1
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Sarkar B, Das A, Pal S, Kundu A, Hasanuzzaman M, Fujita M, Adak MK. Regulation of NADP-Malic Enzyme Activity in Maize ( Zea mays L.) under Salinity with Reference to Light and Darkness. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091836. [PMID: 37176895 PMCID: PMC10181391 DOI: 10.3390/plants12091836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
We revealed the functional characterization of C4-NADP-malic enzyme (NADP-ME), extracted and partially purified from maize (Zea mays L. cv. Kaveri 50). The leaf discs were previously activated under 1000-1200 µE m-2 s-1, incubated in bicarbonate (2.0 mM) solution, and subjected to salt stress (100 mM NaCl). Initially, salt stress was evident from the accumulations of proline, chlorophyll content, carbohydrate profile, and Hill activity influencing the C4 enzyme. Primarily, in illuminated tissues, the activity of the enzyme recorded a reduced trend through salinity irrespective of light and darkness compared to the control. On illumination, the kinetic parameters such as Vmax of the enzyme increased by 1.36-fold compared to in the dark under salinity whereas Km was decreased by 20% under the same condition. The extent of light induction was proportionate to limiting (0.01 mM) and saturated (4.0 mM) malate concentrations for enzyme activity. Moreover, the catalytic properties of the enzyme were also tested on concomitant responses to activator (citrate and succinate) and inhibitor (oxalate and pyruvate) residues. The sensitivity to light and dark effects was also tested for reducing agents such as dithiothreitol, suggesting the effect of the changes in redox on the regulatory properties of the enzyme. The ratio of enzyme activity under light and darkness in the presence or absence of a reducing agent was concomitantly increased with varying malate concentrations. At the molecular level, protein polymorphism of the enzyme represented minor variations in band intensities, however, not in numbers through salinity subjected to light and darkness. Therefore, salinity-induced changes in the decarboxylation reaction, evident by NADP-ME activity, may be based on the redox property of regulatory sites and sensitivity to light and darkness.
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Affiliation(s)
- Bipul Sarkar
- Plant Physiology and Molecular Biology Research Unit, Department of Botany, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Abir Das
- Plant Physiology and Molecular Biology Research Unit, Department of Botany, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Sayan Pal
- Plant Physiology and Molecular Biology Research Unit, Department of Botany, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Ankita Kundu
- Plant Physiology and Molecular Biology Research Unit, Department of Botany, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh
| | - Masayuki Fujita
- Laboratory of Plant Stress Responses, Faculty of Agriculture, Kagawa University, Kita-Gun, Kagawa, Miki-cho 761-0795, Japan
| | - Malay Kumar Adak
- Plant Physiology and Molecular Biology Research Unit, Department of Botany, University of Kalyani, Kalyani 741235, West Bengal, India
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2
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Montanhero Cabrera VI, do Nascimento Sividanes G, Quintiliano NF, Hikari Toyama M, Ghilardi Lago JH, de Oliveira MA. Exploring functional and structural features of chemically related natural prenylated hydroquinone and benzoic acid from Piper crassinervium (Piperaceae) on bacterial peroxiredoxin inhibition. PLoS One 2023; 18:e0281322. [PMID: 36827425 PMCID: PMC9956870 DOI: 10.1371/journal.pone.0281322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 02/26/2023] Open
Abstract
Multiple drug resistance (MDR) bacterial strains are responsible by 1.2 million of human deaths all over the world. The pathogens possess efficient enzymes which are able to mitigate the toxicity of reactive oxygen species (ROS) produced by some antibiotics and the host immune cells. Among them, the bacterial peroxiredoxin alkyl hydroperoxide reductase C (AhpC) is able to decompose efficiently several kinds of hydroperoxides. To decompose their substrates AhpC use a reactive cysteine residue (peroxidatic cysteine-CysP) that together with two other polar residues (Thr/Ser and Arg) comprise the catalytic triad of these enzymes and are involved in the substrate targeting/stabilization to allow a bimolecular nucleophilic substitution (SN2) reaction. Additionally to the high efficiency the AhpC is very abundant in the cells and present virulent properties in some bacterial species. Despite the importance of AhpC in bacteria, few studies aimed at using natural compounds as inhibitors of this class of enzymes. Some natural products were identified as human isoforms, presenting as common characteristics a bulk hydrophobic moiety and an α, β-unsaturated carbonylic system able to perform a thiol-Michael reaction. In this work, we evaluated two chemically related natural products: 1,4-dihydroxy-2-(3',7'-dimethyl-1'-oxo-2'E,6'-octadienyl) benzene (C1) and 4-hydroxy-2-(3',7'-dimethyl-1'-oxo-2'E,6'-octadienyl) benzoic acid (C2), both were isolated from branches Piper crassinervium (Piperaceae), over the peroxidase activity of AhpC from Pseudomonas aeruginosa (PaAhpC) and Staphylococcus epidermidis (SeAhpC). By biochemical assays we show that although both compounds can perform the Michael addition reaction, only compound C2 was able to inhibit the PaAhpC peroxidase activity but not SeAhpC, presenting IC50 = 20.3 μM. SDS-PAGE analysis revealed that the compound was not able to perform a thiol-Michael addition, suggesting another inhibition behavior. Using computer-assisted simulations, we also show that an acidic group present in the structure of compound C2 may be involved in the stabilization by polar interactions with the Thr and Arg residues from the catalytic triad and several apolar interactions with hydrophobic residues. Finally, C2 was not able to interfere in the peroxidase activity of the isoform Prx2 from humans or even the thiol proteins of the Trx reducing system from Escherichia coli (EcTrx and EcTrxR), indicating specificity for P. aeruginosa AhpC.
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Affiliation(s)
| | | | | | - Marcos Hikari Toyama
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente, SP, Brazil
| | - João Henrique Ghilardi Lago
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
- * E-mail: (MAO); (JHGL)
| | - Marcos Antonio de Oliveira
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente, SP, Brazil
- * E-mail: (MAO); (JHGL)
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3
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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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4
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Native state fluctuations in a peroxiredoxin active site match motions needed for catalysis. Structure 2022; 30:278-288.e3. [PMID: 34678159 PMCID: PMC8818020 DOI: 10.1016/j.str.2021.10.001] [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: 05/22/2021] [Revised: 08/10/2021] [Accepted: 09/29/2021] [Indexed: 02/05/2023]
Abstract
Peroxiredoxins are ubiquitous enzymes that detoxify peroxides and regulate redox signaling. During catalysis, a "peroxidatic" cysteine (CP) in the conserved active site reduces peroxide while being oxidized to a CP-sulfenate, prompting a local unfolding event that enables formation of a disulfide with a second, "resolving" cysteine. Here, we use nuclear magnetic resonance spectroscopy to probe the dynamics of the CP-thiolate and disulfide forms of Xanthomonas campestris peroxiredoxin Q. Chemical exchange saturation transfer behavior of the resting enzyme reveals 26 residues in and around the active site exchanging at a rate of 72 s-1 with a locally unfolded, high-energy (2.5% of the population) state. This unequivocally establishes that a catalytically relevant local unfolding equilibrium exists in the enzyme's CP-thiolate form. Also, faster motions imply an active site instability that could promote local unfolding and, based on other work, be exacerbated by CP-sulfenate formation so as to direct the enzyme along a functional catalytic trajectory.
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5
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Troussicot L, Burmann BM, Molin M. Structural determinants of multimerization and dissociation in 2-Cys peroxiredoxin chaperone function. Structure 2021; 29:640-654. [PMID: 33945778 DOI: 10.1016/j.str.2021.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/31/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022]
Abstract
Peroxiredoxins (PRDXs) are abundant peroxidases present in all kingdoms of life. Recently, they have been shown to also carry out additional roles as molecular chaperones. To address this emerging supplementary function, this review focuses on structural studies of 2-Cys PRDX systems exhibiting chaperone activity. We provide a detailed understanding of the current knowledge of structural determinants underlying the chaperone function of PRDXs. Specifically, we describe the mechanisms which may modulate their quaternary structure to facilitate interactions with client proteins and how they are coordinated with the functions of other molecular chaperones. Following an overview of PRDX molecular architecture, we outline structural details of the presently best-characterized peroxiredoxins exhibiting chaperone function and highlight common denominators. Finally, we discuss the remarkable structural similarities between 2-Cys PRDXs, small HSPs, and J-domain-independent Hsp40 holdases in terms of their functions and dynamic equilibria between low- and high-molecular-weight oligomers.
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Affiliation(s)
- Laura Troussicot
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden.
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, 405 30 Göteborg, Sweden.
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6
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Bolduc J, Koruza K, Luo T, Malo Pueyo J, Vo TN, Ezeriņa D, Messens J. Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities. Redox Biol 2021; 42:101959. [PMID: 33895094 PMCID: PMC8113037 DOI: 10.1016/j.redox.2021.101959] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/07/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. Understanding the role of the multiple structural and post-translational modification (PTM) layers that tunes the peroxiredoxin specificities is still a challenge. In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. Armed with numerous cellular and atomic level experimental techniques, we look at the future and ask ourselves what is still needed to give us a clearer view on the cellular operating power of Prdxs in both stress and non-stress conditions.
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Affiliation(s)
- Jesalyn Bolduc
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Katarina Koruza
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Ting Luo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Julia Malo Pueyo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Trung Nghia Vo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Daria Ezeriņa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium.
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7
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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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8
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Chong SMS, Kamariah N, Grüber G. Residues of helix ɑ2 are critical for catalytic efficiency of mycobacterial alkylhydroperoxide reductase subunit C. FEBS Lett 2020; 594:2829-2839. [PMID: 32557576 DOI: 10.1002/1873-3468.13864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 11/05/2022]
Abstract
The ability of Mycobacteria to overcome oxidative stress is of paramount importance for its survival within the host. One of the key enzymes that are involved in protecting the bacterium from reactive oxygen species is the catalase-peroxidase (KatG). However, in strains resistant to the antibiotic isoniazid, KatG is rendered ineffective, which is associated with an increased expression of alkylhydroperoxide reductase subunit C (AhpC). Mycobacterial AhpC possesses a unique helical displacement when compared to its bacterial counterparts. Here, via mutagenesis studies, we demonstrate the importance of this helix for redox modulation of the catalytic activity of AhpC. Along with structural insights from crystallographic data, the impact of critical residues on the structure and flexibility of the helix and on AhpC oligomerization is described.
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Affiliation(s)
- Shi Min Sherilyn Chong
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Republic of Singapore.,Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Republic of Singapore
| | - Neelagandan Kamariah
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
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9
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Abstract
Peroxiredoxins are most central to the cellular adaptation against oxidative stress. They act as oxidant scavengers, stress sensors, transmitters of signals, and chaperones, and they possess a unique quaternary switch that is intimately related to these functions. However, so far it has not been possible to monitor peroxiredoxin structural changes in the intact cellular environment. This study presents genetically encoded probes, based on homo-FRET (Förster resonance energy transfer between identical fluorophores) fluorescence polarization, that allow following these quaternary changes in real time, in living cells. We envisage that these probes can be used to address a broad range of questions related to the function of peroxiredoxins. Peroxiredoxins are central to cellular redox homeostasis and signaling. They serve as peroxide scavengers, sensors, signal transducers, and chaperones, depending on conditions and context. Typical 2-Cys peroxiredoxins are known to switch between different oligomeric states, depending on redox state, pH, posttranslational modifications, and other factors. Quaternary states and their changes are closely connected to peroxiredoxin activity and function but so far have been studied, almost exclusively, outside the context of the living cell. Here we introduce the use of homo-FRET (Förster resonance energy transfer between identical fluorophores) fluorescence polarization to monitor dynamic changes in peroxiredoxin quaternary structure inside the crowded environment of living cells. Using the approach, we confirm peroxide- and thioredoxin-related quaternary transitions to take place in cellulo and observe that the relationship between dimer–decamer transitions and intersubunit disulfide bond formation is more complex than previously thought. Furthermore, we demonstrate the use of the approach to compare different peroxiredoxin isoforms and to identify mutations and small molecules affecting the oligomeric state inside cells. Mutagenesis experiments reveal that the dimer–decamer equilibrium is delicately balanced and can be shifted by single-atom structural changes. We show how to use this insight to improve the design of peroxiredoxin-based redox biosensors.
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10
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Harris RC, Liu R, Shen J. Predicting Reactive Cysteines with Implicit-Solvent-Based Continuous Constant pH Molecular Dynamics in Amber. J Chem Theory Comput 2020; 16:3689-3698. [PMID: 32330035 PMCID: PMC7772776 DOI: 10.1021/acs.jctc.0c00258] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cysteines existing in the deprotonated thiolate form or having a tendency to become deprotonated are important players in enzymatic and cellular redox functions and frequently exploited in covalent drug design; however, most computational studies assume cysteines as protonated. Thus, developing an efficient tool that can make accurate and reliable predictions of cysteine protonation states is timely needed. We recently implemented a generalized Born (GB) based continuous constant pH molecular dynamics (CpHMD) method in Amber for protein pKa calculations on CPUs and GPUs. Here we benchmark the performance of GB-CpHMD for predictions of cysteine pKa's and reactivities using a data set of 24 proteins with both down- and upshifted cysteine pKa's. We found that 10 ns single-pH or 4 ns replica-exchange CpHMD titrations gave root-mean-square errors of 1.2-1.3 and correlation coefficients of 0.8-0.9 with respect to experiment. The accuracy of predicting thiolates or reactive cysteines at physiological pH with single-pH titrations is 86 or 81% with a precision of 100 or 90%, respectively. This performance well surpasses the traditional structure-based methods, particularly a widely used empirical pKa tool that gives an accuracy less than 50%. We discuss simulation convergence, dependence on starting structures, common determinants of the pKa downshifts and upshifts, and the origin of the discrepancies from the structure-based calculations. Our work suggests that CpHMD titrations can be performed on a desktop computer equipped with a single GPU card to predict cysteine protonation states for a variety of applications, from understanding biological functions to covalent drug design.
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Affiliation(s)
- Robert C Harris
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Ruibin Liu
- ComputChem LLC, Baltimore, Maryland 21202, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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11
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Kriznik A, Libiad M, Le Cordier H, Boukhenouna S, Toledano MB, Rahuel-Clermont S. Dynamics of a Key Conformational Transition in the Mechanism of Peroxiredoxin Sulfinylation. ACS Catal 2020; 10:3326-3339. [PMID: 32363077 PMCID: PMC7189429 DOI: 10.1021/acscatal.9b04471] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/14/2020] [Indexed: 12/11/2022]
Abstract
![]()
Peroxiredoxins from
the Prx1 subfamily (Prx) are moonlighting peroxidases
that operate in peroxide signaling and are regulated by sulfinylation.
Prxs offer a major model of protein–thiol oxidative modification.
They react with H2O2 to form a sulfenic acid
intermediate that either engages into a disulfide bond, committing
the enzyme into its peroxidase cycle, or again reacts with peroxide
to produce a sulfinic acid that inactivates the enzyme. Sensitivity
to sulfinylation depends on the kinetics of these two competing reactions
and is critically influenced by a structural transition from a fully
folded (FF) to locally unfolded (LU) conformation. Analysis of the
reaction of the Tsa1 Saccharomyces cerevisiae Prx with H2O2 by Trp fluorescence-based rapid
kinetics revealed a process linked to the FF/LU transition that is
kinetically distinct from disulfide formation and suggested that sulfenate
formation facilitates local unfolding. Use of mutants of distinctive
sensitivities and of different peroxide substrates showed that sulfinylation
sensitivity is not coupled to the resolving step kinetics but depends
only on the sulfenic acid oxidation and FF-to-LU transition rate constants.
In addition, stabilization of the active site FF conformation, the
determinant of sulfinylation kinetics, is only moderately influenced
by the Prx C-terminal tail dynamics that determine the FF →
LU kinetics. From these two parameters, the relative sensitivities
of Prxs toward hyperoxidation with different substrates can be predicted,
as confirmed by in vitro and in vivo patterns of sulfinylation.
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Affiliation(s)
- Alexandre Kriznik
- IMoPA, Université de Lorraine, CNRS, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
- UMS2008 IBSLor, Biophysics and Structural Biology Core Facility, Université de Lorraine, CNRS, INSERM, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
| | - Marouane Libiad
- Laboratoire Stress oxydant et Cancer, Institute for Integrative Biology of the Cell (I2BC), UMR9198, CNRS, CEA-Saclay, Université Paris-Saclay, iBiTecS/SBIGEM, Bat 142, F-91198 Gif-sur-Yvette Cedex, France
| | - Hélène Le Cordier
- IMoPA, Université de Lorraine, CNRS, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
| | - Samia Boukhenouna
- IMoPA, Université de Lorraine, CNRS, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
| | - Michel B. Toledano
- Laboratoire Stress oxydant et Cancer, Institute for Integrative Biology of the Cell (I2BC), UMR9198, CNRS, CEA-Saclay, Université Paris-Saclay, iBiTecS/SBIGEM, Bat 142, F-91198 Gif-sur-Yvette Cedex, France
| | - Sophie Rahuel-Clermont
- IMoPA, Université de Lorraine, CNRS, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
- UMS2008 IBSLor, Biophysics and Structural Biology Core Facility, Université de Lorraine, CNRS, INSERM, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
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12
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Vazquez DS, Zeida A, Agudelo WA, Montes MR, Ferrer-Sueta G, Santos J. Exploring the conformational transition between the fully folded and locally unfolded substates of Escherichia coli thiol peroxidase. Phys Chem Chem Phys 2020; 22:9518-9533. [DOI: 10.1039/d0cp00140f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Temporal acquisition of the fully folded conformational substate of the Escherichia coli thiol peroxidase by accelerated molecular dynamics simulations.
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Affiliation(s)
- Diego S. Vazquez
- Laboratorio de Expresión y Plegado de Proteínas
- Departamento de Ciencia y Tecnología
- Universidad Nacional de Quilmes
- Buenos Aires
- Argentina
| | - Ari Zeida
- Departamento de Bioquímica y Centro de Investigaciones Biomédicas (CEINBIO)
- Facultad de Medicina
- Universidad de la República
- Montevideo
- Uruguay
| | - William A. Agudelo
- Fundación Instituto de Inmunología de Colombia (FIDIC)
- Bogotá D.C
- Colombia
| | - Mónica R. Montes
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB)
- “Prof. Dr Alejandro C. Paladini”
- Universidad de Buenos Aires and CONICET
- Ciudad Autónoma de Buenos Aires
- Argentina
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica
- Instituto de Química Biológica and CEINBIO
- Facultad de Ciencias
- Universidad de la República
- Montevideo
| | - Javier Santos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Ciudad Autónoma de Buenos Aires
- Argentina
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3)
- Departamento de Fisiología y Biología Molecular y Celular
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13
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Perkins A, Tudorica DA, Amieva MR, Remington SJ, Guillemin K. Helicobacter pylori senses bleach (HOCl) as a chemoattractant using a cytosolic chemoreceptor. PLoS Biol 2019; 17:e3000395. [PMID: 31465435 PMCID: PMC6715182 DOI: 10.1371/journal.pbio.3000395] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
The gastric pathogen Helicobacter pylori requires a noncanonical cytosolic chemoreceptor transducer-like protein D (TlpD) for efficient colonization of the mammalian stomach. Here, we reconstituted a complete chemotransduction signaling complex in vitro with TlpD and the chemotaxis (Che) proteins CheW and CheA, enabling quantitative assays for potential chemotaxis ligands. We found that TlpD is selectively sensitive at micromolar concentrations to bleach (hypochlorous acid, HOCl), a potent antimicrobial produced by neutrophil myeloperoxidase during inflammation. HOCl acts as a chemoattractant by reversibly oxidizing a conserved cysteine within a 3His/1Cys Zn-binding motif in TlpD that inactivates the chemotransduction signaling complex. We found that H. pylori is resistant to killing by millimolar concentrations of HOCl and responds to HOCl in the micromolar range by increasing its smooth-swimming behavior, leading to chemoattraction to HOCl sources. We show related protein domains from Salmonella enterica and Escherichia coli possess similar reactivity toward HOCl. We propose that this family of proteins enables host-associated bacteria to sense sites of tissue inflammation, a strategy that H. pylori uses to aid in colonizing and persisting in inflamed gastric tissue.
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Affiliation(s)
- Arden Perkins
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Dan A. Tudorica
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Manuel R. Amieva
- Departments of Pediatrics and of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - S. James Remington
- Department of Physics, University of Oregon, Eugene, Oregon, United States of America
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- Humans and the Microbiome Program, CIFAR, Toronto, Ontario, Canada
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14
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Young D, Pedre B, Ezeriņa D, De Smet B, Lewandowska A, Tossounian MA, Bodra N, Huang J, Astolfi Rosado L, Van Breusegem F, Messens J. Protein Promiscuity in H 2O 2 Signaling. Antioxid Redox Signal 2019; 30:1285-1324. [PMID: 29635930 DOI: 10.1089/ars.2017.7013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SIGNIFICANCE Decrypting the cellular response to oxidative stress relies on a comprehensive understanding of the redox signaling pathways stimulated under oxidizing conditions. Redox signaling events can be divided into upstream sensing of oxidants, midstream redox signaling of protein function, and downstream transcriptional redox regulation. Recent Advances: A more and more accepted theory of hydrogen peroxide (H2O2) signaling is that of a thiol peroxidase redox relay, whereby protein thiols with low reactivity toward H2O2 are instead oxidized through an oxidative relay with thiol peroxidases. CRITICAL ISSUES These ultrareactive thiol peroxidases are the upstream redox sensors, which form the first cellular port of call for H2O2. Not all redox-regulated interactions between thiol peroxidases and cellular proteins involve a transfer of oxidative equivalents, and the nature of redox signaling is further complicated through promiscuous functions of redox-regulated "moonlighting" proteins, of which the precise cellular role under oxidative stress can frequently be obscured by "polygamous" interactions. An ultimate goal of redox signaling is to initiate a rapid response, and in contrast to prokaryotic oxidant-responsive transcription factors, mammalian systems have developed redox signaling pathways, which intersect both with kinase-dependent activation of transcription factors, as well as direct oxidative regulation of transcription factors through peroxiredoxin (Prx) redox relays. FUTURE DIRECTIONS We highlight that both transcriptional regulation and cell fate can be modulated either through oxidative regulation of kinase pathways, or through distinct redox-dependent associations involving either Prxs or redox-responsive moonlighting proteins with functional promiscuity. These protein associations form systems of crossregulatory networks with multiple nodes of potential oxidative regulation for H2O2-mediated signaling.
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Affiliation(s)
- David Young
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Brandan Pedre
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daria Ezeriņa
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Barbara De Smet
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Aleksandra Lewandowska
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria-Armineh Tossounian
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nandita Bodra
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jingjing Huang
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Leonardo Astolfi Rosado
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank Van Breusegem
- 2 Brussels Center for Redox Biology, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Joris Messens
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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15
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Faraj SE, Noguera ME, Delfino JM, Santos J. Global Implications of Local Unfolding Phenomena, Probed by Cysteine Reactivity in Human Frataxin. Sci Rep 2019; 9:1731. [PMID: 30742023 PMCID: PMC6370780 DOI: 10.1038/s41598-019-39429-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 01/18/2019] [Indexed: 12/28/2022] Open
Abstract
Local events that affect specific regions of proteins are of utmost relevance for stability and function. The aim of this study is to quantitatively assess the importance of locally-focused dynamics by means of a simple chemical modification procedure. Taking human Frataxin as a working model, we investigated local fluctuations of the C-terminal region (the last 16 residues of the protein) by means of three L → C replacement mutants: L98C, L200C and L203C. The conformation and thermodynamic stability of each variant was assessed. All the variants exhibited native features and high stabilities: 9.1 (wild type), 8.1 (L198C), 7.0 (L200C) and 10.0 kcal mol-1 (L203C). In addition, kinetic rates of Cys chemical modification by DTNB and DTDPy were measured, conformational dynamics data were extracted and free energy for the local unfolding of the C-terminal region was estimated. The analysis of these results indicates that the conformation of the C-terminal region fluctuates with partial independence from global unfolding events. Additionally, numerical fittings of the kinetic model of the process suggest that the local transition occurs in the seconds to minutes timescale. In fact, standard free energy differences for local unfolding were found to be significantly lower than those of the global unfolding reaction, showing that chemical modification results may not be explained in terms of the global unfolding reaction alone. These results provide unequivocal experimental evidence of local phenomena with global effects and contribute to understanding how global and local stability are linked to protein dynamics.
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Affiliation(s)
- Santiago E Faraj
- Alejandro Paladini Institute of Biological Chemistry and Chemical Physics (UBA-CONICET), Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (C1113AAD), Buenos Aires, Argentina
| | - Martín E Noguera
- Alejandro Paladini Institute of Biological Chemistry and Chemical Physics (UBA-CONICET), Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (C1113AAD), Buenos Aires, Argentina
| | - José María Delfino
- Alejandro Paladini Institute of Biological Chemistry and Chemical Physics (UBA-CONICET), Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (C1113AAD), Buenos Aires, Argentina
| | - Javier Santos
- Alejandro Paladini Institute of Biological Chemistry and Chemical Physics (UBA-CONICET), Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (C1113AAD), Buenos Aires, Argentina. .,Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires. Instituto de Biociencias, Biotecnología y Biomedicina (iB3). Intendente Güiraldes 2160 - Ciudad Universitaria, 1428EGA, C.A.B.A., Argentina.
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16
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Piecing Together How Peroxiredoxins Maintain Genomic Stability. Antioxidants (Basel) 2018; 7:antiox7120177. [PMID: 30486489 PMCID: PMC6316004 DOI: 10.3390/antiox7120177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022] Open
Abstract
Peroxiredoxins, a highly conserved family of thiol oxidoreductases, play a key role in oxidant detoxification by partnering with the thioredoxin system to protect against oxidative stress. In addition to their peroxidase activity, certain types of peroxiredoxins possess other biochemical activities, including assistance in preventing protein aggregation upon exposure to high levels of oxidants (molecular chaperone activity), and the transduction of redox signals to downstream proteins (redox switch activity). Mice lacking the peroxiredoxin Prdx1 exhibit an increased incidence of tumor formation, whereas baker's yeast (Saccharomyces cerevisiae) lacking the orthologous peroxiredoxin Tsa1 exhibit a mutator phenotype. Collectively, these findings suggest a potential link between peroxiredoxins, control of genomic stability, and cancer etiology. Here, we examine the potential mechanisms through which Tsa1 lowers mutation rates, taking into account its diverse biochemical roles in oxidant defense, protein homeostasis, and redox signaling as well as its interplay with thioredoxin and thioredoxin substrates, including ribonucleotide reductase. More work is needed to clarify the nuanced mechanism(s) through which this highly conserved peroxidase influences genome stability, and to determine if this mechanism is similar across a range of species.
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17
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Abstract
The bacterial transcription factor OxyR is a model example of a highly sensitive and specific hydrogen peroxide (H2O2) sensor. H2O2 reduction by its active-site cysteine triggers protein structural changes leading to an increased transcription of antioxidant genes. By solving the crystal structures of full-length OxyR in both reduced and oxidized states, we provide molecular insight into these structural changes. We also present a H2O2-bound structure with a threonine activating the peroxide, and argue that this H2O2-bound structure may be catalytically more relevant than that seen previously in the study of a sulfinic acid-mimic mutant of the active-site cysteine. Finally, we discuss the commonalities and differences between the peroxidatic mechanisms of peroxiredoxins and OxyR. Hydrogen peroxide (H2O2) is a strong oxidant capable of oxidizing cysteinyl thiolates, yet only a few cysteine-containing proteins have exceptional reactivity toward H2O2. One such example is the prokaryotic transcription factor OxyR, which controls the antioxidant response in bacteria, and which specifically and rapidly reduces H2O2. In this study, we present crystallographic evidence for the H2O2-sensing mechanism and H2O2-dependent structural transition of Corynebacterium glutamicum OxyR by capturing the reduced and H2O2-bound structures of a serine mutant of the peroxidatic cysteine, and the full-length crystal structure of disulfide-bonded oxidized OxyR. In the H2O2-bound structure, we pinpoint the key residues for the peroxidatic reduction of H2O2, and relate this to mutational assays showing that the conserved active-site residues T107 and R278 are critical for effective H2O2 reduction. Furthermore, we propose an allosteric mode of structural change, whereby a localized conformational change arising from H2O2-induced intramolecular disulfide formation drives a structural shift at the dimerization interface of OxyR, leading to overall changes in quaternary structure and an altered DNA-binding topology and affinity at the catalase promoter region. This study provides molecular insights into the overall OxyR transcription mechanism regulated by H2O2.
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18
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Langford TF, Huang BK, Lim JB, Moon SJ, Sikes HD. Monitoring the action of redox-directed cancer therapeutics using a human peroxiredoxin-2-based probe. Nat Commun 2018; 9:3145. [PMID: 30087344 PMCID: PMC6081480 DOI: 10.1038/s41467-018-05557-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/29/2018] [Indexed: 01/05/2023] Open
Abstract
Redox cancer therapeutics target the increased reliance on intracellular antioxidant systems and enhanced susceptibility to oxidant-induced stress of some cancer cells compared to normal cells. Many of these therapeutics are thought to perturb intracellular levels of the oxidant hydrogen peroxide (H2O2), a signaling molecule that modulates a number of different processes in human cells. However, fluorescent probes for this species remain limited in their ability to detect the small perturbations induced during successful treatments. We report a fluorescent sensor based upon human peroxiredoxin-2, which acts as the natural indicator of small H2O2 fluctuations in human cells. The new probe reveals peroxide-induced oxidation in human cells below the detection limit of current probes, as well as peroxiredoxin-2 oxidation caused by two different redox cancer therapeutics in living cells. This capability will be useful in elucidating the mechanism of current redox-based therapeutics and in developing new ones.
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Affiliation(s)
- Troy F Langford
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, USA
| | - Beijing K Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, USA
| | - Joseph B Lim
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, USA
| | - Sun Jin Moon
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, USA.
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19
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Bolduc JA, Nelson KJ, Haynes AC, Lee J, Reisz JA, Graff AH, Clodfelter JE, Parsonage D, Poole LB, Furdui CM, Lowther WT. Novel hyperoxidation resistance motifs in 2-Cys peroxiredoxins. J Biol Chem 2018; 293:11901-11912. [PMID: 29884768 PMCID: PMC6066324 DOI: 10.1074/jbc.ra117.001690] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 05/29/2018] [Indexed: 01/07/2023] Open
Abstract
2-Cys peroxiredoxins (Prxs) modulate hydrogen peroxide (H2O2)-mediated cell signaling. At high H2O2 levels, eukaryotic Prxs can be inactivated by hyperoxidation and are classified as sensitive Prxs. In contrast, prokaryotic Prxs are categorized as being resistant to hyperoxidation and lack the GGLG and C-terminal YF motifs present in the sensitive Prxs. Additional molecular determinants that account for the subtle differences in the susceptibility to hyperoxidation remain to be identified. A comparison of a new, 2.15-Å-resolution crystal structure of Prx2 in the oxidized, disulfide-bonded state with the hyperoxidized structure of Prx2 and Prx1 in complex with sulfiredoxin revealed three structural regions that rearrange during catalysis. With these regions in hand, focused sequence analyses were performed comparing sensitive and resistant Prx groups. From this combinatorial approach, we discovered two novel hyperoxidation resistance motifs, motifs A and B, which were validated using mutagenesis of sensitive human Prxs and resistant Salmonella enterica serovar Typhimurium AhpC. Introduction and removal of these motifs, respectively, resulted in drastic changes in the sensitivity to hyperoxidation with Prx1 becoming 100-fold more resistant to hyperoxidation and AhpC becoming 800-fold more sensitive to hyperoxidation. The increased sensitivity of the latter AhpC variant was also confirmed in vivo These results support the function of motifs A and B as primary drivers for tuning the sensitivity of Prxs to different levels of H2O2, thus enabling the initiation of variable signaling or antioxidant responses in cells.
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Affiliation(s)
| | | | | | - Jingyun Lee
- Wake Forest Baptist Comprehensive Cancer Center, and
| | - Julie A. Reisz
- Section on Molecular Medicine, Department of Internal Medicine
| | - Aaron H. Graff
- From the Center for Structural Biology, Department of Biochemistry
| | | | - Derek Parsonage
- From the Center for Structural Biology, Department of Biochemistry
| | - Leslie B. Poole
- From the Center for Structural Biology, Department of Biochemistry, ,Wake Forest Baptist Comprehensive Cancer Center, and ,Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157 and ,Center for Molecular Signaling, Wake Forest University, Winston-Salem, North Carolina 27101
| | - Cristina M. Furdui
- Section on Molecular Medicine, Department of Internal Medicine, ,Wake Forest Baptist Comprehensive Cancer Center, and ,Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157 and ,Center for Molecular Signaling, Wake Forest University, Winston-Salem, North Carolina 27101
| | - W. Todd Lowther
- From the Center for Structural Biology, Department of Biochemistry, ,Wake Forest Baptist Comprehensive Cancer Center, and ,Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157 and ,Center for Molecular Signaling, Wake Forest University, Winston-Salem, North Carolina 27101, To whom correspondence should be addressed:
Center for Structural Biology, Dept. of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157. Tel.:
336-716-7230; Fax:
336-713-1283; E-mail:
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20
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Sharapov MG, Penkov NV, Gudkov SV, Goncharov RG, Novoselov VI, Fesenko EE. The Role of Intermolecular Disulfide Bonds in Stabilizing the Structure of Peroxiredoxins. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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Grosche J, Meißner J, Eble JA. More than a syllable in fib-ROS-is: The role of ROS on the fibrotic extracellular matrix and on cellular contacts. Mol Aspects Med 2018; 63:30-46. [PMID: 29596842 DOI: 10.1016/j.mam.2018.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 01/01/2023]
Abstract
Fibrosis is characterized by excess deposition of extracellular matrix (ECM). However, the ECM changes during fibrosis not only quantitatively but also qualitatively. Thus, the composition is altered as the expression of various ECM proteins changes. Moreover, also posttranslational modifications, secretion, deposition and crosslinkage as well as the proteolytic degradation of ECM components run differently during fibrosis. As several of these processes involve redox reactions and some of them are even redox-regulated, reactive oxygen species (ROS) influence fibrotic diseases. Redox regulation of the ECM has not been studied intensively, although evidences exist that the alteration of the ECM, including the redox-relevant processes of its formation and degradation, may be of key importance not only as a cause but also as a consequence of fibrotic diseases. Myofibroblasts, which have differentiated from fibroblasts during fibrosis, produce most of the ECM components and in return obtain important environmental cues of the ECM, including their redox-dependent fibrotic alterations. Thus, myofibroblast differentiation and fibrotic changes of the ECM are interdependent processes and linked with each other via cell-matrix contacts, which are mediated by integrins and other cell adhesion molecules. These cell-matrix contacts are also regulated by redox processes and by ROS. However, most of the redox-catalyzing enzymes are localized within cells. Little is known about redox-regulating enzymes, especially the ones that control the formation and cleavage of redox-sensitive disulfide bridges within the extracellular space. They are also important players in the redox-regulative crosstalk between ECM and cells during fibrosis.
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Affiliation(s)
- Julius Grosche
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany
| | - Juliane Meißner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany
| | - Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany.
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22
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Portillo-Ledesma S, Randall LM, Parsonage D, Dalla Rizza J, Karplus PA, Poole LB, Denicola A, Ferrer-Sueta G. Differential Kinetics of Two-Cysteine Peroxiredoxin Disulfide Formation Reveal a Novel Model for Peroxide Sensing. Biochemistry 2018; 57:3416-3424. [PMID: 29553725 DOI: 10.1021/acs.biochem.8b00188] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Two-cysteine peroxiredoxins (Prx) have a three-step catalytic cycle consisting of (1) reduction of peroxide and formation of sulfenic acid on the enzyme, (2) condensation of the sulfenic acid with a thiol to form disulfide, also known as resolution, and (3) reduction of the disulfide by a reductant protein. By following changes in protein fluorescence, we have studied the pH dependence of reaction 2 in human peroxiredoxins 1, 2, and 5 and in Salmonella typhimurium AhpC and obtained rate constants for the reaction and p Ka values of the thiol and sulfenic acid involved for each system. The observed reaction 2 rate constant spans 2 orders of magnitude, but in all cases, reaction 2 appears to be slow compared to the same reaction in small-molecule systems, making clear the rates are limited by conformational features of the proteins. For each Prx, reaction 2 will become rate-limiting at some critical steady-state concentration of H2O2 producing the accumulation of Prx as sulfenic acid. When this happens, an alternative and faster-resolving Prx (or other peroxidase) may take over the antioxidant role. The accumulation of sulfenic acid Prx at distinct concentrations of H2O2 is embedded in the kinetic limitations of the catalytic cycle and may constitute the basis of a H2O2-mediated redox signal transduction pathway requiring neither inactivation nor posttranslational modification. The differences in the rate constants of resolution among Prx coexisting in the same compartment may partially explain their complementation in antioxidant function and stepwise sensing of H2O2 concentration.
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Affiliation(s)
| | - Lía M Randall
- Laboratorio de I+D de Moléculas Bioactivas, CENUR Litoral Norte , Universidad de la República , Paysandú , Uruguay
| | - Derek Parsonage
- Department of Biochemistry and Centers for Structural Biology and for Redox Biology and Medicine , Wake Forest School of Medicine , Winston-Salem , North Carolina 27157 , United States
| | | | - P Andrew Karplus
- Department of Biochemistry and Biophysics , Oregon State University , 2011 Agricultural & Life Sciences Building , Corvallis , Oregon 97331 , United States
| | - Leslie B Poole
- Department of Biochemistry and Centers for Structural Biology and for Redox Biology and Medicine , Wake Forest School of Medicine , Winston-Salem , North Carolina 27157 , United States
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23
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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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24
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Stöcker S, Van Laer K, Mijuskovic A, Dick TP. The Conundrum of Hydrogen Peroxide Signaling and the Emerging Role of Peroxiredoxins as Redox Relay Hubs. Antioxid Redox Signal 2018; 28:558-573. [PMID: 28587525 DOI: 10.1089/ars.2017.7162] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
SIGNIFICANCE Hydrogen peroxide (H2O2) is known to act as a messenger in signal transduction. How H2O2 leads to selective and efficient oxidation of specific thiols on specific signaling proteins remains one of the most important open questions in redox biology. Recent Advances: Increasing evidence implicates thiol peroxidases as mediators of protein thiol oxidation. Recently, this evidence has been extended to include the peroxiredoxins (Prxs). Prxs are exceptionally sensitive to H2O2, abundantly expressed and capture most of the H2O2 that is generated inside cells. CRITICAL ISSUES The overall prevalence and importance of Prx-based redox signaling relays are still unknown. The same is true for alternative mechanisms of redox signaling. FUTURE DIRECTIONS It will be important to clarify the relative contributions of Prx-mediated and direct thiol oxidation to H2O2 signaling. Many questions relating to Prx-based redox relays remain to be answered, including their mechanism, structural organization, and the potential role of adaptor proteins. Antioxid. Redox Signal. 28, 558-573.
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Affiliation(s)
- Sarah Stöcker
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ) , Heidelberg, Germany
| | - Koen Van Laer
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ) , Heidelberg, Germany
| | - Ana Mijuskovic
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ) , Heidelberg, Germany
| | - Tobias P Dick
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ) , Heidelberg, Germany
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25
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Pan A, Balakrishna AM, Nartey W, Kohlmeier A, Dip PV, Bhushan S, Grüber G. Atomic structure and enzymatic insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit C. Free Radic Biol Med 2018; 115:252-265. [PMID: 29223533 DOI: 10.1016/j.freeradbiomed.2017.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/14/2017] [Accepted: 12/03/2017] [Indexed: 11/20/2022]
Abstract
The Enterococcus faecalis alkyl hydroperoxide reductase complex (AhpR) with its subunits AhpC (EfAhpC) and AhpF (EfAhpF) are of paramount importance to restore redox homeostasis. Recently, the novel phenomenon of swapping of the catalytic domains of EfAhpF was uncovered. Here, we visualized its counterpart EfAhpC (187 residues) from the vancomycin-resistant E. faecalis (V583) bacterium by electron microscopy and demonstrate, that in contrast to other bacterial AhpCs, EfAhpC forms a stable decamer-ring irrespective of the redox state. The first crystallographic structure (2.8Å resolution) of the C-terminal truncated form (EfAhpC1-172) confirms the decamer ring and provides new insight into a transition state in-between a fully folded to a locally unfolded conformation in the catalytic center due to redox modulation. Amino acid substitutions of residues in the N- and C-termini as well as the oligomeric interphase of EfAhpC provide information into their structural and enzymatic roles. Mutagenesis, enzymatic and biophysical studies reveal the effect of the unusual existence of four cysteines in EfAhpC, which might optimize the functional adaptation of the E. faecalis enzyme under various physiological conditions.
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Affiliation(s)
- Ankita Pan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Asha Manikkoth Balakrishna
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Andreas Kohlmeier
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Phat Vinh Dip
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Shashi Bhushan
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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26
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Haruyama T, Uchihashi T, Yamada Y, Kodera N, Ando T, Konno H. Negatively Charged Lipids Are Essential for Functional and Structural Switch of Human 2-Cys Peroxiredoxin II. J Mol Biol 2018; 430:602-610. [PMID: 29309753 DOI: 10.1016/j.jmb.2017.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/29/2017] [Accepted: 12/31/2017] [Indexed: 10/18/2022]
Abstract
The function of ubiquitous 2-Cys peroxiredoxins (Prxs) can be converted alternatively from peroxidases to molecular chaperones. This conversion has been reported to occur by the formation of high-molecular-weight (HMW) complexes upon overoxidation of or ATP/ADP binding to 2-Cys Prxs, but its mechanism is not well understood. Here, we show that upon binding to phosphatidylserine or phosphatidylglycerol dimeric human 2-Cys PrxII (hPrxII) is assembled to trefoil-shaped small oligomers (possibly hexamers) with full chaperone and null peroxidase activities. Spherical HMW complexes are formed, only when phosphatidylserine or phosphatidylglycerol is bound to overoxidized or ATP/ADP-bound hPrxII. The spherical HMW complexes are lipid vesicles covered with trefoil-shaped oligomers arranged in a hexagonal lattice pattern. Thus, these lipids with a net negative charge, which can be supplied by increased membrane trafficking under oxidative stress, are essential for the structural and functional switch of hPrxII and possibly most 2-Cys Prxs.
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Affiliation(s)
- Takamitsu Haruyama
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takayuki Uchihashi
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan; Department of Physics, Kanazawa University, Kanazawa 920-1192, Japan
| | - Yutaro Yamada
- Graduate School of Natural Science & Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Noriyuki Kodera
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan.
| | - Hiroki Konno
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan.
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27
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Carvalho LAC, Truzzi DR, Fallani TS, Alves SV, Toledo JC, Augusto O, Netto LES, Meotti FC. Urate hydroperoxide oxidizes human peroxiredoxin 1 and peroxiredoxin 2. J Biol Chem 2017; 292:8705-8715. [PMID: 28348082 DOI: 10.1074/jbc.m116.767657] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/27/2017] [Indexed: 12/24/2022] Open
Abstract
Urate hydroperoxide is a product of the oxidation of uric acid by inflammatory heme peroxidases. The formation of urate hydroperoxide might be a key event in vascular inflammation, where there is large amount of uric acid and inflammatory peroxidases. Urate hydroperoxide oxidizes glutathione and sulfur-containing amino acids and is expected to react fast toward reactive thiols from peroxiredoxins (Prxs). The kinetics for the oxidation of the cytosolic 2-Cys Prx1 and Prx2 revealed that urate hydroperoxide oxidizes these enzymes at rates comparable with hydrogen peroxide. The second-order rate constants of these reactions were 4.9 × 105 and 2.3 × 106 m-1 s-1 for Prx1 and Prx2, respectively. Kinetic and simulation data suggest that the oxidation of Prx2 by urate hydroperoxide occurs by a three-step mechanism, where the peroxide reversibly associates with the enzyme; then it oxidizes the peroxidatic cysteine, and finally, the rate-limiting disulfide bond is formed. Of relevance, the disulfide bond formation was much slower in Prx2 (k3 = 0.31 s-1) than Prx1 (k3 = 14.9 s-1). In addition, Prx2 was more sensitive than Prx1 to hyperoxidation caused by both urate hydroperoxide and hydrogen peroxide. Urate hydroperoxide oxidized Prx2 from intact erythrocytes to the same extent as hydrogen peroxide. Therefore, Prx1 and Prx2 are likely targets of urate hydroperoxide in cells. Oxidation of Prxs by urate hydroperoxide might affect cell function and be partially responsible for the pro-oxidant and pro-inflammatory effects of uric acid.
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Affiliation(s)
| | - Daniela R Truzzi
- From the Departamento de Bioquímica, Instituto de Química (IQUSP)
| | | | - Simone V Alves
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências (IB-USP), and
| | - José Carlos Toledo
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo-SP CEP 05508-000, Brazil
| | - Ohara Augusto
- From the Departamento de Bioquímica, Instituto de Química (IQUSP)
| | - Luís E S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências (IB-USP), and
| | - Flavia C Meotti
- From the Departamento de Bioquímica, Instituto de Química (IQUSP),
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28
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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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29
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Abstract
Peroxiredoxins (Prxs) are a large and conserved family of peroxidases that are considered to be the primary cellular guardians against oxidative stress in all living organisms. Prxs share a thioredoxin fold and contain a highly-reactive peroxidatic cysteine in a specialised active-site environment that is able to reduce their peroxide substrates. The minimal functional unit for Prxs are either monomers or dimers, but many dimers assemble into decameric rings. Ring structures can further form a variety of high molecular weight complexes. Many eukaryotic Prxs contain a conserved GGLG and C-terminal YF motif that confer sensitivity to elevated levels of peroxide, leading to hyperoxidation and inactivation. Inactive forms of Prxs can be re-reduced by the enzyme sulfiredoxin, in an ATP-dependent reaction. Cycles of hyperoxidation and reactivation are considered to play an integral role in a variety of H2O2-mediated cell signalling pathways in both stress and non-stress conditions. Prxs are also considered to exhibit chaperone-like properties when cells are under oxidative or thermal stress. The roles of various types of covalent modifications, e.g. acetylation and phosphorylation are also discussed. The ability of Prxs to assemble into ordered arrays such as nanotubes is currently being exploited in nanotechnology.
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Affiliation(s)
- Zhenbo Cao
- Institute of Molecular, Cell and Systems Biology, Davidson Building, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - John Gordon Lindsay
- Institute of Molecular, Cell and Systems Biology, Davidson Building, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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30
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Kamariah N, Sek MF, Eisenhaber B, Eisenhaber F, Grüber G. Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins. Sci Rep 2016; 6:37610. [PMID: 27892488 PMCID: PMC5124861 DOI: 10.1038/srep37610] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/31/2016] [Indexed: 12/26/2022] Open
Abstract
In addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled inactivation mechanism, making it more resistant to high H2O2 concentrations. During peroxide reduction, the active site alternates between reduced, fully folded (FF), and oxidized, locally unfolded (LU) conformations. Here we present novel insights into the divergence of bacterial and human Prxs in robustness and sensitivity to inactivation, respectively. Structural details provide new insights into sub-steps during the catalysis of peroxide reduction, enabling the transition from an FF to a LU conformation. Complementary to mutational and enzymatic results, these data unravel the essential role of the C-terminal tail of bacterial Prxs to act as a molecular switch, mediating the transition from an FF to a LU state. In addition, we propose that the C-terminal tail has influence on the propensity of the disulphide bond formation, indicating that as a consequence on the robustness and sensitivity to over-oxidation. Finally, a physical linkage between the catalytic site, the C-terminal tail and the oligomer interface is described.
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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
| | - Mun Foong Sek
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, 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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31
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Gonchoroski T, Virginio VG, Thompson CE, Paes JA, Machado CX, Ferreira HB. Evolution and function of the Mycoplasma hyopneumoniae peroxiredoxin, a 2-Cys-like enzyme with a single Cys residue. Mol Genet Genomics 2016; 292:297-305. [PMID: 27858147 DOI: 10.1007/s00438-016-1272-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/05/2016] [Indexed: 10/20/2022]
Abstract
The minimal genome of the mollicute Mycoplasma hyopneumoniae, the etiological agent of porcine enzootic pneumonia, encodes a limited repertoire of antioxidant enzymes that include a single and atypical peroxiredoxin (MhPrx), whose evolution and function were studied here. MhPrx has only one catalytic cysteine, in contrast with some of its possible ancestors (2-Cys peroxiredoxins), which have two. Although it is more similar to 2-Cys orthologs, MhPrx can still function with a single peroxidatic cysteine (CysP), using non-thiolic electron donors to reduce it. Therefore, MhPrx could be a representative of a possible group of 2-Cys peroxiredoxins, which have lost the resolving cysteine (CysR) residue without losing their catalytic properties. To further investigate MhPrx evolution, we performed a comprehensive phylogenetic analysis in the context of several bacterial families, including Prxs belonging to Tpx and AhpE families, shedding light on the evolutionary history of Mycoplasmataceae Prxs and giving support to the hypothesis of a relatively recent loss of the CysR within this family. Moreover, mutational analyses provided insights into MhPrx function with one, two, or without catalytic cysteines. While removal of the MhPrx putative CysP caused complete activity loss, confirming its catalytic role, the introduction of a second cysteine in a site correspondent to that of the CysR of a 2-Cys orthologue, as in the MhPrx supposed ancestral form, was compatible with enzyme activity. Overall, our phylogenetic and mutational studies support that MhPrx recently diverged from a 2-Cys Prx ancestor and pave the way for future studies addressing structural, functional, and evolutive aspects of peroxiredoxin subfamilies in Mollicutes and other bacteria.
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Affiliation(s)
- Taylor Gonchoroski
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil.,Grupo de Pesquisa em Plasticidade Neuroglial, Departamento de Bioquímica, UFRGS, Porto Alegre, RS, Brazil
| | - Veridiana G Virginio
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil
| | - Claudia E Thompson
- Unidade de Biologia Teórica e Computacional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Jéssica A Paes
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Cláudio X Machado
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.,Departamento de Criminalística, Instituto Geral de Perícias do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Henrique B Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil. .,Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, RS, Brazil.
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32
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Perkins A, Parsonage D, Nelson KJ, Ogba OM, Cheong PHY, Poole LB, Karplus PA. Peroxiredoxin Catalysis at Atomic Resolution. Structure 2016; 24:1668-1678. [PMID: 27594682 DOI: 10.1016/j.str.2016.07.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/24/2016] [Accepted: 07/17/2016] [Indexed: 12/23/2022]
Abstract
Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases that guard cells against oxidative damage, are virulence factors for pathogens, and are involved in eukaryotic redox regulatory pathways. We have analyzed catalytically active crystals to capture atomic resolution snapshots of a PrxQ subfamily enzyme (from Xanthomonas campestris) proceeding through thiolate, sulfenate, and sulfinate species. These analyses provide structures of unprecedented accuracy for seeding theoretical studies, and reveal conformational intermediates giving insight into the reaction pathway. Based on a highly non-standard geometry seen for the sulfenate intermediate, we infer that the sulfenate formation itself can strongly promote local unfolding of the active site to enhance productive catalysis. Further, these structures reveal that preventing local unfolding, in this case via crystal contacts, results in facile hyperoxidative inactivation even for Prxs normally resistant to such inactivation. This supports previous proposals that conformation-specific inhibitors may be useful for achieving selective inhibition of Prxs that are drug targets.
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Affiliation(s)
- Arden Perkins
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Derek Parsonage
- 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
| | - O Maduka Ogba
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | | | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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33
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Awoonor-Williams E, Rowley CN. Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins. J Chem Theory Comput 2016; 12:4662-73. [DOI: 10.1021/acs.jctc.6b00631] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
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34
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Kim KH, Lee W, Kim EE. Crystal structures of human peroxiredoxin 6 in different oxidation states. Biochem Biophys Res Commun 2016; 477:717-722. [PMID: 27353378 DOI: 10.1016/j.bbrc.2016.06.125] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/24/2016] [Indexed: 11/27/2022]
Abstract
Peroxiredoxins (Prxs) are a family of antioxidant enzymes found ubiquitously. Prxs function not only as H2O2 scavengers but also as highly sensitive H2O2 sensors and signal transducers. Since reactive oxygen species are involved in many cellular metabolic and signaling processes, Prxs play important roles in various diseases. Prxs can be hyperoxidized to the sulfinic acid (SO2H) or sulfonic acid (SO3H) forms in the presence of high concentrations of H2O2. It is known that oligomerization of Prx is changed accompanying oxidation states, and linked to the function. Among the six Prxs in mammals, Prx6 is the only 1-Cys Prx. It is found in all organs in humans, unlike some 2-Cys Prxs, and is present in all species from bacteria to humans. In addition, Prx6 has Ca(2+)-independent phospholipase A2 (PLA2) activity. Thus far only the crystal structure of Prx in the oxidized state has been reported. In this study, we present the crystal structures of human Prx6 in the reduced (SH) and the sulfinic acid (SO2H) forms.
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Affiliation(s)
- Kyung Hee Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.
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35
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Structures of Human Peroxiredoxin 3 Suggest Self-Chaperoning Assembly that Maintains Catalytic State. Structure 2016; 24:1120-9. [PMID: 27238969 DOI: 10.1016/j.str.2016.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/14/2016] [Accepted: 04/09/2016] [Indexed: 01/05/2023]
Abstract
Peroxiredoxins are antioxidant proteins primarily responsible for detoxification of hydroperoxides in cells. On exposure to various cellular stresses, peroxiredoxins can acquire chaperone activity, manifested as quaternary reorganization into a high molecular weight (HMW) form. Acidification, for example, causes dodecameric rings of human peroxiredoxin 3 (HsPrx3) to stack into long helical filaments. In this work, a 4.1-Å resolution structure of low-pH-instigated helical filaments was elucidated, showing a locally unfolded active site and partially folded C terminus. A 2.8-Å crystal structure of HsPrx3 was determined at pH 8.5 under reducing conditions, wherein dodecameric rings are arranged as a short stack, with symmetry similar to low-pH filaments. In contrast to previous observations, the crystal structure displays both a fully folded active site and ordered C terminus, suggesting that the HsPrx3 HMW form maintains catalytic activity. We propose a new role for the HMW form as a self-chaperoning assembly maintaining HsPrx3 function under stress.
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Nielsen MH, Kidmose RT, Jenner LB. Structure of TSA2 reveals novel features of the active-site loop of peroxiredoxins. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:158-67. [DOI: 10.1107/s2059798315023815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/10/2015] [Indexed: 01/05/2023]
Abstract
Saccharomyces cerevisiaeTSA2 belongs to the family of typical 2-Cys peroxiredoxins, a ubiquitously expressed family of redox-active enzymes that utilize a conserved peroxidatic cysteine to reduce peroxides. Typical 2-Cys peroxiredoxins have been shown to be involved in protection against oxidative stress and in hydrogen peroxide signalling. Furthermore, several 2-Cys peroxiredoxins, includingS. cerevisiaeTSA1 and TSA2, are able to switch to chaperone activity upon hyperoxidation of their peroxidatic cysteine. This makes the sensitivity to hyperoxidation of the peroxidatic cysteine a very important determinant for the cellular function of a peroxiredoxin under different cellular conditions. Typical 2-Cys peroxiredoxins exist as dimers, and in the course of the reaction the peroxidatic cysteine forms a disulfide with a resolving cysteine located in the C-terminus of its dimeric partner. This requires a local unfolding of the active site and the C-terminus. The balance between the fully folded and locally unfolded conformations is of key importance for the reactivity and sensitivity to hyperoxidation of the different peroxiredoxins. Here, the structure of a C48S mutant of TSA2 fromS. cerevisiaethat mimics the reduced state of the peroxidatic cysteine has been determined. The structure reveals a novel conformation for the strictly conserved Pro41, which is likely to affect the delicate balance between the fully folded and locally unfolded conformations of the active site, and therefore the reactivity and the sensitivity to hyperoxidation. Furthermore, the structure also explains the observed difference in the pKavalues of the peroxidatic cysteines ofS. cerevisiaeTSA1 and TSA2 despite their very high sequence identity.
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Staudacher V, Djuika CF, Koduka J, Schlossarek S, Kopp J, Büchler M, Lanzer M, Deponte M. Plasmodium falciparum antioxidant protein reveals a novel mechanism for balancing turnover and inactivation of peroxiredoxins. Free Radic Biol Med 2015; 85:228-36. [PMID: 25952724 DOI: 10.1016/j.freeradbiomed.2015.04.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 12/12/2022]
Abstract
Life under aerobic conditions has shaped peroxiredoxins (Prx) as ubiquitous thiol-dependent hydroperoxidases and redox sensors. Structural features that balance the catalytically active or inactive redox states of Prx, and, therefore, their hydroperoxidase or sensor function, have so far been analyzed predominantly for Prx1-type enzymes. Here we identify and characterize two modulatory residues of the Prx5-type model enzyme PfAOP from the malaria parasite Plasmodium falciparum. Gain- and loss-of-function mutants reveal a correlation between the enzyme parameters and the inactivation susceptibility of PfAOP with the size of residue 109 and the presence or absence of a catalytically relevant but nonessential cysteine residue. Based on our kinetic data and the crystal structure of PfAOP(L109M), we suggest a novel mechanism for balancing the hydroperoxidase activity and inactivation susceptibility of Prx5-type enzymes. Our study provides unexpected insights into Prx structure-function relationships and contributes to our understanding of what makes Prx good enzymes or redox sensors.
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Affiliation(s)
- Verena Staudacher
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Carine F Djuika
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Joshua Koduka
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Sarah Schlossarek
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Jürgen Kopp
- Biochemistry Center (BZH), Ruprecht-Karls University, D-69120 Heidelberg, Germany; Cellnetworks Excellence Cluster, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Marleen Büchler
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Michael Lanzer
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Marcel Deponte
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany.
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Perkins A, Nelson KJ, Parsonage D, Poole LB, Karplus PA. Peroxiredoxins: guardians against oxidative stress and modulators of peroxide signaling. Trends Biochem Sci 2015; 40:435-45. [PMID: 26067716 DOI: 10.1016/j.tibs.2015.05.001] [Citation(s) in RCA: 389] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/27/2015] [Accepted: 05/01/2015] [Indexed: 02/08/2023]
Abstract
Peroxiredoxins (Prxs) are a ubiquitous family of cysteine-dependent peroxidase enzymes that play dominant roles in regulating peroxide levels within cells. These enzymes, often present at high levels and capable of rapidly clearing peroxides, display a remarkable array of variations in their oligomeric states and susceptibility to regulation by hyperoxidative inactivation and other post-translational modifications. Key conserved residues within the active site promote catalysis by stabilizing the transition state required for transferring the terminal oxygen of hydroperoxides to the active site (peroxidatic) cysteine residue. Extensive investigations continue to expand our understanding of the scope of their importance as well as the structures and forces at play within these critical defense and regulatory enzymes.
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Affiliation(s)
- Arden Perkins
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97333, USA
| | - Kimberly J Nelson
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97333, USA.
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Cunniff B, Newick K, Nelson KJ, Wozniak AN, Beuschel S, Leavitt B, Bhave A, Butnor K, Koenig A, Chouchani ET, James AM, Haynes AC, Lowther WT, Murphy MP, Shukla A, Heintz NH. Disabling Mitochondrial Peroxide Metabolism via Combinatorial Targeting of Peroxiredoxin 3 as an Effective Therapeutic Approach for Malignant Mesothelioma. PLoS One 2015; 10:e0127310. [PMID: 26011724 PMCID: PMC4444329 DOI: 10.1371/journal.pone.0127310] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 04/14/2015] [Indexed: 01/01/2023] Open
Abstract
Dysregulation of signaling pathways and energy metabolism in cancer cells enhances production of mitochondrial hydrogen peroxide that supports tumorigenesis through multiple mechanisms. To counteract the adverse effects of mitochondrial peroxide many solid tumor types up-regulate the mitochondrial thioredoxin reductase 2 - thioredoxin 2 (TRX2) - peroxiredoxin 3 (PRX3) antioxidant network. Using malignant mesothelioma cells as a model, we show that thiostrepton (TS) irreversibly disables PRX3 via covalent crosslinking of peroxidatic and resolving cysteine residues in homodimers, and that targeting the oxidoreductase TRX2 with the triphenylmethane gentian violet (GV) potentiates adduction by increasing levels of disulfide-bonded PRX3 dimers. Due to the fact that activity of the PRX3 catalytic cycle dictates the rate of adduction by TS, immortalized and primary human mesothelial cells are significantly less sensitive to both compounds. Moreover, stable knockdown of PRX3 reduces mesothelioma cell proliferation and sensitivity to TS. Expression of catalase in shPRX3 mesothelioma cells restores defects in cell proliferation but not sensitivity to TS. In a SCID mouse xenograft model of human mesothelioma, administration of TS and GV together reduced tumor burden more effectively than either agent alone. Because increased production of mitochondrial hydrogen peroxide is a common phenotype of malignant cells, and TS and GV are well tolerated in mammals, we propose that targeting PRX3 is a feasible redox-dependent strategy for managing mesothelioma and other intractable human malignancies.
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Affiliation(s)
- Brian Cunniff
- University of Vermont, College of Medicine, Department of Pathology, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
- * E-mail:
| | - Kheng Newick
- University of Pennsylvania School of Medicine, Division of Pulmonary, Thoracic Oncology Research Laboratory, Philadelphia, PA, 19147, United States of America
| | - Kimberly J. Nelson
- Wake Forest School of Medicine, Department of Biochemistry, Medical Center Boulevard, Winston-Salem, NC, 27157, United States of America
| | - Alexandra N. Wozniak
- University of Vermont, College of Medicine, Department of Pathology, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
| | - Stacie Beuschel
- University of Vermont, College of Medicine, Department of Pathology, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
| | - Bruce Leavitt
- University of Vermont, College of Medicine, Department of Surgery, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
| | - Anant Bhave
- University of Vermont, College of Medicine, Department of Radiology, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
| | - Kelly Butnor
- University of Vermont, College of Medicine, Department of Pathology, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
| | - Andreas Koenig
- University of Vermont, Department of Immunology medicine, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
| | - Edward T. Chouchani
- Medical Research Council, Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 0XY, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 2QQ, United Kingdom
| | - Andrew M. James
- Medical Research Council, Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Alexina C. Haynes
- Wake Forest School of Medicine, Department of Biochemistry, Medical Center Boulevard, Winston-Salem, NC, 27157, United States of America
| | - W. Todd Lowther
- Wake Forest School of Medicine, Department of Biochemistry, Medical Center Boulevard, Winston-Salem, NC, 27157, United States of America
| | - Michael P. Murphy
- Medical Research Council, Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Arti Shukla
- University of Vermont, College of Medicine, Department of Pathology, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
| | - Nicholas H. Heintz
- University of Vermont, College of Medicine, Department of Pathology, 149 Beaumont Ave, Burlington, VT, 05405, United States of America
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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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Parsonage D, Nelson KJ, Ferrer-Sueta G, Alley S, Karplus PA, Furdui CM, Poole LB. Dissecting peroxiredoxin catalysis: separating binding, peroxidation, and resolution for a bacterial AhpC. Biochemistry 2015; 54:1567-75. [PMID: 25633283 PMCID: PMC4489686 DOI: 10.1021/bi501515w] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Peroxiredoxins make up a ubiquitous family of cysteine-dependent peroxidases that reduce hydroperoxide or peroxynitrite substrates through formation of a cysteine sulfenic acid (R-SOH) at the active site. In the 2-Cys peroxiredoxins, a second (resolving) cysteine reacts with the sulfenic acid to form a disulfide bond. For all peroxiredoxins, structural rearrangements in the vicinity of the active site cysteine(s) are necessary to allow disulfide bond formation and subsequent reductive recycling. In this study, we evaluated the rate constants for individual steps in the catalytic cycle of Salmonella typhimurium AhpC. Conserved Trp residues situated close to both peroxidatic and resolving cysteines in AhpC give rise to large changes in fluorescence during the catalytic cycle. For recycling, AhpF very efficiently reduces the AhpC disulfide, with a single discernible step and a rate constant of 2.3 × 10(7) M(-1) s(-1). Peroxide reduction was more complex and could be modeled as three steps, beginning with a reversible binding of H2O2 to the enzyme (k1 = 1.36 × 10(8) M(-1) s(-1), and k-1 = 53 s(-1)), followed by rapid sulfenic acid generation (620 s(-1)) and then rate-limiting disulfide bond formation (75 s(-1)). Using bulkier hydroperoxide substrates with higher Km values, we found that different efficiencies (kcat/Km) for turnover of AhpC with these substrates are primarily caused by their slower rates of binding. Our findings indicate that this bacterial peroxiredoxin exhibits rates for both reducing and oxidizing parts of the catalytic cycle that are among the fastest observed so far for this diverse family of enzymes.
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Affiliation(s)
- Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
- Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Kimberly J. Nelson
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
- Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica and Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
| | - Samantha Alley
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - P. Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 AG Life Sciences Building, Corvallis, Oregon 97331, United States
| | - Cristina M. Furdui
- Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
- Section on Molecular Medicine in Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
- Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
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Perkins A, Poole L, Karplus PA. Tuning of peroxiredoxin catalysis for various physiological roles. Biochemistry 2014; 53:7693-705. [PMID: 25403613 PMCID: PMC4270387 DOI: 10.1021/bi5013222] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 11/12/2014] [Indexed: 12/15/2022]
Abstract
Peroxiredoxins (Prxs) make up an ancient family of enzymes that are the predominant peroxidases for nearly all organisms and play essential roles in reducing hydrogen peroxide, organic hydroperoxides, and peroxynitrite. Even between distantly related organisms, the core protein fold and key catalytic residues related to its cysteine-based catalytic mechanism have been retained. Given that these enzymes appeared early in biology, Prxs have experienced more than 1 billion years of optimization for specific ecological niches. Although their basic enzymatic function remains the same, Prxs have diversified and are involved in roles such as protecting DNA against mutation, defending pathogens against host immune responses, suppressing tumor formation, and--for eukaryotes--helping regulate peroxide signaling via hyperoxidation of their catalytic Cys residues. Here, we review the current understanding of the physiological roles of Prxs by analyzing knockout and knockdown studies from ∼25 different species. We also review what is known about the structural basis for the sensitivity of some eukaryotic Prxs to inactivation by hyperoxidation. In considering the physiological relevance of hyperoxidation, we explore the distribution across species of sulfiredoxin (Srx), the enzyme responsible for rescuing hyperoxidized Prxs. We unexpectedly find that among eukaryotes appearing to have a "sensitive" Prx isoform, some do not contain Srx. Also, as Prxs are suggested to be promising targets for drug design, we discuss the rationale behind recently proposed strategies for their selective inhibition.
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Affiliation(s)
- Arden Perkins
- Department
of Biochemistry and Biophysics, Oregon State
University, Corvallis, Oregon 97331, United
States
| | - Leslie
B. Poole
- Department
of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State
University, Corvallis, Oregon 97331, United
States
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Peroxiredoxin 3 levels regulate a mitochondrial redox setpoint in malignant mesothelioma cells. Redox Biol 2014; 3:79-87. [PMID: 25462069 PMCID: PMC4297934 DOI: 10.1016/j.redox.2014.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/05/2014] [Accepted: 11/07/2014] [Indexed: 12/31/2022] Open
Abstract
Peroxiredoxin 3 (PRX3), a typical 2-Cys peroxiredoxin located exclusively in the mitochondrial matrix, is the principal peroxidase responsible for metabolizing mitochondrial hydrogen peroxide, a byproduct of cellular respiration originating from the mitochondrial electron transport chain. Mitochondrial oxidants are produced in excess in cancer cells due to oncogenic transformation and metabolic reorganization, and signals through FOXM1 and other redox-responsive factors to support a hyper-proliferative state. Over-expression of PRX3 in cancer cells has been shown to counteract oncogene-induced senescence and support tumor cell growth and survival making PRX3 a credible therapeutic target. Using malignant mesothelioma (MM) cells stably expressing shRNAs to PRX3 we show that decreased expression of PRX3 alters mitochondrial structure, function and cell cycle kinetics. As compared to control cells, knockdown of PRX3 expression increased mitochondrial membrane potential, basal ATP production, oxygen consumption and extracellular acidification rates. shPRX3 MM cells failed to progress through the cell cycle compared to wild type controls, with increased numbers of cells in G2/M phase. Diminished PRX3 expression also induced mitochondrial hyperfusion similar to the DRP1 inhibitor mdivi-1. Cell cycle progression and changes in mitochondrial networking were rescued by transient expression of either catalase or mitochondrial-targeted catalase, indicating high levels of hydrogen peroxide contribute to perturbations in mitochondrial structure and function in shPRX3 MM cells. Our results indicate that PRX3 levels establish a redox set point that permits MM cells to thrive in response to increased levels of mROS, and that perturbing the redox status governed by PRX3 impairs proliferation by altering cell cycle-dependent dynamics between mitochondrial networking and energy metabolism. Knockdown of PRX3 in malignant mesothelioma cells increases mitochondrial oxidants. Knockdown of PRX3 induces mitochondrial fusion and an increase in G2/M cells. Overexpression of catalase or mito-catalase rescues G2/M cell cycle block and mitochondrial defects.
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Randall LM, Manta B, Hugo M, Gil M, Batthyàny C, Trujillo M, Poole LB, Denicola A. Nitration transforms a sensitive peroxiredoxin 2 into a more active and robust peroxidase. J Biol Chem 2014; 289:15536-43. [PMID: 24719319 DOI: 10.1074/jbc.m113.539213] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peroxiredoxins (Prx) are efficient thiol-dependent peroxidases and key players in the mechanism of H2O2-induced redox signaling. Any structural change that could affect their redox state, oligomeric structure, and/or interaction with other proteins could have a significant impact on the cascade of signaling events. Several post-translational modifications have been reported to modulate Prx activity. One of these, overoxidation of the peroxidatic cysteine to the sulfinic derivative, inactivates the enzyme and has been proposed as a mechanism of H2O2 accumulation in redox signaling (the floodgate hypothesis). Nitration of Prx has been reported in vitro as well as in vivo; in particular, nitrated Prx2 was identified in brains of Alzheimer disease patients. In this work we characterize Prx2 tyrosine nitration, a post-translational modification on a noncatalytic residue that increases its peroxidase activity and its resistance to overoxidation. Mass spectrometry analysis revealed that treatment of disulfide-oxidized Prx2 with excess peroxynitrite renders mainly mononitrated and dinitrated species. Tyrosine 193 of the YF motif at the C terminus, associated with the susceptibility toward overoxidation of eukaryotic Prx, was identified as nitrated and is most likely responsible for the protection of the peroxidatic cysteine against oxidative inactivation. Kinetic analyses suggest that tyrosine nitration facilitates the intermolecular disulfide formation, transforming a sensitive Prx into a robust one. Thus, tyrosine nitration appears as another mechanism to modulate these enzymes in the complex network of redox signaling.
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Affiliation(s)
- Lía M Randall
- From the Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay, the Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo 11100, Uruguay
| | - Bruno Manta
- From the Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay, the Laboratorio de Biología Redox de Tripanosomas, Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay
| | - Martín Hugo
- the Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo 11100, Uruguay, the Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11100 Montevideo, Uruguay
| | - Magdalena Gil
- the Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay, the Unidad de Bioquímica y Proteómica Analíticas, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, 11600 Montevideo, Uruguay, and
| | - Carlos Batthyàny
- the Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo 11100, Uruguay, the Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11100 Montevideo, Uruguay, the Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay
| | - Madia Trujillo
- the Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo 11100, Uruguay, the Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11100 Montevideo, Uruguay
| | - Leslie B Poole
- the Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Ana Denicola
- From the Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay, the Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo 11100, Uruguay,
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