various diseases and can be an index of oxidative stress.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, 4 Zelwerowicza St., 35-601 Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszów, 4 Zelwerowicza St., 35-601 Rzeszow, Poland
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7
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Villar SF, Dalla-Rizza J, Möller MN, Ferrer-Sueta G, Malacrida L, Jameson DM, Denicola A. Fluorescence Lifetime Phasor Analysis of the Decamer-Dimer Equilibrium of Human Peroxiredoxin 1. Int J Mol Sci 2022; 23:5260. [PMID: 35563654 PMCID: PMC9100220 DOI: 10.3390/ijms23095260] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/22/2022] Open
Abstract
Protein self-assembly is a common feature in biology and is often required for a myriad of fundamental processes, such as enzyme activity, signal transduction, and transport of solutes across membranes, among others. There are several techniques to find and assess homo-oligomer formation in proteins. Naturally, all these methods have their limitations, meaning that at least two or more different approaches are needed to characterize a case study. Herein, we present a new method to study protein associations using intrinsic fluorescence lifetime with phasors. In this case, the method is applied to determine the equilibrium dissociation constant (KD) of human peroxiredoxin 1 (hPrx1), an efficient cysteine-dependent peroxidase, that has a quaternary structure comprised of five head-to-tail homodimers non-covalently arranged in a decamer. The hPrx1 oligomeric state not only affects its activity but also its association with other proteins. The excited state lifetime of hPrx1 has distinct values at high and low concentrations, suggesting the presence of two different species. Phasor analysis of hPrx1 emission lifetime allowed for the identification and quantification of hPrx1 decamers, dimers, and their mixture at diverse protein concentrations. Using phasor algebra, we calculated the fraction of hPrx1 decamers at different concentrations and obtained KD (1.1 × 10-24 M4) and C0.5 (1.36 μM) values for the decamer-dimer equilibrium. The results were validated and compared with size exclusion chromatography. In addition, spectral phasors provided similar results despite the small differences in emission spectra as a function of hPrx1 concentration. The phasor approach was shown to be a highly sensitive and quantitative method to assess protein oligomerization and an attractive addition to the biophysicist's toolkit.
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Affiliation(s)
- Sebastián F. Villar
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Joaquín Dalla-Rizza
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
| | - Matías N. Möller
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Leonel Malacrida
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay;
- Departamento de Fisiopatología, Hospital de Clínicas, Universidad de la República, Montevideo 11600, Uruguay
| | - David M. Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
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8
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Beaussart A, Canonico F, Mazon H, Hidalgo J, Cianférani S, Le Cordier H, Kriznik A, Rahuel-Clermont S. Probing the mechanism of the peroxiredoxin decamer interaction with its reductase sulfiredoxin from the single molecule to the solution scale. NANOSCALE HORIZONS 2022; 7:515-525. [PMID: 35234779 DOI: 10.1039/d2nh00037g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peroxiredoxins from the Prx1 subfamily (Prx) are highly regulated multifunctional proteins involved in oxidative stress response, redox signaling and cell protection. Prx is a homodimer that associates into a decamer. The monomer C-terminus plays intricate roles in Prx catalytic functions, decamer stability and interaction with its redox partner, the small reductase sulfiredoxin (Srx), that regulates the switching between Prx cellular functions. As only static structures of covalent Prx-Srx complexes have been reported, whether Srx binding dissociates the decameric assembly and how Prx subunit flexibility impacts complex formation are unknown. Here, we assessed the non-covalent interaction mechanism and dynamics in the solution of Saccharomyces cerevisiae Srx with the ten subunits of Prx Tsa1 at the decamer level via a combination of multiscale biophysical approaches including native mass spectrometry. We show that the ten subunits of the decamer can be saturated by ten Srx molecules and that the Tsa1 decamer in complex with Srx does not dissociate in solution. Furthermore, the binding events of atomic force microscopy (AFM) tip-grafted Srx molecules to Tsa1 individual subunits were relevant to the interactions between free molecules in solution. Combined with protein engineering and rapid kinetics, the observation of peculiar AFM force-distance signatures revealed that Tsa1 C-terminus flexibility controls Tsa1/Srx two-step binding and dynamics and determines the force-induced dissociation of Srx from each subunit of the decameric complex in a sequential or concerted mode. This combined approach from the solution to the single-molecule level offers promising prospects for understanding oligomeric protein interactions with their partners.
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Affiliation(s)
| | | | - Hortense Mazon
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Jorge Hidalgo
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087 Strasbourg, France
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
| | - Sophie Rahuel-Clermont
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
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9
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Chagot ME, Boutilliat A, Kriznik A, Quinternet M. Structural Analysis of the Plasmodial Proteins ZNHIT3 and NUFIP1 Provides Insights into the Selectivity of a Conserved Interaction. Biochemistry 2022; 61:479-493. [PMID: 35315277 DOI: 10.1021/acs.biochem.1c00792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria is a widespread and lethal disease caused by the Plasmodium parasites that can infect human beings through Anopheles mosquitoes. For that reason, the biology of Plasmodium needs to be studied to develop antimalarial treatments. By determining the three-dimensional structures of macromolecules, structural biology helps to understand the function of proteins and can reveal how interactions occur between biological partners. Here, we studied the ZNHIT3 and NUFIP1 proteins from Plasmodium falciparum, two proteins tightly linked to the ribosome biology. Due to their important functions in post-translational modifications of ribosomal RNAs and in ribophagy, these proteins participate in the survival of cells. In this study, we solved the three-dimensional structure of a thermally stable and species-dependent complex between fragments of these proteins. Our results were compared to the AlphaFold predictions, which motivated the study of the free ZNHIT3 fragment that binds NUFIP1. We showed that the latter fragment multimerized in vitro but also had the inner ability to change its conformation to escape the solvent exposition of key hydrophobic residues involved in the interaction with NUFIP1. Our data could open the gate to selective drug discovery processes involving these two proteins.
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Affiliation(s)
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.,Université de Lorraine, CNRS, INSERM, IBSLor, F-54000 Nancy, France
| | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, F-54000 Nancy, France
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10
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Liebthal M, Kushwah MS, Kukura P, Dietz KJ. Single molecule mass photometry reveals the dynamic oligomerization of human and plant peroxiredoxins. iScience 2021; 24:103258. [PMID: 34765909 PMCID: PMC8571717 DOI: 10.1016/j.isci.2021.103258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/08/2021] [Accepted: 10/08/2021] [Indexed: 12/05/2022] Open
Abstract
Protein oligomerization is central to biological function and regulation, yet its experimental quantification and measurement of dynamic transitions in solution remain challenging. Here, we show that single molecule mass photometry quantifies affinity and polydispersity of heterogeneous protein complexes in solution. We demonstrate these capabilities by studying the functionally relevant oligomeric equilibria of 2-cysteine peroxiredoxins (2CPs). Comparison of the polydispersity of plant and human 2CPs as a function of concentration and redox state revealed features conserved among all 2CPs. In addition, we also find species-specific differences in oligomeric transitions, the occurrence of intermediates and the formation of high molecular weight complexes, which are associated with chaperone activity or act as a storage pool for more efficient dimers outlining the functional differentiation of human 2CPs. Our results point to a diversified functionality of oligomerization for 2CPs and illustrate the power of mass photometry for characterizing heterogeneous oligomeric protein distributions in near native conditions.
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Affiliation(s)
- Michael Liebthal
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, 33615 Bielefeld, Germany
| | - Manish Singh Kushwah
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QZ Oxford, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QZ Oxford, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, 33615 Bielefeld, Germany
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11
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Peskin AV, Meotti FC, Kean KM, Göbl C, Peixoto AS, Pace PE, Horne CR, Heath SG, Crowther JM, Dobson RCJ, Karplus PA, Winterbourn CC. Modifying the resolving cysteine affects the structure and hydrogen peroxide reactivity of peroxiredoxin 2. J Biol Chem 2021; 296:100494. [PMID: 33667550 PMCID: PMC8049995 DOI: 10.1016/j.jbc.2021.100494] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 01/05/2023] Open
Abstract
Peroxiredoxin 2 (Prdx2) is a thiol peroxidase with an active site Cys (C52) that reacts rapidly with H2O2 and other peroxides. The sulfenic acid product condenses with the resolving Cys (C172) to form a disulfide which is recycled by thioredoxin or GSH via mixed disulfide intermediates or undergoes hyperoxidation to the sulfinic acid. C172 lies near the C terminus, outside the active site. It is not established whether structural changes in this region, such as mixed disulfide formation, affect H2O2 reactivity. To investigate, we designed mutants to cause minimal (C172S) or substantial (C172D and C172W) structural disruption. Stopped flow kinetics and mass spectrometry showed that mutation to Ser had minimal effect on rates of oxidation and hyperoxidation, whereas Asp and Trp decreased both by ∼100-fold. To relate to structural changes, we solved the crystal structures of reduced WT and C172S Prdx2. The WT structure is highly similar to that of the published hyperoxidized form. C172S is closely related but more flexible and as demonstrated by size exclusion chromatography and analytical ultracentrifugation, a weaker decamer. Size exclusion chromatography and analytical ultracentrifugation showed that the C172D and C172W mutants are also weaker decamers than WT, and small-angle X-ray scattering analysis indicated greater flexibility with partially unstructured regions consistent with C-terminal unfolding. We propose that these structural changes around C172 negatively impact the active site geometry to decrease reactivity with H2O2. This is relevant for Prdx turnover as intermediate mixed disulfides with C172 would also be disruptive and could potentially react with peroxides before resolution is complete.
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Affiliation(s)
- Alexander V Peskin
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Flavia C Meotti
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Kelsey M Kean
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Christoph Göbl
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Albert Souza Peixoto
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Paul E Pace
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Christopher R Horne
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sarah G Heath
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Jennifer M Crowther
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA.
| | - Christine C Winterbourn
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand.
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12
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Himiyama T, Nakamura T. Disassembly of the ring-type decameric structure of peroxiredoxin from Aeropyrum pernix K1 by amino acid mutation. Protein Sci 2020; 29:1138-1147. [PMID: 32022337 DOI: 10.1002/pro.3837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/13/2022]
Abstract
The quaternary structure of peroxiredoxin from Aeropyrum pernix K1 (ApPrx) is a decamer, in which five homodimers are assembled in a pentagonal ring through hydrophobic interactions. In this study, we determined the amino acid (AA) residues of ApPrx crucial for forming the decamer using AA mutations. The ApPrx0Cys mutant, wherein all cysteine residues were mutated to serine, was prepared as a model protein to remove the influence of the redox states of the cysteines on its assembling behavior. The boundary between each homodimer of ApPrx0Cys contains characteristic aromatic AA residues forming hydrophobic interactions: F46, F80, W88, W210, and W211. We found that a single mutation of F46, F80, or W210 to alanine completely disassembled the ApPrx0Cys decamer to homodimers, which was clarified by gel-filtration chromatography and dynamic light scattering measurements. F46A, F80A, and W210A mutants lacked only one aromatic ring compared with ApPrx0Cys, indicating that the assembly is very sensitive to the surface structure of the protein. X-ray structures revealed two mechanisms of disassembly of the ApPrx decamer: loss of hydrophobicity between homodimers and flip of the arm domain. The AA residues targeted in this study are well conserved in ring-type Prx proteins, suggesting the importance of these residues in the assembly. This study demonstrates the sensitivity and modifiability of peroxiredoxin assembly by a simple AA mutation.
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Affiliation(s)
- Tomoki Himiyama
- National Institute of Advanced Industrial Science and Technology, Ikeda, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Japan
| | - Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology, Ikeda, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Japan
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13
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Ratajczak E, Małecka A, Ciereszko I, Staszak AM. Mitochondria Are Important Determinants of the Aging of Seeds. Int J Mol Sci 2019; 20:E1568. [PMID: 30925807 PMCID: PMC6479606 DOI: 10.3390/ijms20071568] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/17/2022] Open
Abstract
Seeds enable plant survival in harsh environmental conditions, and via seeds, genetic information is transferred from parents to the new generation; this stage provides an opportunity for sessile plants to settle in new territories. However, seed viability decreases over long-term storage due to seed aging. For the effective conservation of gene resources, e.g., in gene banks, it is necessary to understand the causes of decreases in seed viability, not only where the aging process is initiated in seeds but also the sequence of events of this process. Mitochondria are the main source of reactive oxygen species (ROS) production, so they are more quickly and strongly exposed to oxidative damage than other organelles. The mitochondrial antioxidant system is also less active than the antioxidant systems of other organelles, thus such mitochondrial 'defects' can strongly affect various cell processes, including seed aging, which we discuss in this paper.
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Affiliation(s)
- Ewelina Ratajczak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland.
| | - Arleta Małecka
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznań, Poland.
| | - Iwona Ciereszko
- Plant Physiology Department, Institute of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland.
| | - Aleksandra M Staszak
- Plant Physiology Department, Institute of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland.
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14
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Rennie ML, Crowley PB. A Thermodynamic Model of Auto‐regulated Protein Assembly by a Supramolecular Scaffold. Chemphyschem 2019; 20:1011-1017. [DOI: 10.1002/cphc.201900153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
- Present address: Institute of Molecular Cell and System BiologyUniversity of Glasgow University Avenue Glasgow UK
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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15
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Himiyama T, Oshima M, Uegaki K, Nakamura T. Distinct molecular assembly of homologous peroxiredoxins from Pyrococcus horikoshii and Thermococcus kodakaraensis. J Biochem 2019; 166:89-95. [DOI: 10.1093/jb/mvz013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Peroxiredoxins from Pyrococcus horikoshii (PhPrx) and Thermococcus kodakaraensis (TkPrx) are highly homologous proteins sharing 196 of the 216 residues. We previously reported a pentagonal ring-type decameric structure of PhPrx. Here, we present the crystal structure of TkPrx. Despite their homology, unlike PhPrx, the quaternary structure of TkPrx was found to be a dodecamer comprised of six homodimers arranged in a hexagonal ring-type assembly. The possibility of the redox-dependent conversion of the molecular assembly, which had been observed in PhPrx, was excluded for TkPrx based on the crystal structure of a mutant in which all of the cysteine residues were substituted with serine. The monomer structures of the dodecameric TkPrx and decameric PhPrx coincided well, but there was a slight difference in the relative orientation of the two domains. Molecular assembly of PhPrx and TkPrx in solution evaluated by gel-filtration chromatography was consistent with the crystallographic results. For both PhPrx and TkPrx, the gel-filtration elution volume slightly increased with a decrease in the protein concentration, suggesting the existence of an equilibrium state between the decameric/dodecameric ring and lower-order assembly. This structural assembly difference between highly homologous Prxs suggests a significant influence of quaternary structure on function, worthy of further exploration.
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Affiliation(s)
- Tomoki Himiyama
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
| | - Maki Oshima
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
| | - Koichi Uegaki
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Nara, Japan
| | - Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
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16
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Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. Active site C P-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins. Free Radic Biol Med 2018; 118:59-70. [PMID: 29474868 DOI: 10.1016/j.freeradbiomed.2018.02.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/12/2018] [Accepted: 02/17/2018] [Indexed: 01/20/2023]
Abstract
Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (CP) located in a conserved sequence Pxxx(T/S)xxCP motif known as CP-loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the CP-loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the CP-loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the CP-loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the CP-loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the CP-loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted CP-loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the CP-loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles.
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Affiliation(s)
- Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Computer Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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17
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Carrasco K, Boufenzer A, Jolly L, Le Cordier H, Wang G, Heck AJ, Cerwenka A, Vinolo E, Nazabal A, Kriznik A, Launay P, Gibot S, Derive M. TREM-1 multimerization is essential for its activation on monocytes and neutrophils. Cell Mol Immunol 2018; 16:460-472. [PMID: 29568119 DOI: 10.1038/s41423-018-0003-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/01/2018] [Accepted: 01/09/2018] [Indexed: 12/18/2022] Open
Abstract
The triggering receptor expressed on myeloid cells-1 (TREM-1) is a receptor expressed on innate immune cells. By promoting the amplification of inflammatory signals that are initially triggered by Toll-like receptors (TLRs), TREM-1 has been characterized as a major player in the pathophysiology of acute and chronic inflammatory diseases, such as septic shock, myocardial infarction, atherosclerosis, and inflammatory bowel diseases. However, the molecular events leading to the activation of TREM-1 in innate immune cells remain unknown. Here, we show that TREM-1 is activated by multimerization and that the levels of intracellular Ca2+ release, reactive oxygen species, and cytokine production correlate with the degree of TREM-1 aggregation. TREM-1 activation on primary human monocytes by LPS required a two-step process consisting of upregulation followed by clustering of TREM-1 at the cell surface, in contrast to primary human neutrophils, where LPS induced a rapid cell membrane reorganization of TREM-1, which confirmed that TREM-1 is regulated differently in primary human neutrophils and monocytes. In addition, we show that the ectodomain of TREM-1 is able to homooligomerize in a concentration-dependent manner, which suggests that the clustering of TREM-1 on the membrane promotes its oligomerization. We further show that the adapter protein DAP12 stabilizes TREM-1 surface expression and multimerization. TREM-1 multimerization at the cell surface is also mediated by its endogenous ligand, a conclusion supported by the ability of the TREM-1 inhibitor LR12 to limit TREM-1 multimerization. These results provide evidence for ligand-induced, receptor-mediated dimerization of TREM-1. Collectively, our findings uncover the mechanisms necessary for TREM-1 activation in monocytes and neutrophils.
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Affiliation(s)
- Kevin Carrasco
- INOTREM, Vandœuvre-les-Nancy, France.,UMR-S 1116, Defaillance cardiovasculaire aigue et chronique, Vandœuvre-les-Nancy, France
| | | | - Lucie Jolly
- INOTREM, Vandœuvre-les-Nancy, France.,UMR-S 1116, Defaillance cardiovasculaire aigue et chronique, Vandœuvre-les-Nancy, France
| | - Helene Le Cordier
- UMR7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Vandœuvre-les-Nancy, France
| | - Guanbo Wang
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Center, Utrecht University, Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Center, Utrecht University, Utrecht, The Netherlands
| | - Adelheid Cerwenka
- Innate Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | - Alexandre Kriznik
- Service Commun de Biophysique Interactions Moléculaires (SCBIM), FR3209, Biopôle de l'Université de Lorraine, Vandœuvre-les-Nancy, France
| | | | - Sebastien Gibot
- UMR-S 1116, Defaillance cardiovasculaire aigue et chronique, Vandœuvre-les-Nancy, France
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18
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Nelson KJ, Perkins A, Van Swearingen AED, Hartman S, Brereton AE, Parsonage D, Salsbury FR, Karplus PA, Poole LB. Experimentally Dissecting the Origins of Peroxiredoxin Catalysis. Antioxid Redox Signal 2018; 28:521-536. [PMID: 28375740 PMCID: PMC5806077 DOI: 10.1089/ars.2016.6922] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AIMS Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases involved in oxidant defense and signal transduction. Despite much study, the precise roles of conserved residues remain poorly defined. In this study, we carried out extensive functional and structural characterization of 10 variants of such residues in a model decameric bacterial Prx. RESULTS Three active site proximal mutations of Salmonella typhimurium AhpC, T43V, R119A, and E49Q, lowered catalytic efficiency with hydrogen peroxide by 4-5 orders of magnitude, but did not affect reactivity toward their reductant, AhpF. pKa values of the peroxidatic cysteine were also shifted up by 1-1.3 pH units for these and a decamer disruption mutant, T77I. Except for the decamer-stabilizing T77V, all mutations destabilized decamers in the reduced form. In the oxidized form, three mutants-T77V, T43A, and T43S-exhibited stabilized decamers and were more efficiently reduced by AhpF than wild-type AhpC. Crystal structures of most mutants were solved and many showed alterations in stability of the fully folded active site loop. INNOVATION This is the first study of Prx mutants to comprehensively assess the effects of mutations on catalytic activities, the active site cysteine pKa, and the protein structure and oligomeric status. CONCLUSION The Arg119 side chain must be properly situated for efficient catalysis, but for other debilitating variants, the functional defects could be explained by structural perturbations and/or associated decamer destabilization rather than direct effects. This underscores the importance of our comprehensive approach. A remarkable new finding was the preference of the reductant for decamers. Antioxid. Redox Signal. 28, 521-536.
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Affiliation(s)
- Kimberly J Nelson
- 1 Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina.,2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
| | - Arden Perkins
- 3 Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon
| | - Amanda E D Van Swearingen
- 1 Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina.,2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
| | - Steven Hartman
- 3 Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon
| | - Andrew E Brereton
- 3 Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon
| | - Derek Parsonage
- 1 Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina.,2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
| | - Freddie R Salsbury
- 2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina.,4 Department of Physics, Wake Forest University , Winston-Salem, North Carolina
| | - P Andrew Karplus
- 3 Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon
| | - Leslie B Poole
- 1 Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina.,2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
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19
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Veal EA, Underwood ZE, Tomalin LE, Morgan BA, Pillay CS. Hyperoxidation of Peroxiredoxins: Gain or Loss of Function? Antioxid Redox Signal 2018; 28:574-590. [PMID: 28762774 DOI: 10.1089/ars.2017.7214] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE In 2003, structural studies revealed that eukaryotic 2-Cys peroxiredoxins (Prx) have evolved to be sensitive to inactivation of their thioredoxin peroxidase activity by hyperoxidation (sulfinylation) of their peroxide-reacting catalytic cysteine. This was accompanied by the unexpected discovery, that the sulfinylation of this cysteine was reversible in vivo and the identification of a new enzyme, sulfiredoxin, that had apparently co-evolved specifically to reduce hyperoxidized 2-Cys Prx, restoring their peroxidase activity. Together, these findings have provided the impetus for multiple studies investigating the purpose of this reversible, Prx hyperoxidation. Recent Advances: It has been suggested that inhibition of the thioredoxin peroxidase activity by hyperoxidation can both promote and inhibit peroxide signal transduction, depending on the context. Prx hyperoxidation has also been proposed to protect cells against reactive oxygen species (ROS)-induced damage, by preserving reduced thioredoxin and/or by increasing non-peroxidase chaperone or signaling activities of Prx. CRITICAL ISSUES Here, we will review the evidence in support of each of these proposed functions, in view of the in vivo contexts in which Prx hyperoxidation occurs, and the role of sulfiredoxin. Thus, we will attempt to explain the basis for seemingly contradictory roles for Prx hyperoxidation in redox signaling. FUTURE DIRECTIONS We provide a rationale, based on modeling and experimental studies, for why Prx hyperoxidation should be considered a suitable, early biomarker for damaging levels of ROS. We discuss the implications that this has for the role of Prx in aging and the detection of hyperoxidized Prx as a conserved feature of circadian rhythms. Antioxid. Redox Signal. 28, 574-590.
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Affiliation(s)
- Elizabeth A Veal
- 1 Institute for Cell and Molecular Biosciences, Newcastle University , Newcastle upon Tyne, United Kingdom .,2 Newcastle University Institute for Ageing, Newcastle University , Newcastle upon Tyne, United Kingdom
| | - Zoe E Underwood
- 1 Institute for Cell and Molecular Biosciences, Newcastle University , Newcastle upon Tyne, United Kingdom .,2 Newcastle University Institute for Ageing, Newcastle University , Newcastle upon Tyne, United Kingdom
| | - Lewis E Tomalin
- 1 Institute for Cell and Molecular Biosciences, Newcastle University , Newcastle upon Tyne, United Kingdom .,2 Newcastle University Institute for Ageing, Newcastle University , Newcastle upon Tyne, United Kingdom
| | - Brian A Morgan
- 1 Institute for Cell and Molecular Biosciences, Newcastle University , Newcastle upon Tyne, United Kingdom
| | - Ché S Pillay
- 3 School of Life Sciences, University of KwaZulu-Natal , Pietermartizburg, South Africa
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20
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Spigolon D, Gallagher DT, Velazquez-Campoy A, Bulone D, Narang J, San Biagio PL, Cappello F, Macario AJL, Conway de Macario E, Robb FT. Quantitative analysis of the impact of a human pathogenic mutation on the CCT5 chaperonin subunit using a proxy archaeal ortholog. Biochem Biophys Rep 2017; 12:66-71. [PMID: 29552646 PMCID: PMC5851525 DOI: 10.1016/j.bbrep.2017.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/21/2017] [Accepted: 07/26/2017] [Indexed: 01/20/2023] Open
Abstract
The human chaperonin complex is a ~ 1 MDa nanomachine composed of two octameric rings formed from eight similar but non-identical subunits called CCT. Here, we are elucidating the mechanism of a heritable CCT5 subunit mutation that causes profound neuropathy in humans. In previous work, we introduced an equivalent mutation in an archaeal chaperonin that assembles into two octameric rings like in humans but in which all subunits are identical. We reported that the hexadecamer formed by the mutant subunit is unstable with impaired chaperoning functions. This study quantifies the loss of structural stability in the hexadecamer due to the pathogenic mutation, using differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). The disassembly of the wild type complex, which is tightly coupled with subunit denaturation, was decoupled by the mutation without affecting the stability of individual subunits. Our results verify the effectiveness of the homo-hexadecameric archaeal chaperonin as a proxy to assess the impact of subtle defects in heterologous systems with mutations in a single subunit. A crippling hereditary neuropathy was addressed at the molecular level. The archaeal/CCT5 model represents a promising testbed for subtle defects. The homomeric archaeal model amplifies the effect of the mutation. The mutation decouples assembly without destabilizing individual subunits.
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Affiliation(s)
- Dario Spigolon
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA.,Institute of Biophysics, UOS Palermo, National Research Council, Italy.,Department of Physics and Chemistry, University of Palermo, Palermo, Italy
| | - D Travis Gallagher
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units: BIFI-IQFR and GBsC-CSIC,Universidad de Zaragoza, Zaragoza, Spain.,Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Fundacion ARAID, Government of Aragon, Zaragoza, Spain
| | - Donatella Bulone
- Institute of Biophysics, UOS Palermo, National Research Council, Italy
| | - Jatin Narang
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA
| | | | - Francesco Cappello
- Department of Biomedicine and Clinical Neurosciences, Human Anatomy Section, University of Palermo, Palermo, Italy.,Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Alberto J L Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy.,Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, USA.,Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD, USA
| | - Everly Conway de Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy.,Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, USA.,Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD, USA
| | - Frank T Robb
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA.,Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, USA.,Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD, USA
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21
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Nakamura T, Oshima M, Yasuda M, Shimamura A, Morita J, Uegaki K. Alteration of molecular assembly of peroxiredoxins from hyperthermophilic archaea. J Biochem 2017; 162:415-422. [DOI: 10.1093/jb/mvx045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/09/2017] [Indexed: 11/14/2022] Open
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22
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Morais MAB, Giuseppe PO, Souza TACB, Castro H, Honorato RV, Oliveira PSL, Netto LES, Tomas AM, Murakami MT. Calcium and magnesium ions modulate the oligomeric state and function of mitochondrial 2-Cys peroxiredoxins in Leishmania parasites. J Biol Chem 2017; 292:7023-7039. [PMID: 28292930 PMCID: PMC5409470 DOI: 10.1074/jbc.m116.762039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/07/2017] [Indexed: 12/16/2022] Open
Abstract
Leishmania parasites have evolved a number of strategies to cope with the harsh environmental changes during mammalian infection. One of these mechanisms involves the functional gain that allows mitochondrial 2-Cys peroxiredoxins to act as molecular chaperones when forming decamers. This function is critical for parasite infectivity in mammals, and its activation has been considered to be controlled exclusively by the enzyme redox state under physiological conditions. Herein, we have revealed that magnesium and calcium ions play a major role in modulating the ability of these enzymes to act as molecular chaperones, surpassing the redox effect. These ions are directly involved in mitochondrial metabolism and participate in a novel mechanism to stabilize the decameric form of 2-Cys peroxiredoxins in Leishmania mitochondria. Moreover, we have demonstrated that a constitutively dimeric Prx1m mutant impairs the survival of Leishmania under heat stress, supporting the central role of the chaperone function of Prx1m for Leishmania parasites during the transition from insect to mammalian hosts.
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Affiliation(s)
- Mariana A B Morais
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil
| | - Priscila O Giuseppe
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil
| | - Tatiana A C B Souza
- the Proteomics and Protein Engineering Laboratory, Carlos Chagas Institute, Fiocruz, Rua Professor Algacyr Munhoz Mader 2135, 81310-020 Curitiba/PR, Brazil
| | - Helena Castro
- the i3S-Institute for Investigation and Innovation in Health, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- the Institute of Molecular and Cell Biology (IBMC), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Rodrigo V Honorato
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil
| | - Paulo S L Oliveira
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil
| | - Luis E S Netto
- the Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of the State of São Paulo, Rua do Matão 14, 05508-090 São Paulo/SP, Brazil, and
| | - Ana M Tomas
- the i3S-Institute for Investigation and Innovation in Health, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- the Institute of Molecular and Cell Biology (IBMC), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- the Abel Salazar Biomedical Sciences Institute, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Mario T Murakami
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil,
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Ledgerwood EC, Marshall JW, Weijman JF. The role of peroxiredoxin 1 in redox sensing and transducing. Arch Biochem Biophys 2017; 617:60-67. [DOI: 10.1016/j.abb.2016.10.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/06/2016] [Accepted: 10/14/2016] [Indexed: 12/11/2022]
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Si M, Wang T, Pan J, Lin J, Chen C, Wei Y, Lu Z, Wei G, Shen X. Graded Response of the Multifunctional 2-Cysteine Peroxiredoxin, CgPrx, to Increasing Levels of Hydrogen Peroxide in Corynebacterium glutamicum. Antioxid Redox Signal 2017; 26:1-14. [PMID: 27324811 DOI: 10.1089/ars.2016.6650] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIMS Eukaryotic typical 2-cysteine (Cys) peroxiredoxins (Prxs) are multifunctional proteins subjected to complex regulation and play important roles in oxidative stress resistance, hydrogen peroxide (H2O2) signaling modulation, aging, and cancer, but the information on the biochemical functions and regulation mechanisms of prokaryotic atypical 2-Cys Prxs is largely lacking. RESULTS In this study, we show that at low peroxide concentrations, the atypical 2-Cys Prx in Corynebacterium glutamicum (CgPrx) mainly exists as monomers and displays thioredoxin (Trx)-dependent peroxidase activity. Moderate oxidative stress causes reversible S-mycothiolation of the H2O2-sensing Cys63 residue, which keeps CgPrx exclusively in dimer form with neither peroxidase nor chaperone activity. Then, the increased levels of H2O2 could act as a messenger to oxidize the redox-sensitive regulator hydrogen peroxide-inducible gene activator, leading to activation of expression of the more efficient mycothiol peroxidase and catalase to eliminate excessive peroxide. If oxidative stress is too severe, the H2O2-sensing Cys63 becomes hyperoxidized to sulfonic acid, which irreversibly inactivates the peroxidase activity, and most of CgPrx will be converted to multimeric chaperones for salvage of damaged proteins. INNOVATION We demonstrate for the first time that atypical 2-Cys CgPrx acts as both a Trx-dependent peroxidase and a molecular chaperone and plays a regulatory role in modulating the peroxide-mediated signaling cascades. CONCLUSION These results reveal that CgPrx functions as a multifunctional protein crucial for adapting appropriate responses to different levels of oxidative challenge in C. glutamicum. Antioxid. Redox Signal. 26, 1-14.
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Affiliation(s)
- Meiru Si
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University , Yangling, China .,2 College of Plant Protection, Northwest A&F University , Yangling, China
| | - Tietao Wang
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University , Yangling, China
| | - Junfeng Pan
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University , Yangling, China
| | - Jinshui Lin
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University , Yangling, China
| | - Can Chen
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University , Yangling, China
| | - Yahong Wei
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University , Yangling, China
| | - Zhiqiang Lu
- 2 College of Plant Protection, Northwest A&F University , Yangling, China
| | - Gehong Wei
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University , Yangling, China
| | - Xihui Shen
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University , Yangling, China
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Chung MC, Alem F, Hamer SG, Narayanan A, Shatalin K, Bailey C, Nudler E, Hakami RM. S-nitrosylation of peroxiredoxin 1 contributes to viability of lung epithelial cells during Bacillus anthracis infection. Biochim Biophys Acta Gen Subj 2016; 1861:3019-3029. [PMID: 27612662 DOI: 10.1016/j.bbagen.2016.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/30/2016] [Accepted: 09/04/2016] [Indexed: 11/24/2022]
Abstract
BACKGROUND Using Bacillus anthracis as a model gram-positive bacterium, we investigated the effects of host protein S-nitrosylation during bacterial infection. B. anthracis possesses a bacterial nitric oxide synthase (bNOS) that is important for its virulence and survival. However, the role of S-nitrosylation of host cell proteins during B. anthracis infection has not been determined. METHODS Nitrosoproteomic analysis of human small airway epithelial cells (HSAECs) infected with toxigenic B. anthracis Sterne was performed, identifying peroxiredoxin 1 (Prx1) as one predominant target. Peroxidase activity of Prx during infection was measured using 2-Cys-Peroxiredoxin activity assay. Chaperone activity of S-nitrosylated Prx1 was measured by insulin aggregation assay, and analysis of formation of multimeric species using Native PAGE. Griess assay and DAF-2DA fluorescence assay were used to measure NO production. Cell viability was measured using the Alamar Blue assay and the ATPlite assay (Perkin Elmer). RESULTS S-nitrosylation of Prx1 in Sterne-infected HSAECs leads to a decrease in its peroxidase activity while enhancing its chaperone function. Treatment with bNOS inhibitor, or infection with bNOS deletion strain, reduces S-nitrosylation of Prx1 and decreases host cell survival. Consistent with this, siRNA knockdown of Prx1 lowers bNOS-dependent protection of HSAEC viability. CONCLUSIONS Anthrax infection results in S-nitrosylation of multiple host proteins, including Prx1. The nitrosylation-dependent decrease in peroxidase activity of Prx1 and increase in its chaperone activity is one factor contributing to enhancing infected cell viability. GENERAL SIGNIFICANCE These results provide a new venue of mechanistic investigation for inhalational anthrax that could lead to novel and potentially effective countermeasures.
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Affiliation(s)
- Myung-Chul Chung
- School of Systems Biology, and the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA
| | - Farhang Alem
- School of Systems Biology, and the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA
| | - Sarah G Hamer
- School of Systems Biology, and the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA
| | - Aarthi Narayanan
- School of Systems Biology, and the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA
| | - Konstantin Shatalin
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Charles Bailey
- School of Systems Biology, and the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Ramin M Hakami
- School of Systems Biology, and the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA.
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Liebthal M, Strüve M, Li X, Hertle Y, Maynard D, Hellweg T, Viehhauser A, Dietz KJ. Redox-Dependent Conformational Dynamics of Decameric 2-Cysteine Peroxiredoxin and its Interaction with Cyclophilin 20-3. PLANT & CELL PHYSIOLOGY 2016; 57:1415-1425. [PMID: 26872837 DOI: 10.1093/pcp/pcw031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/23/2016] [Indexed: 05/20/2023]
Abstract
2-Cysteine peroxiredoxins (2-CysPrxs) switch between functions as a thiol peroxidase, chaperone, an interaction partner and possibly a proximity-based oxidase in a redox-dependent manner. In photosynthetic eukaryotes, 2-CysPrx localizes to the plastid, functions in the context of photosynthesis and enables an ascorbate peroxidase-independent water-water cycle for detoxifying H2O2 The high degree of evolutionary conservation of 2-CysPrx suggests that the switching is an essential characteristic and needed to transduce redox information to downstream pathways and regulation. The study aimed at exploring the dissociation behavior of 2-CysPrx and its interactions with cyclophilin depending on bulk phase conditions. Isothermal titration microcalorimetry (ITC), dynamic light scattering and size exclusion chromatography (SEC) proved the previously suggested model that reduced 2-CysPrx below a critical transition concentration (CTC) exists in its dimeric state, and above the CTC adopts the decameric state. The presence of cyclophilin 20-3 (Cyp20-3) affected the CTC of a 2-CysPrx decamer suggesting interaction which was further quantified by direct titration of 2-CysPrx with Cyp20-3, and in overlays. Finally catalytic inactivation assays showed the higher catalytic efficiency of 2-CysPrx at pH 8 compared with pH 7.2, but also revealed increased inactivation by hyperoxidation at pH 8. Interestingly, calculation of the average turnover number until inactivation gave rather similar values of 243 and 268 catalytic cycles at pH 8 and pH 7.2, respectively. These quantitative data support a model where 2-CysPrx and Cyp20-3, by interaction, form a redox-sensitive regulatory module in the chloroplast which is under control of the photosynthesis-linked stromal pH value, the redox state and additional stromal protein factor(s).
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Affiliation(s)
- Michael Liebthal
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Germany
| | - Marcel Strüve
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Germany
| | - Xin Li
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Germany
| | - Yvonne Hertle
- Department of Physical and Biophysical Chemistry, Faculty of Chemistry, University of Bielefeld, Germany
| | - Daniel Maynard
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Germany
| | - Thomas Hellweg
- Department of Physical and Biophysical Chemistry, Faculty of Chemistry, University of Bielefeld, Germany
| | - Andrea Viehhauser
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Germany
| | - Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, Germany
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Poole LB, Nelson KJ. Distribution and Features of the Six Classes of Peroxiredoxins. Mol Cells 2016; 39:53-9. [PMID: 26810075 PMCID: PMC4749874 DOI: 10.14348/molcells.2016.2330] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 12/09/2015] [Indexed: 12/03/2022] Open
Abstract
Peroxiredoxins are cysteine-dependent peroxide reductases that group into 6 different, structurally discernable classes. In 2011, our research team reported the application of a bioinformatic approach called active site profiling to extract active site-proximal sequence segments from the 29 distinct, structurally-characterized peroxiredoxins available at the time. These extracted sequences were then used to create unique profiles for the six groups which were subsequently used to search GenBank(nr), allowing identification of ∼3500 peroxiredoxin sequences and their respective subgroups. Summarized in this minireview are the features and phylogenetic distributions of each of these peroxiredoxin subgroups; an example is also provided illustrating the use of the web accessible, searchable database known as PREX to identify subfamily-specific peroxiredoxin sequences for the organism Vitis vinifera (grape).
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Affiliation(s)
- Leslie B. Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157,
USA
| | - Kimberly J. Nelson
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157,
USA
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109,
USA
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Toledano MB, Huang B. Microbial 2-Cys Peroxiredoxins: Insights into Their Complex Physiological Roles. Mol Cells 2016; 39:31-9. [PMID: 26813659 PMCID: PMC4749871 DOI: 10.14348/molcells.2016.2326] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 11/27/2022] Open
Abstract
The peroxiredoxins (Prxs) constitute a very large and highly conserved family of thiol-based peroxidases that has been discovered only very recently. We consider here these enzymes through the angle of their discovery, and of some features of their molecular and physiological functions, focusing on complex phenotypes of the gene mutations of the 2-Cys Prxs subtype in yeast. As scavengers of the low levels of H2O2 and as H2O2 receptors and transducers, 2-Cys Prxs have been highly instrumental to understand the biological impact of H2O2, and in particular its signaling function. 2-Cys Prxs can also become potent chaperone holdases, and unveiling the in vivo relevance of this function, which is still not established, should further increase our knowledge of the biological impact and toxicity of H2O2. The diverse molecular functions of 2-Cys Prx explain the often-hard task of relating them to peroxiredoxin genes phenotypes, which underscores the pleiotropic physiological role of these enzymes and complex biologic impact of H2O2.
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Affiliation(s)
- Michel B. Toledano
- CEA, DSV, IBITECS, SBIGEM, Laboratoire Stress Oxydant et Cancer (LSOC), CEA-Saclay, 91191 Gif-sur-Yvette,
France
| | - Bo Huang
- CEA, DSV, IBITECS, SBIGEM, Laboratoire Stress Oxydant et Cancer (LSOC), CEA-Saclay, 91191 Gif-sur-Yvette,
France
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29
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Kinetic analysis of structural influences on the susceptibility of peroxiredoxins 2 and 3 to hyperoxidation. Biochem J 2015; 473:411-21. [PMID: 26614766 DOI: 10.1042/bj20150572] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/27/2015] [Indexed: 02/06/2023]
Abstract
Mammalian 2-cysteine peroxiredoxins (Prxs) are susceptible to hyperoxidation by excess H2O2. The cytoplasmic family member Prx2 hyperoxidizes more readily than mitochondrial Prx3 due to slower dimerization of the sulfenic acid (SpOH) intermediate. Four variant amino acids near the C-terminus have been shown to contribute to this difference. We have performed kinetic analysis of the relationship between hyperoxidation and disulfide formation, using whole-protein MS and comparing wild-type (WT) Prx2 and Prx3 with tail-swap mutants in which the four amino acids were reversed. These changes make Prx3 more sensitive and Prx2 less sensitive to hyperoxidation and accounted for ∼70% of the difference between the two proteins. The tail swap mutant of Prx3 was also more susceptible when expressed in the mitochondria of HeLa cells. The hyperoxidized product at lower excesses of H2O2 was a semi-hyperoxidized dimer with one active site disulfide and the other a sulfinic acid. For Prx2, increasing the H2O2 concentration resulted in complete hyperoxidation. In contrast, only approximately half the Prx3 active sites underwent hyperoxidation and, even with high H2O2, the predominant product was the hyperoxidized dimer. Size exclusion chromatography (SEC) showed that the oligomeric forms of all redox states of Prx3 dissociated more readily into dimeric units than their Prx2 counterparts. Notably the species with one disulfide and one hyperoxidized active site was decameric for Prx2 and dimeric for Prx3. Reduction and re-oxidation of the hyperoxidized dimer of Prx3 produced hyperoxidized monomers, implying dissociation and rearrangement of the subunits of the functional homodimer.
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30
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Noichri Y, Palais G, Ruby V, D'Autreaux B, Delaunay-Moisan A, Nyström T, Molin M, Toledano MB. In vivo parameters influencing 2-Cys Prx oligomerization: The role of enzyme sulfinylation. Redox Biol 2015; 6:326-333. [PMID: 26335398 PMCID: PMC4556779 DOI: 10.1016/j.redox.2015.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 11/28/2022] Open
Abstract
2-Cys Prxs are H2O2-specific antioxidants that become inactivated by enzyme hyperoxidation at elevated H2O2 levels. Although hyperoxidation restricts the antioxidant physiological role of these enzymes, it also allows the enzyme to become an efficient chaperone holdase. The critical molecular event allowing the peroxidase to chaperone switch is thought to be the enzyme assembly into high molecular weight (HMW) structures brought about by enzyme hyperoxidation. How hyperoxidation promotes HMW assembly is not well understood and Prx mutants allowing disentangling its peroxidase and chaperone functions are lacking. To begin addressing the link between enzyme hyperoxidation and HMW structures formation, we have evaluated the in vivo 2-Cys Prxs quaternary structure changes induced by H2O2 by size exclusion chromatography (SEC) on crude lysates, using wild type (Wt) untagged and Myc-tagged S. cerevisiae 2-Cys Prx Tsa1 and derivative Tsa1 mutants or genetic conditions known to inactivate peroxidase or chaperone activity or altering the enzyme sensitivity to hyperoxidation. Our data confirm the strict causative link between H2O2-induced hyperoxidation and HMW formation/stabilization, also raising the question of whether CP hyperoxidation triggers the assembly of HMW structures by the stacking of decamers, which is the prevalent view of the literature, or rather, the stabilization of preassembled stacked decamers.
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Affiliation(s)
- Y Noichri
- Oxidative Stress and Cancer, IBITECS, SBIGEM, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - G Palais
- Oxidative Stress and Cancer, IBITECS, SBIGEM, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - V Ruby
- Oxidative Stress and Cancer, IBITECS, SBIGEM, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - B D'Autreaux
- Oxidative Stress and Cancer, IBITECS, SBIGEM, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - A Delaunay-Moisan
- Oxidative Stress and Cancer, IBITECS, SBIGEM, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - T Nyström
- Department of Chemistry and Molecular Biology (CMB), University of Gothenburg, Medicinaregatan 9C, S-413 90 Göteborg, Sweden
| | - M Molin
- Department of Chemistry and Molecular Biology (CMB), University of Gothenburg, Medicinaregatan 9C, S-413 90 Göteborg, Sweden
| | - M B Toledano
- Oxidative Stress and Cancer, IBITECS, SBIGEM, CEA-Saclay, 91191 Gif-sur-Yvette, France.
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31
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Dip PV, Kamariah N, Nartey W, Beushausen C, Kostyuchenko VA, Ng TS, Lok SM, Saw WG, Eisenhaber F, Eisenhaber B, Grüber G. Key roles of the Escherichia coli AhpC C-terminus in assembly and catalysis of alkylhydroperoxide reductase, an enzyme essential for the alleviation of oxidative stress. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1837:1932-1943. [PMID: 25193562 DOI: 10.1016/j.bbabio.2014.08.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/19/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
2-Cys peroxiredoxins (Prxs) are a large family of peroxidases, responsible for antioxidant function and regulation in cell signaling, apoptosis and differentiation. The Escherichia coli alkylhydroperoxide reductase (AhpR) is a prototype of the Prxs-family, and is composed of an NADH-dependent AhpF reductase (57 kDa) and AhpC (21 kDa), catalyzing the reduction of H2O2. We show that the E. coli AhpC (EcAhpC, 187 residues) forms a decameric ring structure under reduced and close to physiological conditions, composed of five catalytic dimers. Single particle analysis of cryo-electron micrographs of C-terminal truncated (EcAhpC1 -172 and EcAhpC1 -182) and mutated forms of EcAhpC reveals the loss of decamer formation, indicating the importance of the very C-terminus of AhpC in dimer to decamer transition. The crystallographic structures of the truncated EcAhpC1 -172 and EcAhpC1 -182 demonstrate for the first time that, in contrast to the reduced form, the very C-terminus of the oxidized EcAhpC is oriented away from the AhpC dimer interface and away from the catalytic redox-center, reflecting structural rearrangements during redox-modulation and -oligomerization. Furthermore, using an ensemble of different truncated and mutated EcAhpC protein constructs the importance of the very C-terminus in AhpC activity and in AhpC-AhpF assembly has been demonstrated.
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Affiliation(s)
- Phat Vinh Dip
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551; Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, KTP Building, 8 College Road, Singapore 169857; Center for Bioimaging Sciences, Dept. of Biological Sciences, National University of Singapore, Singapore 119077
| | - Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551
| | - Claudia Beushausen
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551
| | - Victor A Kostyuchenko
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, KTP Building, 8 College Road, Singapore 169857; Center for Bioimaging Sciences, Dept. of Biological Sciences, National University of Singapore, Singapore 119077
| | - Thiam-Seng Ng
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, KTP Building, 8 College Road, Singapore 169857; Center for Bioimaging Sciences, Dept. of Biological Sciences, National University of Singapore, Singapore 119077
| | - Shee-Mei Lok
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, KTP Building, 8 College Road, Singapore 169857; Center for Bioimaging Sciences, Dept. of Biological Sciences, National University of Singapore, Singapore 119077
| | - Wuan Geok Saw
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671; School of Computer Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553; Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore 117597
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551; Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.
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Camejo D, Ortiz-Espín A, Lázaro JJ, Romero-Puertas MC, Lázaro-Payo A, Sevilla F, Jiménez A. Functional and structural changes in plant mitochondrial PrxII F caused by NO. J Proteomics 2015; 119:112-25. [PMID: 25682994 DOI: 10.1016/j.jprot.2015.01.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 01/16/2015] [Accepted: 01/29/2015] [Indexed: 11/17/2022]
Abstract
Peroxiredoxins (Prxs) have emerged as important factors linking reactive oxygen species (ROS) metabolism to redox-dependent signaling events. Together with ROS, nitric oxide (NO) is a free radical product of the cell metabolism that is essential in the signal transduction. S-Nitrosylation is emerging as a fundamental protein modification for the transduction of NO bioactivity. Using recombinant pea mitochondrial PsPrxII F (PrxII F), the effect of S-nitrosoglutathione (GSNO) and sodium nitroprusside dehydrate (SNP), which are known to mediate protein S-nitrosylation processes, was studied. S-Nitrosylation of the PrxII F was demonstrated using the biotin switch method and LC ESI-QTOF tandem MS analysis. S-nitrosylated PrxII F decreased its peroxidase activity and acquired a new transnitrosylase activity, preventing the thermal aggregation of citrate synthase (CS). For the first time, we demonstrate the dual function for PrxII F as peroxidase and transnitrosylase. This switch was accompanied by a conformational change of the protein that could favor the protein-protein interaction CS-PrxII F. The observed in vivo S-nitrosylation of PrxII F could probably function as a protective mechanism under oxidative and nitrosative stress, such as occurs under salinity. We conclude that we are dealing with a novel regulatory mechanism for this protein by NO. BIOLOGICAL SIGNIFICANCE S-Nitrosylation is a post-translational modification that is increasingly viewed as fundamental for the signal transduction role of NO in plants. This study demonstrates that S-nitrosylation of the mitochondrial peroxiredoxin PrxII F induces a conformational change in the protein and provokes a reduction in its peroxidase activity, while acquiring a novel function as transnitrosylase. The implication of this mechanism will increase our understanding of the role of posttranslational modifications in the protein function in plants under stress situations such as salinity, in which NO could act as signaling molecule.
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Affiliation(s)
- Daymi Camejo
- CEBAS-CSIC, Department of Stress Biology and Plant Pathology, E-30100 Murcia, Spain.
| | - Ana Ortiz-Espín
- CEBAS-CSIC, Department of Stress Biology and Plant Pathology, E-30100 Murcia, Spain.
| | - Juan J Lázaro
- EEZ-CSIC, Department of Biochemistry, Cellular and Molecular Biology of Plants, E-18080 Granada, Spain.
| | - María C Romero-Puertas
- EEZ-CSIC, Department of Biochemistry, Cellular and Molecular Biology of Plants, E-18080 Granada, Spain.
| | - Alfonso Lázaro-Payo
- EEZ-CSIC, Department of Biochemistry, Cellular and Molecular Biology of Plants, E-18080 Granada, Spain.
| | - Francisca Sevilla
- CEBAS-CSIC, Department of Stress Biology and Plant Pathology, E-30100 Murcia, Spain.
| | - Ana Jiménez
- CEBAS-CSIC, Department of Stress Biology and Plant Pathology, E-30100 Murcia, Spain.
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Abstract
Peroxiredoxins were not recognized as a family of enzymes until the 1990s but are now known to be the dominant peroxidases in most organisms. Here, the history and fundamental properties of peroxiredoxins are briefly reviewed, with a special focus on describing how an exquisitely tunable balance between fully folded and locally unfolded conformations plays a large role in peroxiredoxin catalytic properties.
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Affiliation(s)
- P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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34
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Mitochondrial peroxiredoxin functions as crucial chaperone reservoir in Leishmania infantum. Proc Natl Acad Sci U S A 2015; 112:E616-24. [PMID: 25646478 DOI: 10.1073/pnas.1419682112] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cytosolic eukaryotic 2-Cys-peroxiredoxins have been widely reported to act as dual-function proteins, either detoxifying reactive oxygen species or acting as chaperones to prevent protein aggregation. Several stimuli, including peroxide-mediated sulfinic acid formation at the active site cysteine, have been proposed to trigger the chaperone activity. However, the mechanism underlying this activation and the extent to which the chaperone function is crucial under physiological conditions in vivo remained unknown. Here we demonstrate that in the vector-borne protozoan parasite Leishmania infantum, mitochondrial peroxiredoxin (Prx) exerts intrinsic ATP-independent chaperone activity, protecting a wide variety of different proteins against heat stress-mediated unfolding in vitro and in vivo. Activation of the chaperone function appears to be induced by temperature-mediated restructuring of the reduced decamers, promoting binding of unfolding client proteins in the center of Prx's ringlike structure. Client proteins are maintained in a folding-competent conformation until restoration of nonstress conditions, upon which they are released and transferred to ATP-dependent chaperones for refolding. Interference with client binding impairs parasite infectivity, providing compelling evidence for the in vivo importance of Prx's chaperone function. Our results suggest that reduced Prx provides a mitochondrial chaperone reservoir, which allows L. infantum to deal successfully with protein unfolding conditions during the transition from insect to the mammalian hosts and to generate viable parasites capable of perpetuating infection.
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Bernal-Bayard P, Ojeda V, Hervás M, Cejudo FJ, Navarro JA, Velázquez-Campoy A, Pérez-Ruiz JM. Molecular recognition in the interaction of chloroplast 2-Cys peroxiredoxin with NADPH-thioredoxin reductase C (NTRC) and thioredoxinx. FEBS Lett 2014; 588:4342-7. [DOI: 10.1016/j.febslet.2014.09.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 09/25/2014] [Accepted: 09/25/2014] [Indexed: 12/30/2022]
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Benfeitas R, Selvaggio G, Antunes F, Coelho PMBM, Salvador A. Hydrogen peroxide metabolism and sensing in human erythrocytes: a validated kinetic model and reappraisal of the role of peroxiredoxin II. Free Radic Biol Med 2014; 74:35-49. [PMID: 24952139 DOI: 10.1016/j.freeradbiomed.2014.06.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/26/2014] [Accepted: 06/10/2014] [Indexed: 01/09/2023]
Abstract
Hydrogen peroxide (H2O2) metabolism in human erythrocytes has been thoroughly investigated, but unclear points persist. By integrating the available data into a mathematical model that accurately represents the current understanding and comparing computational predictions to observations we sought to (a) identify inconsistencies in present knowledge, (b) propose resolutions, and (c) examine their functional implications. The systematic confrontation of computational predictions with experimental observations of the responses of intact erythrocytes highlighted the following important discrepancy. The high rate constant (10(7)-10(8) M(-1) s(-1)) for H2O2 reduction determined for purified peroxiredoxin II (Prx2) and the high abundance of this protein indicate that under physiological conditions it consumes practically all the H2O2. However, this is inconsistent with extensive evidence that Prx2's contribution to H2O2 elimination is comparable to that of catalase. Models modified such that Prx2's effective peroxidase activity is just 10(5) M(-1) s(-1) agree near quantitatively with extensive experimental observations. This low effective activity is probably due to a strong but readily reversible inhibition of Prx2's peroxidatic activity in intact cells, implying that the main role of Prx2 in human erythrocytes is not to eliminate peroxide substrates. Simulations of the responses to physiological H2O2 stimuli highlight that a design combining abundant Prx2 with a low effective peroxidase activity spares NADPH while improving potential signaling properties of the Prx2/thioredoxin/thioredoxin reductase system.
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Affiliation(s)
- Rui Benfeitas
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Gianluca Selvaggio
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Fernando Antunes
- Departamento de Química e Bioquímica and Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro M B M Coelho
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Armindo Salvador
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; Coimbra Chemistry Center, University of Coimbra, 3004-535 Coimbra, Portugal.
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Kabiri M, Bushnak I, McDermot MT, Unsworth LD. Toward a Mechanistic Understanding of Ionic Self-Complementary Peptide Self-Assembly: Role of Water Molecules and Ions. Biomacromolecules 2013; 14:3943-50. [DOI: 10.1021/bm401077b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | | | - Mark T. McDermot
- NanoLife
Group, National Institute for Nanotechnology, National Research Council (Canada), Edmonton, Alberta, Canada
| | - Larry D. Unsworth
- NanoLife
Group, National Institute for Nanotechnology, National Research Council (Canada), Edmonton, Alberta, Canada
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König J, Galliardt H, Jütte P, Schäper S, Dittmann L, Dietz KJ. The conformational bases for the two functionalities of 2-cysteine peroxiredoxins as peroxidase and chaperone. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3483-97. [PMID: 23828546 PMCID: PMC3733160 DOI: 10.1093/jxb/ert184] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
2-Cysteine peroxiredoxins (2-CysPrxs) are ubiquitous and highly abundant proteins that serve multiple functions as peroxidases, chaperones, and thiol oxidases and in redox-dependent cell signalling. The chloroplast protein plays a role in seedling development and protection of the photosynthetic apparatus. This study aimed to unequivocally link conformation and function. To this end, a set of non-tagged site-directed mutagenized At2-CysPrx variants was engineered, which mimicked the conformational states and their specific functions: hyperoxidized form (C54D), reduced form (C54S, C176S), oxidized form (C54DC176K), phosphorylated form (T92D), reduced ability for oligomerization by interfering with the dimer-dimer interface (F84R) and a C-terminally truncated form [ΔC (-20 aa)]. These variants were fully or partly fixed in their quaternary structure and function, respectively, and were analysed for their conformational state and peroxidase and chaperone activity, as well as for their sensitivity to hyperoxidation. The presence of a His6-tag strongly influenced the properties of the protein. The ΔC variant became insensitive to hyperoxidation, while T92D and F84R became more sensitive. The C54D variant revealed the highest chaperone activity. The highest peroxidase activity was observed for the F84R and ΔC variants. Efficient interaction with NADP-dependent thioredoxin reductase C depended on the presence of Cys residues and the C-terminal tail. The results suggest that the structural flexibility is important for the switch between peroxidase and chaperone function and that evolution has conserved the functional switch instead of maximizing a single function. These variants are ideal tools for future conformation-specific studies in vivo and in vitro.
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Saccoccia F, Di Micco P, Boumis G, Brunori M, Koutris I, Miele AE, Morea V, Sriratana P, Williams DL, Bellelli A, Angelucci F. Moonlighting by different stressors: crystal structure of the chaperone species of a 2-Cys peroxiredoxin. Structure 2012; 20:429-39. [PMID: 22405002 DOI: 10.1016/j.str.2012.01.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/02/2011] [Accepted: 01/03/2012] [Indexed: 11/29/2022]
Abstract
2-Cys peroxiredoxins (Prxs) play two different roles depending on the physiological status of the cell. They are thioredoxin-dependent peroxidases under low oxidative stress and ATP-independent chaperones upon exposure to high peroxide concentrations. These alternative functions have been associated with changes in the oligomerization state from low-(LMW) to high-molecular-weight (HMW) species. Here we present the structures of Schistosoma mansoni PrxI in both states: the LMW decamer and the HMW 20-mer formed by two stacked decamers. The latter is the structure of a 2-Cys Prx chaperonic form. Comparison of the structures sheds light on the mechanism by which chemical stressors, such as high H(2)O(2) concentration and acidic pH, are sensed and translated into a functional switch in this protein family. We also propose a model to account for the in vivo formation of long filaments of stacked Prx rings.
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Affiliation(s)
- Fulvio Saccoccia
- Department of Biochemical Sciences, Sapienza University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185 Rome, Italy
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40
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Abstract
Peroxiredoxins (Prx) are central elements of the antioxidant defense system and the dithiol-disulfide redox regulatory network of the plant and cyanobacterial cell. They employ a thiol-based catalytic mechanism to reduce H2O2, alkylhydroperoxide, and peroxinitrite. In plants and cyanobacteria, there exist 2-CysPrx, 1-CysPrx, PrxQ, and type II Prx. Higher plants typically contain at least one plastid 2-CysPrx, one nucleo-cytoplasmic 1-CysPrx, one chloroplast PrxQ, and one each of cytosolic, mitochondrial, and plastidic type II Prx. Cyanobacteria express variable sets of three or more Prxs. The catalytic cycle consists of three steps: (i) peroxidative reduction, (ii) resolving step, and (iii) regeneration using diverse electron donors such as thioredoxins, glutaredoxins, cyclophilins, glutathione, and ascorbic acid. Prx proteins undergo major conformational changes in dependence of their redox state. Thus, they not only modulate cellular reactive oxygen species- and reactive nitrogen species-dependent signaling, but depending on the Prx type they sense the redox state, transmit redox information to binding partners, and function as chaperone. They serve in context of photosynthesis and respiration, but also in metabolism and development of all tissues, for example, in nodules as well as during seed and fruit development. The article surveys the current literature and attempts a mostly comprehensive coverage of present day knowledge and concepts on Prx mechanism, regulation, and function and thus on the whole Prx systems in plants.
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Affiliation(s)
- Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Bielefeld University, Bielefeld, Germany.
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41
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Abstract
Peroxiredoxins (Prx) are central elements of the antioxidant defense system and the dithiol-disulfide redox regulatory network of the plant and cyanobacterial cell. They employ a thiol-based catalytic mechanism to reduce H2O2, alkylhydroperoxide, and peroxinitrite. In plants and cyanobacteria, there exist 2-CysPrx, 1-CysPrx, PrxQ, and type II Prx. Higher plants typically contain at least one plastid 2-CysPrx, one nucleo-cytoplasmic 1-CysPrx, one chloroplast PrxQ, and one each of cytosolic, mitochondrial, and plastidic type II Prx. Cyanobacteria express variable sets of three or more Prxs. The catalytic cycle consists of three steps: (i) peroxidative reduction, (ii) resolving step, and (iii) regeneration using diverse electron donors such as thioredoxins, glutaredoxins, cyclophilins, glutathione, and ascorbic acid. Prx proteins undergo major conformational changes in dependence of their redox state. Thus, they not only modulate cellular reactive oxygen species- and reactive nitrogen species-dependent signaling, but depending on the Prx type they sense the redox state, transmit redox information to binding partners, and function as chaperone. They serve in context of photosynthesis and respiration, but also in metabolism and development of all tissues, for example, in nodules as well as during seed and fruit development. The article surveys the current literature and attempts a mostly comprehensive coverage of present day knowledge and concepts on Prx mechanism, regulation, and function and thus on the whole Prx systems in plants.
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Affiliation(s)
- Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Bielefeld University, Bielefeld, Germany.
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Nirudodhi S, Parsonage D, Karplus PA, Poole LB, Maier CS. Conformational studies of the robust 2-Cys peroxiredoxin Salmonella typhimurium AhpC by solution phase hydrogen/deuterium (H/D) exchange monitored by electrospray ionization mass spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 302:93-100. [PMID: 21516234 PMCID: PMC3079231 DOI: 10.1016/j.ijms.2010.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This is the first comprehensive HX-MS study of a "robust" 2-Cys peroxiredoxin (Prx), namely Salmonella typhimurium AhpC (StAhpC). Prx proteins control intracellular peroxide levels and are abundant antioxidant proteins in eukaryotes, archaea and bacteria. Crystal structural analyses and structure/activity studies of several bacterial and mammalian 2-Cys Prxs have revealed that the activity of 2-Cys Prxs is regulated by redox-dependent oligmerization and a sensitivity of the active site cysteine residue to overoxidation. The propensity to overoxidation is linked to the conformational flexibility of the peroxidatic active site loop. The HX-MS results emphasize the modulation of the conformational motility of the active site loop by disulfide formation. To obtain information on the conformational impact of decamer formation on the active site loop motility, mutants with Thr77 substituted by Ile, a decamer-disrupting mutation or by Val, a decamer-stabilizing mutation, were studied. For the isoleucine mutant, enhanced mobility was observed for regions encompassing the α4 helix located in the dimer-dimer interface and regions surrounding the peroxidatic loop. In contrast, the T77V mutation resulted in an increase in conformational stability in most regions of the protein except for the active site loop and the region encompassing the resolving cysteine.
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Affiliation(s)
- Sasidhar Nirudodhi
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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43
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Dietz KJ, Pfannschmidt T. Novel regulators in photosynthetic redox control of plant metabolism and gene expression. PLANT PHYSIOLOGY 2011; 155:1477-85. [PMID: 21205617 PMCID: PMC3091116 DOI: 10.1104/pp.110.170043] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 12/23/2010] [Indexed: 05/18/2023]
Affiliation(s)
- Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany.
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44
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Iglesias-Baena I, Barranco-Medina S, Sevilla F, Lázaro JJ. The dual-targeted plant sulfiredoxin retroreduces the sulfinic form of atypical mitochondrial peroxiredoxin. PLANT PHYSIOLOGY 2011; 155:944-55. [PMID: 21139087 PMCID: PMC3032478 DOI: 10.1104/pp.110.166504] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 12/05/2010] [Indexed: 05/19/2023]
Abstract
Sulfiredoxin (Srx) couples the energy of ATP hydrolysis to the energetically unfavorable process of reducing the inactive sulfinic form of 2-cysteine peroxiredoxins (Prxs) to regenerate its active form. In plants, Srx as well as typical 2-cysteine Prx have been considered as enzymes with exclusive chloroplast localization. This work explores the subcellular localization of Srx in pea (Pisum sativum) and Arabidopsis (Arabidopsis thaliana). Immunocytochemistry, analysis of protein extracts from isolated intact organelles, and cell-free posttranslational import assays demonstrated that plant Srx also localizes to the mitochondrion in addition to plastids. The dual localization was in line with the prediction of a signal peptide for dual targeting. Activity tests and microcalorimetric data proved the interaction between Srx and its mitochondrial targets Prx IIF and thioredoxin. Srx catalyzed the retroreduction of the inactive sulfinic form of atypical Prx IIF using thioredoxin as reducing agent. Arabidopsis Srx also reduced overoxidized human Prx V. These results suggest that plant Srx could play a crucial role in the regulation of Prx IIF activity by controlling the regeneration of its overoxidized form in mitochondria, which are sites of efficient reactive oxygen species production in plants.
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Affiliation(s)
| | | | | | - Juan-José Lázaro
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E–18008, Granada, Spain (I.I.-B., S.B.-M., J.-J.L.); and Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, E–30080, Murcia, Spain (F.S.)
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45
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Dietz KJ, Jacquot JP, Harris G. Hubs and bottlenecks in plant molecular signalling networks. THE NEW PHYTOLOGIST 2010; 188:919-38. [PMID: 20958306 DOI: 10.1111/j.1469-8137.2010.03502.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Conditional control of plant cell function and development relies on appropriate signal perception, signal integration and processing. The development of high throughput technologies such as proteomics and interactomics has enabled the identification of protein interaction networks that mediate signal processing from inputs to appropriate outputs. Such networks can be depicted in graphical representations using nodes and edges allowing for the immediate visualization and analysis of the network's topology. Hubs are network elements characterized by many edges (often degree grade k ≥ 5) which confer a degree of topological importance to them. The review introduces the concept of networks, hubs and bottlenecks and describes four examples from plant science in more detail, namely hubs in the redox regulatory network of the chloroplast with ferredoxin, thioredoxin and peroxiredoxin, in mitogen activated protein (MAP) kinase signal processing, in photomorphogenesis with the COP9 signalosome, COP1 and CDD, and monomeric GTPase function. Some guidance is provided to appropriate internet resources, web repositories, databases and their use. Plant networks can be generated from existing public databases and this type of analysis is valuable in support of existing hypotheses, or to allow for the generation of new concepts or ideas. However, intensive manual curating of in silico networks is still always necessary.
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Affiliation(s)
- Karl-Josef Dietz
- Plant Biochemistry and Physiology, Bielefeld University, D-33501 Bielefeld, Germany.
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46
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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47
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Iglesias-Baena I, Barranco-Medina S, Lázaro-Payo A, López-Jaramillo FJ, Sevilla F, Lázaro JJ. Characterization of plant sulfiredoxin and role of sulphinic form of 2-Cys peroxiredoxin. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:1509-21. [PMID: 20176891 PMCID: PMC2837264 DOI: 10.1093/jxb/erq016] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 01/19/2010] [Accepted: 01/19/2010] [Indexed: 05/20/2023]
Abstract
The antioxidant function of 2-Cys peroxiredoxin (Prx) involves the oxidation of its conserved peroxidatic cysteine to sulphenic acid that is recycled by a reductor agent. In conditions of oxidative stress, the peroxidatic cysteine can be overoxidized to sulphinic acid inactivating the Prx. An enzyme recently discovered, named sulfiredoxin (Srx), reduces the sulphinic 2-Cys Prx (Prx-SO(2)H). To explore the physiological functions of Srx in plants we have cloned, expressed and purified to homogeneity a Srx from Arabidopsis thaliana (AtSrx), as well as five variants by site-directed mutagenesis on amino acids involved in its activity. The activity of sulfiredoxin, determined by a new method, is dependent on the concentration of the sulphinic form of Prx and the conserved Srx is capable of regenerating the functionality of both pea and Arabidopsis Prx-SO(2)H. Molecular modelling of AtSrx and the facts that the R28Q variant shows a partial inactivation, that the activity of the E76A variant is equivalent to that of the native enzyme and that the double mutation R28Q/E76A abolishes the enzymatic activity suggests that the pair His100-Glu76 may be involved in the activation of C72 in the absence of R28. The knock-out mutant plants without Srx or 2-Cys Prx exhibited phenotypical differences under growth conditions of 16 h light, probably due to the signalling role of the sulphinic form of Prx. These mutants showed more susceptibility to oxidative stress than wild-type plants. This work presents the first systematic biochemical characterization of the Srx/Prx system from plants and contributes to a better understanding of its physiological function.
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Affiliation(s)
- Iván Iglesias-Baena
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - Sergio Barranco-Medina
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - Alfonso Lázaro-Payo
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, E-18008 Granada, Spain
| | | | - Francisca Sevilla
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, E-30080 Murcia, Spain
| | - Juan-José Lázaro
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, E-18008 Granada, Spain
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48
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Mitochondrial peroxiredoxin involvement in antioxidant defence and redox signalling. Biochem J 2009; 425:313-25. [PMID: 20025614 DOI: 10.1042/bj20091541] [Citation(s) in RCA: 375] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Prxs (peroxiredoxins) are a family of proteins that are extremely effective at scavenging peroxides. The Prxs exhibit a number of intriguing properties that distinguish them from conventional antioxidants, including a susceptibility to inactivation by hyperoxidation in the presence of excess peroxide and the ability to form complex oligomeric structures. These properties, combined with a high cellular abundance and reactivity with hydrogen peroxide, have led to speculation that the Prxs function as redox sensors that transmit signals as part of the cellular response to oxidative stress. Multicellular organisms express several different Prxs that can be categorized by their subcellular distribution. In mammals, Prx 3 and Prx 5 are targeted to the mitochondrial matrix. Mitochondria are a major source of hydrogen peroxide, and this oxidant is implicated in the damage associated with aging and a number of pathologies. Hydrogen peroxide can also act as a second messenger, and is linked with signalling events in mitochondria, including the induction of apoptosis. A simple kinetic competition analysis estimates that Prx 3 will be the target for up to 90% of hydrogen peroxide generated in the matrix. Therefore, mitochondrial Prxs have the potential to play a major role in mitochondrial redox signalling, but the extent of this role and the mechanisms involved are currently unclear.
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49
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Barranco-Medina S, Dietz KJ. Thermodynamics of 2-Cys peroxiredoxin assembly determined by isothermal titration calorimetry. Methods Enzymol 2009; 466:409-30. [PMID: 21609870 DOI: 10.1016/s0076-6879(09)66017-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Oligomerization is a frequently encountered physical characteristic of biological molecules that occurs for a wide number of transcription factors, ion channels, oxygen-carrying macromolecules such as hemocyanin and enzymes. On the other hand, unwanted protein oligomerization can lead to the formation of pathogenic structures related with Alzheimer and other diseases. Self-assembly is also a well-described phenomenon within peroxiredoxins, a family of thiol peroxidases. Peroxiredoxin hyperaggregate formation is the key mechanism that triggers the switch between Prx activity as peroxidase and chaperone. The oligomerization process is fundamental for understanding the multiple peroxiredoxin function. The chapter gives a detailed description of typical 2-Cys Peroxiredoxin oligomerization using isothermal titration calorimetry (ITC) and provides a recipe for studying the thermodynamic parameters of peroxiredoxin assembly, that is, association and dissociation constant, enthalpy, entropy, and the Gibbs free energy of the process.
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50
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Muthuramalingam M, Seidel T, Laxa M, Nunes de Miranda SM, Gärtner F, Ströher E, Kandlbinder A, Dietz KJ. Multiple redox and non-redox interactions define 2-Cys peroxiredoxin as a regulatory hub in the chloroplast. MOLECULAR PLANT 2009; 2:1273-88. [PMID: 19995730 DOI: 10.1093/mp/ssp089] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In plants, the highly abundant 2-cysteine peroxiredoxin (2-CysPrx) is associated with the chloroplast and involved in protecting photosynthesis. This work addresses the multiple interactions of the 2-CysPrx in the chloroplast, which depend on its redox state. Transcript co-regulation analysis showed a strong linkage to the peptidyl-prolyl-cis/trans isomerase Cyclophilin 20-3 (Cyp20-3) and other components of the photosynthetic apparatus. Co-expression in protoplasts and quantification of fluorescence resonance energy transfer (FRET) efficiency in vivo confirmed protein interactions of 2-CysPrx with Cyp20-3 as well as NADPH-dependent thioredoxin reductase C (NTRC), while thioredoxin x (Trx-x) did not form complexes that could enable FRET. Likewise, changes in FRET of fluorescently labeled 2-CysPrx in vitro and in vivo proved redox dependent dynamics of 2-CysPrx. Addition of Cyp20-3 to an in vitro peroxidase assay with 2-CysPrx had no significant effect on peroxide reduction. Also, in the presence of NTRC, addition of Cyp20-3 did not further enhance peroxide reduction. In addition, 2-CysPrx functioned as chaperone and inhibited aggregation of citrate synthase during heat treatment. This activity was partly inhibited by Cyp20-3. As a new interaction partner of decameric 2-CysPrx, photosystem II could be identified after chloroplast fractionation and in pull-down assays after reconstitution. In summary, the data indicate a dynamic function of plant 2-CysPrx as redox sensor, chaperone, and regulator in the chloroplast with diverse functions beyond its role as thiol peroxidase.
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