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Farjallah A, Boubakri H, Barhoumi F, Brahmi R, Gandour M. Systematic analysis of Prx genes in the Brachypodium genus and their expression pattern under abiotic constraints. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:93-105. [PMID: 37991495 DOI: 10.1111/plb.13592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Peroxiredoxins (Prx) are ubiquitous peroxidases required for the removal of excess free radicals produced under stress conditions. Peroxiredoxin genes (Prx) in the Brachypodium genus were identified using bioinformatics tools and their expression profiles were determined under abiotic stress using RT-qPCR. The promoter regions of Prx genes contain several cis-acting elements related to stress response. In silico expression analysis showed that B. distachyon Prx genes (BdPrx) are tissue specific. RT-qPCR analysis revealed their differential expression when exposed to salt or PEG-induced dehydration stress. In addition, the upregulation of BdPrx genes was accompanied by accumulation of H2 O2 . Exogenous application of H2 O2 induced expression of almost all BdPrx genes. The identified molecular interaction network indicated that Prx proteins may contribute to abiotic stress tolerance by regulating key enzymes involved in lignin biosynthesis. Overall, our findings suggest the potential role of Prx genes in abiotic stress tolerance and lay the foundation for future functional analyses aiming to engineer genetically improved cereal lines.
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Affiliation(s)
- A Farjallah
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences and Technics of Sidi Bouzid, University of Kairouan, Kairouan, Tunisia
| | - H Boubakri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - F Barhoumi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - R Brahmi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - M Gandour
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences and Technics of Sidi Bouzid, University of Kairouan, Kairouan, Tunisia
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2
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Lang L, Wolf AC, Riedel M, Thibol L, Geissel F, Feld K, Zimmermann J, Morgan B, Manolikakes G, Deponte M. Substrate Promiscuity and Hyperoxidation Susceptibility as Potential Driving Forces for the Co-evolution of Prx5-Type and Prx6-Type 1-Cys Peroxiredoxin Mechanisms. ACS Catal 2023. [DOI: 10.1021/acscatal.2c04896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Lukas Lang
- Faculty of Chemistry, TU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Ann-Cathrin Wolf
- Faculty of Chemistry, TU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Mareike Riedel
- Faculty of Chemistry, TU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Lea Thibol
- Faculty of Chemistry, TU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Fabian Geissel
- Faculty of Chemistry, TU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Kristina Feld
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Jannik Zimmermann
- Institute of Biochemistry, Centre for Human and Molecular Biology (ZHMB), Saarland University, D-66123 Saarbrücken, Germany
| | - Bruce Morgan
- Institute of Biochemistry, Centre for Human and Molecular Biology (ZHMB), Saarland University, D-66123 Saarbrücken, Germany
| | - Georg Manolikakes
- Faculty of Chemistry, TU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Marcel Deponte
- Faculty of Chemistry, TU Kaiserslautern, D-67663 Kaiserslautern, Germany
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3
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Hewitt OH, Degnan SM. Antioxidant enzymes that target hydrogen peroxide are conserved across the animal kingdom, from sponges to mammals. Sci Rep 2023; 13:2510. [PMID: 36781921 PMCID: PMC9925728 DOI: 10.1038/s41598-023-29304-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
Oxygen is the sustenance of aerobic life and yet is highly toxic. In early life, antioxidants functioned solely to defend against toxic effects of reactive oxygen species (ROS). Later, as aerobic metabolisms evolved, ROS became essential for signalling. Thus, antioxidants are multifunctional and must detoxify, but also permit ROS signalling for vital cellular processes. Here we conduct metazoan-wide genomic assessments of three enzymatic antioxidant families that target the predominant ROS signaller, hydrogen peroxide: namely, monofunctional catalases (CAT), peroxiredoxins (PRX), and glutathione peroxidases (GPX). We reveal that the two most evolutionary ancient families, CAT and PRX, exhibit metazoan-wide conservation. In the basal animal lineage, sponges (phylum Porifera), we find all three antioxidant families, but with GPX least abundant. Poriferan CATs are distinct from bilaterian CATs, but the evolutionary divergence is small. Amongst PRXs, subfamily PRX6 is the most conserved, whilst subfamily AhpC-PRX1 is the largest; PRX4 is the only core member conserved from sponges to mammals and may represent the ancestral animal AhpC-PRX1. Conversely, for GPX, the most recent family to arise, only the cysteine-dependent subfamily GPX7 is conserved across metazoans, and common across Porifera. Our analyses illustrate that the fundamental functions of antioxidants have resulted in gene conservation throughout the animal kingdom.
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Affiliation(s)
- Olivia H Hewitt
- School of Biological Sciences and Centre for Marine Science, University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Sandie M Degnan
- School of Biological Sciences and Centre for Marine Science, University of Queensland, St Lucia, QLD, 4072, Australia.
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4
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Bioinformatic Analyses of Peroxiredoxins and RF-Prx: A Random Forest-Based Predictor and Classifier for Prxs. Methods Mol Biol 2022; 2499:155-176. [PMID: 35696080 PMCID: PMC9844236 DOI: 10.1007/978-1-0716-2317-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Peroxiredoxins (Prxs) are a protein superfamily, present in all organisms, that play a critical role in protecting cellular macromolecules from oxidative damage but also regulate intracellular and intercellular signaling processes involving redox-regulated proteins and pathways. Bioinformatic approaches using computational tools that focus on active site-proximal sequence fragments (known as active site signatures) and iterative clustering and searching methods (referred to as TuLIP and MISST) have recently enabled the recognition of over 38,000 peroxiredoxins, as well as their classification into six functionally relevant groups. With these data providing so many examples of Prxs in each class, machine learning approaches offer an opportunity to extract additional information about features characteristic of these protein groups.In this study, we developed a novel computational method named "RF-Prx" based on a random forest (RF) approach integrated with K-space amino acid pairs (KSAAP) to identify peroxiredoxins and classify them into one of six subgroups. Our process performed in a superior manner compared to other machine learning classifiers. Thus the RF approach integrated with K-space amino acid pairs enabled the detection of class-specific conserved sequences outside the known functional centers and with potential importance. For example, drugs designed to target Prx proteins would likely suffer from cross-reactivity among distinct Prxs if targeted to conserved active sites, but this may be avoidable if remote, class-specific regions could be targeted instead.
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5
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Peroxiredoxin Asp f3 Is Essential for Aspergillus fumigatus To Overcome Iron Limitation during Infection. mBio 2021; 12:e0097621. [PMID: 34399627 PMCID: PMC8406167 DOI: 10.1128/mbio.00976-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspergillus fumigatus is an important fungal pathogen that causes allergic reactions but also life-threatening infections. One of the most abundant A. fumigatus proteins is Asp f3. This peroxiredoxin is a major fungal allergen and known for its role as a virulence factor, vaccine candidate, and scavenger of reactive oxygen species. Based on the hypothesis that Asp f3 protects A. fumigatus against killing by immune cells, we investigated the susceptibility of a conditional aspf3 mutant by employing a novel assay. Surprisingly, Asp f3-depleted hyphae were killed as efficiently as the wild type by human granulocytes. However, we identified an unexpected growth defect of mutants that lack Asp f3 under low-iron conditions, which explains the avirulence of the Δaspf3 deletion mutant in a murine infection model. A. fumigatus encodes two Asp f3 homologues which we named Af3l (Asp f3-like) 1 and Af3l2. Inactivation of Af3l1, but not of Af3l2, exacerbated the growth defect of the conditional aspf3 mutant under iron limitation, which ultimately led to death of the double mutant. Inactivation of the iron acquisition repressor SreA partially compensated for loss of Asp f3 and Af3l1. However, Asp f3 was not required for maintaining iron homeostasis or siderophore biosynthesis. Instead, we show that it compensates for a loss of iron-dependent antioxidant enzymes. Iron supplementation restored the virulence of the Δaspf3 deletion mutant in a murine infection model. Our results unveil the crucial importance of Asp f3 to overcome nutritional immunity and reveal a new biological role of peroxiredoxins in adaptation to iron limitation.
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6
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Rauer C, Sen N, Waman VP, Abbasian M, Orengo CA. Computational approaches to predict protein functional families and functional sites. Curr Opin Struct Biol 2021; 70:108-122. [PMID: 34225010 DOI: 10.1016/j.sbi.2021.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 01/06/2023]
Abstract
Understanding the mechanisms of protein function is indispensable for many biological applications, such as protein engineering and drug design. However, experimental annotations are sparse, and therefore, theoretical strategies are needed to fill the gap. Here, we present the latest developments in building functional subclassifications of protein superfamilies and using evolutionary conservation to detect functional determinants, for example, catalytic-, binding- and specificity-determining residues important for delineating the functional families. We also briefly review other features exploited for functional site detection and new machine learning strategies for combining multiple features.
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Affiliation(s)
- Clemens Rauer
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Neeladri Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Vaishali P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Mahnaz Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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7
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Martínez J, Nevado A, Suñén E, Gabriel M, Vélez-Del-Burgo A, Sánchez P, Postigo I. The Aspergillus niger Major Allergen (Asp n 3) DNA-Specific Sequence Is a Reliable Marker to Identify Early Fungal Contamination and Postharvest Damage in Mangifera indica Fruit. Front Microbiol 2021; 12:663323. [PMID: 34262539 PMCID: PMC8273346 DOI: 10.3389/fmicb.2021.663323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/25/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of this work was to study the value of the main allergen Asp n 3 of Aspergillus niger as a molecular marker of allergenicity and pathogenicity with the potential to be used in the identification of A. niger as a contaminant and cause of spoilage of Mangifera indica. Real-time polymerase chain reaction (RT-PCR) was used for the amplification of Asp n 3 gene. Two pairs of primers were designed: one for the amplification of the entire sequence and another one for the amplification of the most conserved region of this peroxisomal protein. The presence of A. niger was demonstrated by the early detection of the allergenic protein Asp n 3 coding gene, which could be considered a species-specific marker. The use of primers designed based on the conserved region of the Asp n 3 encoding gene allowed us to identify the presence of the closely related fungal species Aspergillus fumigatus by detecting Asp n 3 homologous protein, which can be cross-reactive. The use of conserved segments of the Asp n 3 gene or its entire sequence allows us to detect phylogenetically closely related species within the Aspergilaceae family or to identify species-specific contaminating fungi.
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Affiliation(s)
- Jorge Martínez
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria-Gasteiz, Spain
| | - Ander Nevado
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria-Gasteiz, Spain
| | - Ester Suñén
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria-Gasteiz, Spain
| | - Marta Gabriel
- INEGI, Institute of Science and Innovation in Mechanical and Industrial Engineering, Porto, Portugal
| | - Ainara Vélez-Del-Burgo
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria-Gasteiz, Spain
| | - Patricia Sánchez
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria-Gasteiz, Spain
| | - Idoia Postigo
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy and Laboratory of Parasitology and Allergy, Lascaray Research Centre, University of the Basque Country, Vitoria-Gasteiz, Spain
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8
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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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9
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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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10
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Rosen MR, Leuthaeuser JB, Parish CA, Fetrow JS. Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters. Biochemistry 2020; 59:4262-4284. [PMID: 33135415 DOI: 10.1021/acs.biochem.0c00651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active site similarities, some ArsC can function as low-molecular weight protein tyrosine phosphatases (LMW-PTPs). Broad superfamily classifications align with redox partners (Trx- or Grx-linked). To understand this superfamily's mechanistic diversity, the ArsC superfamily is classified on the basis of active site features utilizing the tools TuLIP (two-level iterative clustering process) and autoMISST (automated multilevel iterative sequence searching technique). This approach identified nine functionally relevant (perhaps isofunctional) protein groups. Five groups exhibit distinct ArsC mechanisms. Three are Grx-linked: group 4AA (classical ArsC), group 3AAA (YffB-like), and group 5BAA. Two are Trx-linked: groups 6AAAAA and 7AAAAAAAA. One is an Spx-like transcriptional regulatory group, group 5AAA. Three are potential LMW-PTP groups: groups 7BAAAA, and 7AAAABAA, which have not been previously identified, and the well-studied LMW-PTP family group 8AAA. Molecular dynamics simulations were utilized to explore functional site details. In several families, we confirm and add detail to literature-based mechanistic information. Mechanistic roles are hypothesized for conserved active site residues in several families. In three families, simulations of the unliganded structure sample specific conformational ensembles, which are proposed to represent either a more ligand-binding-competent conformation or a pathway toward a more binding-competent state; these active sites may be designed to traverse high-energy barriers to the lower-energy conformations necessary to more readily bind ligands. This more detailed biochemical understanding of ArsC and ArsC-like PTP mechanisms opens possibilities for further understanding of arsenate bioremediation and the LMW-PTP mechanism.
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Affiliation(s)
- Mikaela R Rosen
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Janelle B Leuthaeuser
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Carol A Parish
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
| | - Jacquelyn S Fetrow
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States
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11
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Teixeira F, Tse E, Castro H, Makepeace KAT, Meinen BA, Borchers CH, Poole LB, Bardwell JC, Tomás AM, Southworth DR, Jakob U. Chaperone activation and client binding of a 2-cysteine peroxiredoxin. Nat Commun 2019; 10:659. [PMID: 30737390 PMCID: PMC6368585 DOI: 10.1038/s41467-019-08565-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 01/14/2019] [Indexed: 02/02/2023] Open
Abstract
Many 2-Cys-peroxiredoxins (2-Cys-Prxs) are dual-function proteins, either acting as peroxidases under non-stress conditions or as chaperones during stress. The mechanism by which 2-Cys-Prxs switch functions remains to be defined. Our work focuses on Leishmania infantum mitochondrial 2-Cys-Prx, whose reduced, decameric subpopulation adopts chaperone function during heat shock, an activity that facilitates the transition from insects to warm-blooded host environments. Here, we have solved the cryo-EM structure of mTXNPx in complex with a thermally unfolded client protein, and revealed that the flexible N-termini of mTXNPx form a well-resolved central belt that contacts and encapsulates the unstructured client protein in the center of the decamer ring. In vivo and in vitro cross-linking studies provide further support for these interactions, and demonstrate that mTXNPx decamers undergo temperature-dependent structural rearrangements specifically at the dimer-dimer interfaces. These structural changes appear crucial for exposing chaperone-client binding sites that are buried in the peroxidase-active protein.
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Affiliation(s)
- Filipa Teixeira
- Department of Molecular, Cellular and Developmental, University of Michigan, Ann Arbor, 48109-1085, MI, USA.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200-135, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, 4050-313, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, 4050-313, Portugal
| | - Eric Tse
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, 94158, CA, USA
| | - Helena Castro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200-135, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, 4050-313, Portugal
| | - Karl A T Makepeace
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, V8P 5C2, BC, Canada.,Genome British Columbia Proteomics Centre, University of Victoria, Victoria, V8Z 7X8, BC, Canada
| | - Ben A Meinen
- Department of Molecular, Cellular and Developmental, University of Michigan, Ann Arbor, 48109-1085, MI, USA.,Howard Hughes Medical Institute, Ann Arbor, 48109-1085, MI, USA
| | - Christoph H Borchers
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, V8P 5C2, BC, Canada.,Genome British Columbia Proteomics Centre, University of Victoria, Victoria, V8Z 7X8, BC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, H4A 3T2, QC, Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, Montreal, H3T 1E2, QC, Canada
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, 27157, NC, USA
| | - James C Bardwell
- Department of Molecular, Cellular and Developmental, University of Michigan, Ann Arbor, 48109-1085, MI, USA.,Howard Hughes Medical Institute, Ann Arbor, 48109-1085, MI, USA
| | - Ana M Tomás
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200-135, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, 4050-313, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, 4050-313, Portugal
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, 94158, CA, USA.
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental, University of Michigan, Ann Arbor, 48109-1085, MI, USA.
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12
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Forshaw TE, Holmila R, Nelson KJ, Lewis JE, Kemp ML, Tsang AW, Poole LB, Lowther WT, Furdui CM. Peroxiredoxins in Cancer and Response to Radiation Therapies. Antioxidants (Basel) 2019; 8:antiox8010011. [PMID: 30609657 PMCID: PMC6356878 DOI: 10.3390/antiox8010011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/23/2018] [Accepted: 12/25/2018] [Indexed: 12/11/2022] Open
Abstract
Peroxiredoxins have a long-established cellular function as regulators of redox metabolism by catalyzing the reduction of peroxides (e.g., H2O2, lipid peroxides) with high catalytic efficiency. This activity is also critical to the initiation and relay of both phosphorylation and redox signaling in a broad range of pathophysiological contexts. Under normal physiological conditions, peroxiredoxins protect normal cells from oxidative damage that could promote oncogenesis (e.g., environmental stressors). In cancer, higher expression level of peroxiredoxins has been associated with both tumor growth and resistance to radiation therapies. However, this relationship between the expression of peroxiredoxins and the response to radiation is not evident from an analysis of data in The Cancer Genome Atlas (TCGA) or NCI60 panel of cancer cell lines. The focus of this review is to summarize the current experimental knowledge implicating this class of proteins in cancer, and to provide a perspective on the value of targeting peroxiredoxins in the management of cancer. Potential biases in the analysis of the TCGA data with respect to radiation resistance are also highlighted.
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Affiliation(s)
- Tom E Forshaw
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Reetta Holmila
- Department of Internal Medicine, Section on Molecular Medicine, 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.
| | - Joshua E Lewis
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
| | - Melissa L Kemp
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
| | - Allen W Tsang
- Department of Internal Medicine, Section on Molecular Medicine, 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.
| | - W Todd Lowther
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
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Analyses of the three 1-Cys Peroxiredoxins from Aspergillus fumigatus reveal that cytosolic Prx1 is central to H 2O 2 metabolism and virulence. Sci Rep 2018; 8:12314. [PMID: 30120327 PMCID: PMC6098058 DOI: 10.1038/s41598-018-30108-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
Standing among the front defense strategies against pathogens, host phagocytic cells release various oxidants. Therefore, pathogens have to cope with stressful conditions at the site of infection. Peroxiredoxins (Prx) are highly reactive and abundant peroxidases that can support virulence and persistence of pathogens in distinct hosts. Here, we revealed that the opportunistic human pathogen A. fumigatus presents three 1-Cys Prx (Prx6 subfamily), which is unprecedented. We showed that PrxB and PrxC were in mitochondria, while Prx1 was in cytosol. As observed for other Prxs, recombinant Prx1 and PrxC decomposed H2O2 at elevated velocities (rate constants in the 107 M−1s−1 range). Deletion mutants for each Prx displayed higher sensitivity to oxidative challenge in comparison with the wild-type strain. Additionally, cytosolic Prx1 was important for A. fumigatus survival upon electron transport dysfunction. Expression of Prxs was dependent on the SakAHOG1 MAP kinase and the Yap1YAP1 transcription factor, a global regulator of the oxidative stress response in fungi. Finally, cytosolic Prx1 played a major role in pathogenicity, since it is required for full virulence, using a neutropenic mouse infection model. Our data indicate that the three 1-Cys Prxs act together to maintain the redox balance of A. fumigatus.
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14
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Affiliation(s)
- Jacquelyn S. Fetrow
- Office of the President, Albright College, Reading, Pennsylvania, United States of America
- * E-mail:
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
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Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. Active site C P-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins. Free Radic Biol Med 2018; 118:59-70. [PMID: 29474868 DOI: 10.1016/j.freeradbiomed.2018.02.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/12/2018] [Accepted: 02/17/2018] [Indexed: 01/20/2023]
Abstract
Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (CP) located in a conserved sequence Pxxx(T/S)xxCP motif known as CP-loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the CP-loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the CP-loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the CP-loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the CP-loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the CP-loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted CP-loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the CP-loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles.
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Affiliation(s)
- Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Computer Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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16
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Voth W, Jakob U. Stress-Activated Chaperones: A First Line of Defense. Trends Biochem Sci 2017; 42:899-913. [PMID: 28893460 DOI: 10.1016/j.tibs.2017.08.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 10/18/2022]
Abstract
Proteins are constantly challenged by environmental stress conditions that threaten their structure and function. Especially problematic are oxidative, acid, and severe heat stress which induce very rapid and widespread protein unfolding and generate conditions that make canonical chaperones and/or transcriptional responses inadequate to protect the proteome. We review here recent advances in identifying and characterizing stress-activated chaperones which are inactive under non-stress conditions but become potent chaperones under specific protein-unfolding stress conditions. We discuss the post-translational mechanisms by which these chaperones sense stress, and consider the role that intrinsic disorder plays in their regulation and function. We examine their physiological roles under both non-stress and stress conditions, their integration into the cellular proteostasis network, and their potential as novel therapeutic targets.
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Affiliation(s)
- Wilhelm Voth
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular Biology, Universitätsmedizin Göttingen, 37073 Göttingen, Germany
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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17
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Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci 2017; 26:677-699. [PMID: 28054422 PMCID: PMC5368075 DOI: 10.1002/pro.3112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023]
Abstract
Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.
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Affiliation(s)
- Stacy T. Knutson
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Brian M. Westwood
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Janelle B. Leuthaeuser
- Molecular Genetics and Genomics ProgramWake Forest School of MedicineWinston‐SalemNorth Carolina27157
| | - Brandon E. Turner
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Don Nguyendac
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Gabrielle Shea
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Kiran Kumar
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Julia D. Hayden
- Biochemistry Program, Dickinson CollegeCarlislePennsylvania17013
| | - Angela F. Harper
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Shoshana D. Brown
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - John H. Morris
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - Thomas E. Ferrin
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - Patricia C. Babbitt
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
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