1
|
Goncalves D, Duy DL, Peffer S, Morano KA. Cytoplasmic redox imbalance in the thioredoxin system activates Hsf1 and results in hyperaccumulation of the sequestrase Hsp42 with misfolded proteins. Mol Biol Cell 2024; 35:ar53. [PMID: 38381577 PMCID: PMC11064659 DOI: 10.1091/mbc.e23-07-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Cells employ multiple systems to maintain homeostasis when experiencing environmental stress. For example, the folding of nascent polypeptides is exquisitely sensitive to proteotoxic stressors including heat, pH, and oxidative stress, and is safeguarded by a network of protein chaperones that concentrate potentially toxic misfolded proteins into transient assemblies to promote folding or degradation. The redox environment itself is buffered by both cytosolic and organellar thioredoxin and glutathione pathways. How these systems are linked is poorly understood. Here, we determine that specific disruption of the cytosolic thioredoxin system resulted in constitutive activation of the heat shock response in Saccharomyces cerevisiae and accumulation of the sequestrase Hsp42 into an exaggerated and persistent juxtanuclear quality control (JUNQ) compartment. Terminally misfolded proteins also accumulated in this compartment in thioredoxin reductase (TRR1)-deficient cells, despite apparently normal formation and dissolution of transient cytoplasmic quality control (CytoQ) bodies during heat shock. Notably, cells lacking TRR1 and HSP42 exhibited severe synthetic slow growth exacerbated by oxidative stress, signifying a critical role for Hsp42 under redox-challenged conditions. Finally, we demonstrated that Hsp42 localization patterns in trr1∆ cells mimic those observed in chronically aging and glucose-starved cells, linking nutrient depletion and redox imbalance with management of misfolded proteins via a process of long-term sequestration.
Collapse
Affiliation(s)
- Davi Goncalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
| | - Duong Long Duy
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
| | - Sara Peffer
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
- Microbiology and Infectious Disease Program, MD Anderson UTHealth Graduate School at UTHealth Houston, Houston, TX 77030
| | - Kevin A. Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
| |
Collapse
|
2
|
Gonçalves D, Peffer S, Morano KA. Cytoplasmic redox imbalance in the thioredoxin system activates Hsf1 and results in hyperaccumulation of the sequestrase Hsp42 with misfolded proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546610. [PMID: 37425817 PMCID: PMC10327208 DOI: 10.1101/2023.06.26.546610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cells employ multiple systems to maintain homeostasis when experiencing environmental stress. For example, the folding of nascent polypeptides is exquisitely sensitive to proteotoxic stressors including heat, pH and oxidative stress, and is safeguarded by a network of protein chaperones that concentrate potentially toxic misfolded proteins into transient assemblies to promote folding or degradation. The redox environment itself is buffered by both cytosolic and organellar thioredoxin and glutathione pathways. How these systems are linked is poorly understood. Here, we determine that specific disruption of the cytosolic thioredoxin system resulted in constitutive activation of the heat shock response in Saccharomyces cerevisiae and accumulation of the sequestrase Hsp42 into an exaggerated and persistent juxtanuclear quality control (JUNQ) compartment. Terminally misfolded proteins also accumulated in this compartment in thioredoxin reductase (TRR1)-deficient cells, despite apparently normal formation and dissolution of transient cytoplasmic quality control (CytoQ) bodies during heat shock. Notably, cells lacking TRR1 and HSP42 exhibited severe synthetic slow growth exacerbated by oxidative stress, signifying a critical role for Hsp42 under redox-challenged conditions. Finally, we demonstrated that Hsp42 localization patterns in trr1∆ cells mimic those observed in chronically aging and glucose-starved cells, linking nutrient depletion and redox imbalance with management of misfolded proteins via a mechanism of long-term sequestration.
Collapse
Affiliation(s)
- Davi Gonçalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX USA
- Current address: Cemvita Factory, Houston, TX USA
| | - Sara Peffer
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX USA
- MD Anderson UTHealth Graduate School at UTHealth Houston, Houston, TX USA
- Current address: Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Kevin A. Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX USA
| |
Collapse
|
3
|
Wu T, Li ST, Ran Y, Lin Y, Liu L, Zhang X, Zhou L, Zhang L, Wu D, Yang B, Tang S. Mapping protein direct interactome of oxidoreductases with small molecular chemical cross-linkers in live cells. Redox Biol 2023; 61:102642. [PMID: 36863169 PMCID: PMC9986639 DOI: 10.1016/j.redox.2023.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Identifying direct substrates of enzymes has been a long-term challenge. Here, we present a strategy using live cell chemical cross-linking and mass spectrometry to identify the putative substrates of enzymes for further biochemical validation. Compared with other methods, our strategy is based on the identification of cross-linked peptides supported by high-quality MS/MS spectra, which eliminates false-positive discoveries of indirect binders. Additionally, cross-linking sites allow the analysis of interaction interfaces, providing further information for substrate validation. We demonstrated this strategy by identifying direct substrates of thioredoxin in both E. coli and HEK293T cells using two bis-vinyl sulfone chemical cross-linkers BVSB and PDES. We confirmed that BVSB and PDES have high specificity in cross-linking the active site of thioredoxin with its substrates both in vitro and in live cells. Applying live cell cross-linking, we identified 212 putative substrates of thioredoxin in E. coli and 299 putative S-nitrosylation (SNO) substrates of thioredoxin in HEK293T cells. In addition to thioredoxin, we have shown that this strategy can be applied to other proteins in the thioredoxin superfamily. Based on these results, we believe future development of cross-linking techniques will further advance cross-linking mass spectrometry in identifying substrates of other classes of enzymes.
Collapse
Affiliation(s)
- Ting Wu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Shang-Tong Li
- Glbizzia Biosciences Co., Ltd, Beijing, 102601, China
| | - Yu Ran
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Yinuo Lin
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Lu Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiajun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Donghai Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
| | - Shibing Tang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| |
Collapse
|
4
|
West JD. Experimental Approaches for Investigating Disulfide-Based Redox Relays in Cells. Chem Res Toxicol 2022; 35:1676-1689. [PMID: 35771680 DOI: 10.1021/acs.chemrestox.2c00123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reversible oxidation of cysteine residues within proteins occurs naturally during normal cellular homeostasis and can increase during oxidative stress. Cysteine oxidation often leads to the formation of disulfide bonds, which can impact protein folding, stability, and function. Work in both prokaryotic and eukaryotic models over the past five decades has revealed several multiprotein systems that use thiol-dependent oxidoreductases to mediate disulfide bond reduction, formation, and/or rearrangement. Here, I provide an overview of how these systems operate to carry out disulfide exchange reactions in different cellular compartments, with a focus on their roles in maintaining redox homeostasis, transducing redox signals, and facilitating protein folding. Additionally, I review thiol-independent and thiol-dependent approaches for interrogating what proteins partner together in such disulfide-based redox relays. While the thiol-independent approaches rely either on predictive measures or standard procedures for monitoring protein-protein interactions, the thiol-dependent approaches include direct disulfide trapping methods as well as thiol-dependent chemical cross-linking. These strategies may prove useful in the systematic characterization of known and newly discovered disulfide relay mechanisms and redox switches involved in oxidant defense, protein folding, and cell signaling.
Collapse
Affiliation(s)
- James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| |
Collapse
|
5
|
Freije BJ, Freije WM, Do TU, Adkins GE, Bruch A, Hurtig JE, Morano KA, Schaffrath R, West JD. Identifying Interaction Partners of Yeast Protein Disulfide Isomerases Using a Small Thiol-Reactive Cross-Linker: Implications for Secretory Pathway Proteostasis. Chem Res Toxicol 2022; 35:326-336. [PMID: 35084835 PMCID: PMC8860869 DOI: 10.1021/acs.chemrestox.1c00376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein disulfide isomerases (PDIs) function in forming the correct disulfide bonds in client proteins, thereby aiding the folding of proteins that enter the secretory pathway. Recently, several PDIs have been identified as targets of organic electrophiles, yet the client proteins of specific PDIs remain largely undefined. Here, we report that PDIs expressed in Saccharomyces cerevisiae are targets of divinyl sulfone (DVSF) and other thiol-reactive protein cross-linkers. Using DVSF, we identified the interaction partners that were cross-linked to Pdi1 and Eug1, finding that both proteins form cross-linked complexes with other PDIs, as well as vacuolar hydrolases, proteins involved in cell wall biosynthesis and maintenance, and many ER proteostasis factors involved ER stress signaling and ER-associated protein degradation (ERAD). The latter discovery prompted us to examine the effects of DVSF on ER quality control, where we found that DVSF inhibits the degradation of the ERAD substrate CPY*, in addition to covalently modifying Ire1 and blocking the activation of the unfolded protein response. Our results reveal that DVSF targets many proteins within the ER proteostasis network and suggest that these proteins may be suitable targets for covalent therapeutic development in the future.
Collapse
Affiliation(s)
- Benjamin J. Freije
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA
| | - Wilson M. Freije
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA
| | - To Uyen Do
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA
| | - Grace E. Adkins
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA
| | - Alexander Bruch
- Fachgebiet Mikrobiologie; Institut für Biologie; Universität Kassel; Kassel, Germany
| | - Jennifer E. Hurtig
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA,Department of Microbiology & Molecular Genetics; McGovern Medical School; University of Texas at Houston; Houston, TX USA
| | - Kevin A. Morano
- Department of Microbiology & Molecular Genetics; McGovern Medical School; University of Texas at Houston; Houston, TX USA
| | - Raffael Schaffrath
- Fachgebiet Mikrobiologie; Institut für Biologie; Universität Kassel; Kassel, Germany
| | - James D. West
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA,Corresponding author , phone: 330-263-2368
| |
Collapse
|
6
|
Cobb DW, Woods GS, Muralidharan V. Activity-based Crosslinking to Identify Substrates of Thioredoxin-domain Proteinsin Malaria Parasites. Bio Protoc 2022; 12:e4322. [PMID: 35340291 PMCID: PMC8899546 DOI: 10.21769/bioprotoc.4322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 08/17/2021] [Accepted: 12/14/2021] [Indexed: 08/07/2023] Open
Abstract
Malaria remains a major public health issue, infecting nearly 220 million people every year. The spread of drug-resistant strains of Plasmodium falciparum around the world threatens the progress made against this disease. Therefore, identifying druggable and essential pathways in P. falciparum parasites remains a major area of research. One poorly understood area of parasite biology is the formation of disulfide bonds, which is an essential requirement for the folding of numerous proteins. Specialized chaperones with thioredoxin (Trx) domains catalyze the redox functions necessary for breaking incorrect and forming correct disulfide bonds in proteins. Defining the substrates of these redox chaperones is difficult and immunoprecipitation based assays cannot distinguish between substrates and interacting partners. Further, the substrate or client interactions with the redox chaperones are usually transient in nature. Activity based crosslinkers that rely on the nucleophilic cysteines on Trx domains and the disulfide bond forming cysteines on clients provide an easily scalable method to trap and identify the substrates of Trx-domain containing chaperones. The cell permeable crosslinker divinyl sulfone (DVSF) is active only in the presence of nucleophilic cysteines in proteins and, therefore, traps Trx domains with their substrates, as they form mixed disulfide bonds during the course of their catalytic activity. This allows the identification of substrates that rely on Trx activity for their folding, as well as discovering small molecules that interfere with Trx domain activity. Graphic abstract: Identification of thioredoxin domain substrates via divinylsulfone crosslinking and immunoprecipitation-mass spectrometry.
Collapse
Affiliation(s)
- David W. Cobb
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- Department of Cellular BIology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Grace S. Woods
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Vasant Muralidharan
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- Department of Cellular BIology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| |
Collapse
|
7
|
Vicker SL, Maina EN, Showalter AK, Tran N, Davidson EE, Bailey MR, McGarry SW, Freije WM, West JD. Broader than expected tolerance for substitutions in the WCGPCK catalytic motif of yeast thioredoxin 2. Free Radic Biol Med 2022; 178:308-313. [PMID: 34530076 DOI: 10.1016/j.freeradbiomed.2021.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/29/2022]
Abstract
Thioredoxins constitute a key class of oxidant defense enzymes that facilitate disulfide bond reduction in oxidized substrate proteins. While thioredoxin's WCGPCK active site motif is highly conserved in traditional model organisms, predicted thioredoxins from newly sequenced genomes show variability in this motif, making ascertaining which genes encode functional thioredoxins with robust activity a challenge. To address this problem, we generated a semi-saturation mutagenesis library of approximately 70 thioredoxin variants harboring mutations adjacent to their catalytic cysteines, making substitutions in the Saccharomyces cerevisiae thioredoxin Trx2. Using this library, we determined how such substitutions impact oxidant defense in yeast along with how they influence disulfide reduction and interaction with binding partners in vivo. The majority of thioredoxin variants screened rescued the slow growth phenotype that accompanies deletion of the yeast cytosolic thioredoxins; however, the ability of these mutant proteins to protect against H2O2-mediated toxicity, facilitate disulfide reduction, and interact with redox partners varied widely, depending on the site being mutated and the substitution made. We report that thioredoxin is less tolerant of substitutions at its conserved tryptophan and proline in the active site motif, while it is more amenable to substitutions at the conserved glycine and lysine. Our work highlights a noteworthy plasticity within the active site of this critical oxidant defense enzyme.
Collapse
Affiliation(s)
- Shayna L Vicker
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - Eran N Maina
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - Abigail K Showalter
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - Nghi Tran
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - Emma E Davidson
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - Morgan R Bailey
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - Stephen W McGarry
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - Wilson M Freije
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA.
| |
Collapse
|
8
|
Kaduhr L, Brachmann C, Ravichandran KE, West JD, Glatt S, Schaffrath R. Urm1, not quite a ubiquitin-like modifier? MICROBIAL CELL 2021; 8:256-261. [PMID: 34782858 PMCID: PMC8561144 DOI: 10.15698/mic2021.11.763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/27/2022]
Abstract
Ubiquitin related modifier 1 (Urm1) is a unique eukaryotic member of the ubiquitin-fold (UbF) protein family and conserved from yeast to humans. Urm1 is dual-functional, acting both as a sulfur carrier for thiolation of tRNA anticodons and as a protein modifier in a lysine-directed Ub-like conjugation also known as urmylation. Although Urm1 conjugation coincides with oxidative stress and targets proteins like 2-Cys peroxiredoxins from yeast (Ahp1) and fly (Prx5), it was unclear how urmylation proceeds molecularly and whether it is affected by the activity of these antioxidant enzymes. An in-depth study of Ahp1 urmylation in yeast from our laboratory (Brachmann et al., 2020) uncovered that promiscuous lysine target sites and specific redox requirements determine the Urm1 acceptor activity of the peroxiredoxin. The results clearly show that the dimer interface and the 2-Cys based redox-active centers of Ahp1 are affecting the Urm1 conjugation reaction. Together with in vivo assays demonstrating that high organic peroxide concentrations can prevent Ahp1 from being urmylated, Brachmann et al. provide insights into a potential link between Urm1 utilization and oxidant defense of cells. Here, we highlight these major findings and discuss wider implications with regards to an emerging link between Urm1 conjugation and redox biology. Moreover, from these studies we propose to redefine our perspective on Urm1 and the molecular nature of urmylation, a post-translational conjugation that may not be that ubiquitin-like after all.
Collapse
Affiliation(s)
- Lars Kaduhr
- Universität Kassel, Institut für Biologie, Fachgebiet Mikrobiologie, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Cindy Brachmann
- Universität Kassel, Institut für Biologie, Fachgebiet Mikrobiologie, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Keerthiraju Ethiraju Ravichandran
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Postgraduate School of Molecular Medicine, 02-091 Warsaw, Poland
| | - James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, USA
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raffael Schaffrath
- Universität Kassel, Institut für Biologie, Fachgebiet Mikrobiologie, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| |
Collapse
|
9
|
Fassler R, Zuily L, Lahrach N, Ilbert M, Reichmann D. The Central Role of Redox-Regulated Switch Proteins in Bacteria. Front Mol Biosci 2021; 8:706039. [PMID: 34277710 PMCID: PMC8282892 DOI: 10.3389/fmolb.2021.706039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/18/2021] [Indexed: 01/11/2023] Open
Abstract
Bacteria possess the ability to adapt to changing environments. To enable this, cells use reversible post-translational modifications on key proteins to modulate their behavior, metabolism, defense mechanisms and adaptation of bacteria to stress. In this review, we focus on bacterial protein switches that are activated during exposure to oxidative stress. Such protein switches are triggered by either exogenous reactive oxygen species (ROS) or endogenous ROS generated as by-products of the aerobic lifestyle. Both thiol switches and metal centers have been shown to be the primary targets of ROS. Cells take advantage of such reactivity to use these reactive sites as redox sensors to detect and combat oxidative stress conditions. This in turn may induce expression of genes involved in antioxidant strategies and thus protect the proteome against stress conditions. We further describe the well-characterized mechanism of selected proteins that are regulated by redox switches. We highlight the diversity of mechanisms and functions (as well as common features) across different switches, while also presenting integrative methodologies used in discovering new members of this family. Finally, we point to future challenges in this field, both in uncovering new types of switches, as well as defining novel additional functions.
Collapse
Affiliation(s)
- Rosi Fassler
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lisa Zuily
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Nora Lahrach
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Marianne Ilbert
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
10
|
da Motta KP, Lemos BB, Paltian JJ, Reis ASD, Blödorn GB, Alves D, Luchese C, Wilhelm EA. 7-Chloro-4-(phenylselanyl) quinoline reduces renal oxidative stress induced by oxaliplatin in mice. Can J Physiol Pharmacol 2021; 99:1102-1111. [PMID: 34015230 DOI: 10.1139/cjpp-2021-0090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The object of this study was to evaluate the relationship between oxidative damage induced by oxaliplatin (OXA) and the therapeutic potential of 7-chloro-4-(phenylselanyl) quinoline (4-PSQ) in kidney of mice. Mice received OXA (10 mg/kg) or vehicle intraperitoneally (days 0 and 2). Oral administration of 4-PSQ (1 mg/kg) or vehicle was performed on days 2 to 14. On day 15 the animals were euthanized and the kidneys and blood were collected. The effect of OXA and (or) 4-PSQ on urea, thiobarbituric acid reactive species, nonprotein thiol (NPSH), and protein carbonyl (PC) levels were investigated. Moreover, renal superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione reductase (GR), glutathione S-transferase (GST), δ-aminolevulinic acid dehydratase (δ-ALA-D), and Na+,K+ ATPase activities were evaluated. Our findings revealed an increase on urea levels and significant renal oxidative damage in OXA-induced mice. OXA exposure increased SOD, GPx, and GST activities and caused a reduction on NPSH levels and CAT and GR activities. Na+,K+ ATPase and δ-ALA-D activities were reduced by OXA. 4-PSQ decreased plasmatic urea levels and renal oxidative damage. SOD, GPx, CAT, GR, and Na+,K+ ATPase activities were restored by 4-PSQ. 4-PSQ may be a good prototype for the treatment of OXA-induced renal injury.
Collapse
Affiliation(s)
- Ketlyn P da Motta
- Laboratório de Pesquisa em Farmacologia Bioquímica - LaFarBio, CCQFA - Universidade Federal de Pelotas, UFPel, P.O. Box 354 - 96010-900, Pelotas, RS, Brazil.,Curso de Bacharelado em Química Forense, Centro de Ciências Químicas, Farmacêuticas e de Alimentos - Universidade Federal de Pelotas, UFPel, P.O. CEP 96010-900 Pelotas, RS, Brazil
| | - Briana B Lemos
- Laboratório de Pesquisa em Farmacologia Bioquímica - LaFarBio, CCQFA - Universidade Federal de Pelotas, UFPel, P.O. Box 354 - 96010-900, Pelotas, RS, Brazil.,Curso de Bacharelado em Química Forense, Centro de Ciências Químicas, Farmacêuticas e de Alimentos - Universidade Federal de Pelotas, UFPel, P.O. CEP 96010-900 Pelotas, RS, Brazil
| | - Jaini J Paltian
- Laboratório de Pesquisa em Farmacologia Bioquímica - LaFarBio, CCQFA - Universidade Federal de Pelotas, UFPel, P.O. Box 354 - 96010-900, Pelotas, RS, Brazil
| | - Angélica S Dos Reis
- Laboratório de Pesquisa em Farmacologia Bioquímica - LaFarBio, CCQFA - Universidade Federal de Pelotas, UFPel, P.O. Box 354 - 96010-900, Pelotas, RS, Brazil
| | - Gustavo B Blödorn
- Laboratório de Síntese Orgânica Limpa - LASOL, CCQFA - Universidade Federal de Pelotas, UFPel, P.O. Box 354 - 96010-900, Pelotas, RS, Brazil
| | - Diego Alves
- Laboratório de Síntese Orgânica Limpa - LASOL, CCQFA - Universidade Federal de Pelotas, UFPel, P.O. Box 354 - 96010-900, Pelotas, RS, Brazil
| | - Cristiane Luchese
- Laboratório de Pesquisa em Farmacologia Bioquímica - LaFarBio, CCQFA - Universidade Federal de Pelotas, UFPel, P.O. Box 354 - 96010-900, Pelotas, RS, Brazil
| | - Ethel A Wilhelm
- Laboratório de Pesquisa em Farmacologia Bioquímica - LaFarBio, CCQFA - Universidade Federal de Pelotas, UFPel, P.O. Box 354 - 96010-900, Pelotas, RS, Brazil.,Curso de Bacharelado em Química Forense, Centro de Ciências Químicas, Farmacêuticas e de Alimentos - Universidade Federal de Pelotas, UFPel, P.O. CEP 96010-900 Pelotas, RS, Brazil
| |
Collapse
|
11
|
Cobb DW, Kudyba HM, Villegas A, Hoopmann MR, Baptista RP, Bruton B, Krakowiak M, Moritz RL, Muralidharan V. A redox-active crosslinker reveals an essential and inhibitable oxidative folding network in the endoplasmic reticulum of malaria parasites. PLoS Pathog 2021; 17:e1009293. [PMID: 33534803 PMCID: PMC7886143 DOI: 10.1371/journal.ppat.1009293] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/16/2021] [Accepted: 01/07/2021] [Indexed: 12/18/2022] Open
Abstract
Malaria remains a major global health problem, creating a constant need for research to identify druggable weaknesses in P. falciparum biology. As important components of cellular redox biology, members of the Thioredoxin (Trx) superfamily of proteins have received interest as potential drug targets in Apicomplexans. However, the function and essentiality of endoplasmic reticulum (ER)-localized Trx-domain proteins within P. falciparum has not been investigated. We generated conditional mutants of the protein PfJ2—an ER chaperone and member of the Trx superfamily—and show that it is essential for asexual parasite survival. Using a crosslinker specific for redox-active cysteines, we identified PfJ2 substrates as PfPDI8 and PfPDI11, both members of the Trx superfamily as well, which suggests a redox-regulatory role for PfJ2. Knockdown of these PDIs in PfJ2 conditional mutants show that PfPDI11 may not be essential. However, PfPDI8 is required for asexual growth and our data suggest it may work in a complex with PfJ2 and other ER chaperones. Finally, we show that the redox interactions between these Trx-domain proteins in the parasite ER and their substrates are sensitive to small molecule inhibition. Together these data build a model for how Trx-domain proteins in the P. falciparum ER work together to assist protein folding and demonstrate the suitability of ER-localized Trx-domain proteins for antimalarial drug development. One of the leading and persistent causes of childhood mortality in the world is malaria, which is caused by parasites from the genus Plasmodium. Unfortunately, the parasite has developed resistance to all available drugs, making the discovery of new drug targets and potential small molecule inhibitors of essential parasite biology a top priority. A critical pathway required for many different biological processes in the parasite is oxidative folding which requires members of the Thioredoxin (Trx) superfamily of proteins. But we know almost nothing about the function and essentiality of Trx-domain proteins that localize to the endoplasmic reticulum, the origin of the secretory pathway, within P. falciparum. Here we show that a network of Trx-domain containing proteins function together and are essential for parasite survival within human red blood cells. Further, we identify a small molecule inhibitor of the redox activities of these Trx-domain containing proteins. This study demonstrates the suitability of this pathway for future antimalarial drug development.
Collapse
Affiliation(s)
- David W. Cobb
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
| | - Heather M. Kudyba
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
| | - Alejandra Villegas
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
| | - Michael R. Hoopmann
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Rodrigo P. Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Georgia, United States of America
| | - Baylee Bruton
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
| | - Michelle Krakowiak
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Vasant Muralidharan
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
- * E-mail:
| |
Collapse
|
12
|
Sunyer-Figueres M, Vázquez J, Mas A, Torija MJ, Beltran G. Transcriptomic Insights into the Effect of Melatonin in Saccharomyces cerevisiae in the Presence and Absence of Oxidative Stress. Antioxidants (Basel) 2020; 9:E947. [PMID: 33019712 PMCID: PMC7650831 DOI: 10.3390/antiox9100947] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
Abstract
Melatonin is a ubiquitous indolamine that plays important roles in various aspects of biological processes in mammals. In Saccharomyces cerevisiae, melatonin has been reported to exhibit antioxidant properties and to modulate the expression of some genes involved in endogenous defense systems. The aim of this study was to elucidate the role of supplemented melatonin at the transcriptional level in S. cerevisiae in the presence and absence of oxidative stress. This was achieved by exposing yeast cells pretreated with different melatonin concentrations to hydrogen peroxide and assessing the entry of melatonin into the cell and the yeast response at the transcriptional level (by microarray and qPCR analyses) and the physiological level (by analyzing changes in the lipid composition and mitochondrial activity). We found that exogenous melatonin crossed cellular membranes at nanomolar concentrations and modulated the expression of many genes, mainly downregulating the expression of mitochondrial genes in the absence of oxidative stress, triggering a hypoxia-like response, and upregulating them under stress, mainly the cytochrome complex and electron transport chain. Other categories that were enriched by the effect of melatonin were related to transport, antioxidant activity, signaling, and carbohydrate and lipid metabolism. The overall results suggest that melatonin is able to reprogram the cellular machinery to achieve tolerance to oxidative stress.
Collapse
Affiliation(s)
| | | | | | - María-Jesús Torija
- Departament de Bioquímica i Biotecnologia, Grup de Biotecnologia Enològica, Facultat d’Enologia, Universitat Rovira i Virgili, C/Marcel·lí Domingo, 1. 43007 Tarragona, Catalunya, Spain; (M.S.-F.); (J.V.); (A.M.); (G.B.)
| | | |
Collapse
|
13
|
Redox requirements for ubiquitin-like urmylation of Ahp1, a 2-Cys peroxiredoxin from yeast. Redox Biol 2020; 30:101438. [PMID: 32004955 PMCID: PMC7016264 DOI: 10.1016/j.redox.2020.101438] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023] Open
Abstract
The yeast peroxiredoxin Ahp1, like related anti-oxidant enzymes in other species, undergoes urmylation, a lysine-directed conjugation to ubiquitin-like modifier Urm1. Ahp1 assembles into a homodimer that detoxifies peroxides via forming intersubunit disulfides between peroxidatic and resolving cysteines that are subsequently reduced by the thioredoxin system. Although urmylation coincides with oxidative stress, it is unclear how this modification happens on a molecular level and whether it affects peroxiredoxin activity. Here, we report that thioredoxin mutants decrease Ahp1 urmylation in yeast and each subunit of the oxidized Ahp1 dimer is modified by Urm1 suggesting coupling of urmylation to dimerization. Consistently, Ahp1 mutants unable to form dimers, fail to be urmylated as do mutants that lack the peroxidatic cysteine. Moreover, Ahp1 urmylation involves at least two lysine residues close to the catalytic cysteines and can be prevented in yeast cells exposed to high organic peroxide concentrations. Our results elucidate redox requirements and molecular determinants critical for Ahp1 urmylation, thus providing insights into a potential link between oxidant defense and Urm1 utilization in cells.
Collapse
|
14
|
Loberg MA, Hurtig JE, Graff AH, Allan KM, Buchan JA, Spencer MK, Kelly JE, Clodfelter JE, Morano KA, Lowther WT, West JD. Aromatic Residues at the Dimer-Dimer Interface in the Peroxiredoxin Tsa1 Facilitate Decamer Formation and Biological Function. Chem Res Toxicol 2019; 32:474-483. [PMID: 30701970 DOI: 10.1021/acs.chemrestox.8b00346] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To prevent the accumulation of reactive oxygen species and limit associated damage to biological macromolecules, cells express a variety of oxidant-detoxifying enzymes, including peroxiredoxins. In Saccharomyces cerevisiae, the peroxiredoxin Tsa1 plays a key role in peroxide clearance and maintenance of genome stability. Five homodimers of Tsa1 can assemble into a toroid-shaped decamer, with the active sites in the enzyme being shared between individual dimers in the decamer. Here, we have examined whether two conserved aromatic residues at the decamer-building interface promote Tsa1 oligomerization, enzymatic activity, and biological function. When substituting either or both of these aromatic residues at the decamer-building interface with either alanine or leucine, we found that the Tsa1 decamer is destabilized, favoring dimeric species instead. These proteins exhibit varying abilities to rescue the phenotypes of oxidant sensitivity and genomic instability in yeast lacking Tsa1 and Tsa2, with the individual leucine substitutions at this interface partially complementing the deletion phenotypes. The ability of Tsa1 decamer interface variants to partially rescue peroxidase function in deletion strains is temperature-dependent and correlates with their relative rate of reactivity with hydrogen peroxide and their ability to interact with thioredoxin. Based on the combined results of in vitro and in vivo assays, our findings indicate that multiple steps in the catalytic cycle of Tsa1 may be impaired by introducing substitutions at its decamer-building interface, suggesting a multifaceted biological basis for its assembly into decamers.
Collapse
Affiliation(s)
- Matthew A Loberg
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Jennifer E Hurtig
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States.,Department of Microbiology & Molecular Genetics, McGovern Medical School , The University of Texas Health Science Center at Houston , Houston , Texas 77030 , United States
| | - Aaron H Graff
- Department of Biochemistry and Center for Structural Biology , Wake Forest School of Medicine , Winston-Salem , North Carolina 27101 , United States
| | - Kristin M Allan
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - John A Buchan
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Matthew K Spencer
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Joseph E Kelly
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Jill E Clodfelter
- Department of Biochemistry and Center for Structural Biology , Wake Forest School of Medicine , Winston-Salem , North Carolina 27101 , United States
| | - Kevin A Morano
- Department of Microbiology & Molecular Genetics, McGovern Medical School , The University of Texas Health Science Center at Houston , Houston , Texas 77030 , United States
| | - W Todd Lowther
- Department of Biochemistry and Center for Structural Biology , Wake Forest School of Medicine , Winston-Salem , North Carolina 27101 , United States
| | - James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| |
Collapse
|
15
|
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.
Collapse
|
16
|
Araki K, Ushioda R, Kusano H, Tanaka R, Hatta T, Fukui K, Nagata K, Natsume T. A crosslinker-based identification of redox relay targets. Anal Biochem 2016; 520:22-26. [PMID: 28048978 DOI: 10.1016/j.ab.2016.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/16/2016] [Accepted: 12/30/2016] [Indexed: 12/23/2022]
Abstract
Thiol-based redox control is among the most important mechanisms for maintaining cellular redox homeostasis, with essential participation of cysteine thiols of oxidoreductases. To explore cellular redox regulatory networks, direct interactions among active cysteine thiols of oxidoreductases and their targets must be clarified. We applied a recently described thiol-ene crosslinking-based strategy, named divinyl sulfone (DVSF) method, enabling identification of new potential redox relay partners of the cytosolic oxidoreductases thioredoxin (TXN) and thioredoxin domain containing 17 (TXNDC17). Applying multiple methods, including classical substrate-trapping techniques, will increase understanding of redox regulatory mechanisms in cells.
Collapse
Affiliation(s)
- Kazutaka Araki
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.
| | - Ryo Ushioda
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-Ku, Kyoto 603-8555, Japan
| | - Hidewo Kusano
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Riko Tanaka
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | | | - Kazuhiko Fukui
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Kazuhiro Nagata
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-Ku, Kyoto 603-8555, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan; Robotic Biology Institute, Inc., Tokyo 135-0064, Japan
| |
Collapse
|