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Muñoz-Villagrán C, Acevedo-Arbunic J, Härtig E, Issotta F, Mascayano C, Jahn D, Jahn M, Levicán G. The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress. Int J Mol Sci 2024; 25:6905. [PMID: 39000017 PMCID: PMC11241051 DOI: 10.3390/ijms25136905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Extreme acidophilic bacteria like Leptospirillum sp. require an efficient enzyme system to counteract strong oxygen stress conditions in their natural habitat. The genome of Leptospirillum sp. CF-1 encodes the thioredoxin-fold protein TFP2, which exhibits a high structural similarity to the thioredoxin domain of E. coli CnoX. CnoX from Escherichia coli is a chaperedoxin that protects protein substrates from oxidative stress conditions using its holdase function and a subsequent transfer to foldase chaperones for refolding. Recombinantly produced and purified Leptospirillum sp. TFP2 possesses both thioredoxin and chaperone holdase activities in vitro. It can be reduced by thioredoxin reductase (TrxR). The tfp2 gene co-locates with genes for the chaperone foldase GroES/EL on the chromosome. The "tfp2 cluster" (ctpA-groES-groEL-hyp-tfp2-recN) was found between 1.9 and 8.8-fold transcriptionally up-regulated in response to 1 mM hydrogen peroxide (H2O2). Leptospirillum sp. tfp2 heterologously expressed in E. coli wild type and cnoX mutant strains lead to an increased tolerance of these E. coli strains to H2O2 and significantly reduced intracellular protein aggregates. Finally, a proteomic analysis of protein aggregates produced in E. coli upon exposition to oxidative stress with 4 mM H2O2, showed that Leptospirillum sp. tfp2 expression caused a significant decrease in the aggregation of 124 proteins belonging to fifteen different metabolic categories. These included several known substrates of DnaK and GroEL/ES. These findings demonstrate that Leptospirillum sp. TFP2 is a chaperedoxin-like protein, acting as a key player in the control of cellular proteostasis under highly oxidative conditions that prevail in extreme acidic environments.
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Affiliation(s)
- Claudia Muñoz-Villagrán
- Laboratorio de Microbiología Básica y Aplicada, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Javiera Acevedo-Arbunic
- Laboratorio de Microbiología Básica y Aplicada, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Elisabeth Härtig
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (E.H.)
| | - Francisco Issotta
- Departamento Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago 8331150, Chile
| | - Carolina Mascayano
- Laboratorio de Simulación Computacional y Diseño Racional de Fármacos, Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (E.H.)
- Braunschweig Integrated Centre of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (E.H.)
| | - Gloria Levicán
- Laboratorio de Microbiología Básica y Aplicada, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
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Liu DD, Ding W, Cheng JT, Wei Q, Lin Y, Zhu TY, Tian J, Sun K, Zhang L, Lu P, Yang F, Liu C, Tang S, Yang B. Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids. Nat Commun 2024; 15:5221. [PMID: 38890329 PMCID: PMC11189575 DOI: 10.1038/s41467-024-49517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Latent bioreactive unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identification of protein interactors, such as proteins, DNA, RNA and carbohydrates. However, it is challenging to perform high-throughput identification of Uaa cross-linking products due to the complexities of protein samples and the data analysis processes. Enrichable Uaas can effectively reduce the complexities of protein samples and simplify data analysis, but few cross-linked peptides were identified from mammalian cell samples with these Uaas. Here we develop an enrichable and multiple amino acids reactive Uaa, eFSY, and demonstrate that eFSY is MS cleavable when eFSY-Lys and eFSY-His are the cross-linking products. An identification software, AixUaa is developed to decipher eFSY mass cleavable data. We systematically identify direct interactomes of Thioredoxin 1 (Trx1) and Selenoprotein M (SELM) with eFSY and AixUaa.
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Affiliation(s)
- Dan-Dan Liu
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wenlong Ding
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jin-Tao Cheng
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qiushi Wei
- School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Yinuo Lin
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Tian-Yi Zhu
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Tian
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Ke Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Long Zhang
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Peilong Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Chao Liu
- School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, 100191, China.
| | - Shibing Tang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China.
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China.
| | - Bing Yang
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Anjou C, Lotoux A, Morvan C, Martin-Verstraete I. From ubiquity to specificity: The diverse functions of bacterial thioredoxin systems. Environ Microbiol 2024; 26:e16668. [PMID: 38899743 DOI: 10.1111/1462-2920.16668] [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: 02/27/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
The thioredoxin (Trx) system, found universally, is responsible for the regeneration of reversibly oxidized protein thiols in living cells. This system is made up of a Trx and a Trx reductase, and it plays a central role in maintaining thiol-based redox homeostasis by reducing oxidized protein thiols, such as disulfide bonds in proteins. Some Trxs also possess a chaperone function that is independent of thiol-disulfide exchange, in addition to their thiol-disulfide reductase activity. These two activities of the Trx system are involved in numerous physiological processes in bacteria. This review describes the diverse physiological roles of the Trx system that have emerged throughout bacterial evolution. The Trx system is essential for responding to oxidative and nitrosative stress. Beyond this primary function, the Trx system also participates in redox regulation and signal transduction, and in controlling metabolism, motility, biofilm formation, and virulence. This range of functions has evolved alongside the diversity of bacterial lifestyles and their specific constraints. This evolution can be characterized by the multiplication of the systems and by the specialization of cofactors or targets to adapt to the constraints of atypical lifestyles, such as photosynthesis, insect endosymbiosis, or spore-forming bacteria.
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Affiliation(s)
- Cyril Anjou
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Aurélie Lotoux
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Claire Morvan
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
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Dagah OMA, Silaa BB, Zhu M, Pan Q, Qi L, Liu X, Liu Y, Peng W, Ullah Z, Yudas AF, Muhammad A, Zhang X, Lu J. Exploring Immune Redox Modulation in Bacterial Infections: Insights into Thioredoxin-Mediated Interactions and Implications for Understanding Host-Pathogen Dynamics. Antioxidants (Basel) 2024; 13:545. [PMID: 38790650 PMCID: PMC11117976 DOI: 10.3390/antiox13050545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Bacterial infections trigger a multifaceted interplay between inflammatory mediators and redox regulation. Recently, accumulating evidence has shown that redox signaling plays a significant role in immune initiation and subsequent immune cell functions. This review addresses the crucial role of the thioredoxin (Trx) system in the initiation of immune reactions and regulation of inflammatory responses during bacterial infections. Downstream signaling pathways in various immune cells involve thiol-dependent redox regulation, highlighting the pivotal roles of thiol redox systems in defense mechanisms. Conversely, the survival and virulence of pathogenic bacteria are enhanced by their ability to counteract oxidative stress and immune attacks. This is achieved through the reduction of oxidized proteins and the modulation of redox-sensitive signaling pathways, which are functions of the Trx system, thereby fortifying bacterial resistance. Moreover, some selenium/sulfur-containing compounds could potentially be developed into targeted therapeutic interventions for pathogenic bacteria. Taken together, the Trx system is a key player in redox regulation during bacterial infection, and contributes to host-pathogen interactions, offering valuable insights for future research and therapeutic development.
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Affiliation(s)
- Omer M. A. Dagah
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Billton Bryson Silaa
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Minghui Zhu
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Qiu Pan
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Linlin Qi
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Xinyu Liu
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Yuqi Liu
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Wenjing Peng
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Zakir Ullah
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Appolonia F. Yudas
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | - Amir Muhammad
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
| | | | - Jun Lu
- Engineering Research Center of Coptis Development and Utilization/Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (O.M.A.D.); (B.B.S.); (M.Z.); (Q.P.); (L.Q.); (X.L.); (Y.L.); (W.P.); (Z.U.); (A.F.Y.); (A.M.)
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Ntallis C, Tzoupis H, Tselios T, Chasapis CT, Vlamis-Gardikas A. Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands. Antioxidants (Basel) 2023; 13:15. [PMID: 38275635 PMCID: PMC10812433 DOI: 10.3390/antiox13010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
In silico approaches were employed to examine the characteristics of interactions between human mitochondrial thioredoxin 2 (HsTrx2) and its 38 previously identified mitochondrial protein ligands. All interactions appeared driven mainly by electrostatic forces. The statistically significant residues of HsTrx2 for interactions were characterized as "contact hot spots". Since these were identical/adjacent to putative thermodynamic hot spots, an energy network approach identified their neighbors to highlight possible contact interfaces. Three distinct areas for binding emerged: (i) one around the active site for covalent interactions, (ii) another antipodal to the active site for strong non-covalent interactions, and (iii) a third area involved in both kinds of interactions. The contact interfaces of HsTrx2 were projected as respective interfaces for Escherichia coli Trx1 (EcoTrx1), 2, and HsTrx1. Comparison of the interfaces and contact hot spots of HsTrx2 to the contact residues of EcoTx1 and HsTrx1 from existing crystal complexes with protein ligands supported the hypothesis, except for a part of the cleft/groove adjacent to Trp30 preceding the active site. The outcomes of this study raise the possibility for the rational design of selective inhibitors for the interactions of HsTrx2 with specific protein ligands without affecting the entirety of the functions of the Trx system.
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Affiliation(s)
- Charalampos Ntallis
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Haralampos Tzoupis
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Theodore Tselios
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou 48, 11635 Athens, Greece;
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Huang J, Staes A, Impens F, Demichev V, Van Breusegem F, Gevaert K, Willems P. CysQuant: Simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry. Redox Biol 2023; 67:102908. [PMID: 37793239 PMCID: PMC10562924 DOI: 10.1016/j.redox.2023.102908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function. Accurate quantification of cysteine oxidation is therefore crucial for decoding protein redox regulation. Here, we present CysQuant, a novel approach for simultaneous quantification of cysteine oxidation degrees and protein abundancies. CysQuant involves light/heavy iodoacetamide isotopologues for differential labeling of reduced and reversibly oxidized cysteines analyzed by data-dependent acquisition (DDA) or data-independent acquisition mass spectrometry (DIA-MS). Using plexDIA with in silico predicted spectral libraries, we quantified an average of 18% cysteine oxidation in Arabidopsis thaliana by DIA-MS, including a subset of highly oxidized cysteines forming disulfide bridges in AlphaFold2 predicted structures. Applying CysQuant to Arabidopsis seedlings exposed to excessive light, we successfully quantified the well-established increased reduction of Calvin-Benson cycle enzymes and discovered yet uncharacterized redox-sensitive disulfides in chloroplastic enzymes. Overall, CysQuant is a highly versatile tool for assessing the cysteine modification status that can be widely applied across various mass spectrometry platforms and organisms.
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Affiliation(s)
- Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - An Staes
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium; VIB Proteomics Core, 9052, Ghent, Belgium
| | - Francis Impens
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium; VIB Proteomics Core, 9052, Ghent, Belgium
| | - Vadim Demichev
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
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7
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chem Biol 2023; 30:811-827.e7. [PMID: 37419112 PMCID: PMC10510412 DOI: 10.1016/j.chembiol.2023.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/01/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Ashley R Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Andréa B Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Kaitlyn B Nguyễn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Stephanie L Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
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9
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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.
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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.
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10
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525042. [PMID: 36711448 PMCID: PMC9882296 DOI: 10.1101/2023.01.22.525042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxiCat, Biotin Switch, and SP3-Rox, they typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. To obviate requirements for laborious biochemical fractionation, here, we develop and apply an unprecedented two step cysteine capture method to establish the Local Cysteine Capture (Cys-LoC), and Local Cysteine Oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole cell proteomic analysis. Application of the Cys-LOx method to LPS stimulated murine immortalized bone marrow-derived macrophages (iBMDM), revealed previously unidentified mitochondria-specific inflammation-induced cysteine oxidative modifications including those associated with oxidative phosphorylation. These findings shed light on post-translational mechanisms regulating mitochondrial function during the cellular innate immune response.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Ashley R. Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Anthony E. Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Andréa B. Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Lisa M. Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Alexandra C. Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Stephanie L. Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Heta S. Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Ajit S. Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M. Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA.,DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA.,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
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11
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Romero ML, Garcia Seisdedos H, Ibarra‐Molero B. Active site center redesign increases protein stability preserving catalysis in thioredoxin. Protein Sci 2022. [PMCID: PMC9601870 DOI: 10.1002/pro.4417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The stabilization of natural proteins is a long‐standing desired goal in protein engineering. Optimizing the hydrophobicity of the protein core often results in extensive stability enhancements. However, the presence of totally or partially buried catalytic charged residues, essential for protein function, has limited the applicability of this strategy. Here, focusing on the thioredoxin, we aimed to augment protein stability by removing buried charged residues in the active site without loss of catalytic activity. To this end, we performed a charged‐to‐hydrophobic substitution of a buried and functional group, resulting in a significant stability increase yet abolishing catalytic activity. Then, to simulate the catalytic role of the buried ionizable group, we designed a combinatorial library of variants targeting a set of seven surface residues adjacent to the active site. Notably, more than 50% of the library variants restored, to some extent, the catalytic activity. The combination of experimental study of 2% of the library with the prediction of the whole mutational space by partial least squares regression revealed that a single point mutation at the protein surface is sufficient to fully restore the catalytic activity without thermostability cost. As a result, we engineered one of the highest thermal stabilities reported for a protein with a natural occurring fold (137°C). Further, our hyperstable variant preserves the catalytic activity both in vitro and in vivo.
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Affiliation(s)
- Maria Luisa Romero
- Departamento de Química Física Universidad de Granada Granada
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Hector Garcia Seisdedos
- Departamento de Química Física Universidad de Granada Granada
- Department of Structural Biology Weizmann Institute of Science Rehovot Israel
- Department of Structural Biology Instituto de Biologia Molecular de Barcelona (IBMB‐CSIC) Barcelona Spain
| | - Beatriz Ibarra‐Molero
- Departamento de Química Física Universidad de Granada Granada
- Department of Structural Biology Instituto de Biologia Molecular de Barcelona (IBMB‐CSIC) Barcelona Spain
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12
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Rouyère C, Serrano T, Frémont S, Echard A. Oxidation and reduction of actin: Origin, impact in vitro and functional consequences in vivo. Eur J Cell Biol 2022; 101:151249. [PMID: 35716426 DOI: 10.1016/j.ejcb.2022.151249] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/13/2022] [Accepted: 06/06/2022] [Indexed: 11/15/2022] Open
Abstract
Actin is among the most abundant proteins in eukaryotic cells and assembles into dynamic filamentous networks regulated by many actin binding proteins. The actin cytoskeleton must be finely tuned, both in space and time, to fulfill key cellular functions such as cell division, cell shape changes, phagocytosis and cell migration. While actin oxidation by reactive oxygen species (ROS) at non-physiological levels are known for long to impact on actin polymerization and on the cellular actin cytoskeleton, growing evidence shows that direct and reversible oxidation/reduction of specific actin amino acids plays an important and physiological role in regulating the actin cytoskeleton. In this review, we describe which actin amino acid residues can be selectively oxidized and reduced in many different ways (e.g. disulfide bond formation, glutathionylation, carbonylation, nitration, nitrosylation and other oxidations), the cellular enzymes at the origin of these post-translational modifications, and the impact of actin redox modifications both in vitro and in vivo. We show that the regulated balance of oxidation and reduction of key actin amino acid residues contributes to the control of actin filament polymerization and disassembly at the subcellular scale and highlight how improper redox modifications of actin can lead to pathological conditions.
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Affiliation(s)
- Clémentine Rouyère
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015 Paris, France; Sorbonne Université, Collège Doctoral, F-75005 Paris, France
| | - Thomas Serrano
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015 Paris, France
| | - Stéphane Frémont
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015 Paris, France
| | - Arnaud Echard
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015 Paris, France.
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13
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Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance. Antioxidants (Basel) 2022; 11:antiox11030561. [PMID: 35326211 PMCID: PMC8945050 DOI: 10.3390/antiox11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 12/10/2022] Open
Abstract
Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.
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14
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Comparative kinetic analysis of ascorbate (Vitamin-C) recycling dehydroascorbate reductases from plants and humans. Biochem Biophys Res Commun 2021; 591:110-117. [PMID: 35007834 DOI: 10.1016/j.bbrc.2021.12.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 12/26/2021] [Indexed: 11/20/2022]
Abstract
Ascorbate is an important cellular antioxidant that gets readily oxidized to dehydroascorbate (DHA). Recycling of DHA is therefore paramount in the maintenance of cellular homeostasis and preventing oxidative stress. Dehydroascorbate reductases (DHARs), in conjunction with glutathione (GSH), carry out this vital process in eukaryotes, among which plant DHARs have garnered considerable attention. A detailed kinetic analysis of plant DHARs relative to their human counterparts is, however, lacking. Chloride intracellular channels (HsCLICs) are close homologs of plant DHARs, recently demonstrated to share their enzymatic activity. This study reports the highest turnover rate for a plant DHAR from stress adapted Pennisetum glaucum (PgDHAR). In comparison, HsCLICs 1, 3, and 4 reduced DHA at a significantly lower rate. We further show that the catalytic cysteine from both homologs was susceptible to varying degrees of oxidation, validated by crystal structures and mass-spectrometry. Our findings may have broader implications on crop improvement using pearl millet DHAR vis-à-vis discovery of cancer therapeutics targeting Vitamin-C recycling capability of human CLICs.
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15
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Napolitano S, Pokharna A, Glockshuber R, Gossert AD. The trans-to-cis proline isomerization in E. coli Trx folding is accelerated by trans prolines. Biophys J 2021; 120:5207-5218. [PMID: 34736898 DOI: 10.1016/j.bpj.2021.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/17/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022] Open
Abstract
The conserved fold of thioredoxin (Trx)-like thiol/disulfide oxidoreductases contains an invariant cis-proline residue (P76 in Escherichia coli Trx) that is essential for Trx function and that is responsible for the folding rate-limiting step. E. coli Trx contains four additional prolines, which are all in the trans conformation in the native state. Notably, a recent study revealed that replacement of all four trans prolines in Trx by alanines (Trx variant Trx1P) further slowed the rate-limiting step 25-fold, indicating that one or several of the four trans prolines accelerate the trans-to-cis transition of P76 in Trx wild-type (wt). Here, we characterized the folding kinetics of Trx variants containing cisP76 and one or several of the natural trans prolines of Trx wt with NMR spectroscopy. First, we demonstrate that the isomerization reaction in Trx1P is a pure two-state transition between two distinct tertiary structures, in which all observed NMR resonances changes follow the same first-order kinetics. Moreover, we show that trans-P68 is the critical residue responsible for the faster folding of wt Trx relative to the single-proline (P76) variant Trx1P, as the two-proline variant Trx2P(P76P68) already folds seven times faster than Trx1P. trans-P34 also accelerates trans-to-cis isomerization of P76, albeit to a smaller extent. Overall, the results demonstrate that trans prolines can significantly modulate the kinetics of rate-limiting trans-to-cis proline isomerization in protein folding. Finally, we discuss possible mechanisms of acceleration and the potential significance of a protein-internal folding acceleration mechanism for Trx in a living cell.
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Affiliation(s)
| | - Aditya Pokharna
- Institute of Molecular Biology and Biophysics, Zürich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Zürich, Switzerland.
| | - Alvar D Gossert
- Institute of Molecular Biology and Biophysics, Zürich, Switzerland; Biomolecular NMR Spectroscopy Platform, Department of Biology, ETH Zürich, Zürich, Switzerland.
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16
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Role of the Redox State of Human Peroxiredoxin-5 on Its TLR4-Activating DAMP Function. Antioxidants (Basel) 2021; 10:antiox10121902. [PMID: 34943005 PMCID: PMC8750366 DOI: 10.3390/antiox10121902] [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: 11/12/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
Human peroxiredoxin-5 (PRDX5) is a unique redox-sensitive protein that plays a dual role in brain ischemia-reperfusion injury. While intracellular PRDX5 has been reported to act as a neuroprotective antioxidative enzyme by scavenging peroxides, once released extracellularly from necrotic brain cells, the protein aggravates neural cell death by inducing expression of proinflammatory cytokines in macrophages through activation of Toll-like receptor (TLR) 2 (TLR2) and 4 (TLR4). Although recent evidence showed that PRDX5 was able to interact directly with TLR4, little is known regarding the role of the cysteine redox state of PRDX5 on its DAMP function. To gain insights into the role of PRDX5 redox-active cysteine residues in the TLR4-dependent proinflammatory activity of the protein, we used a recombinant human PRDX5 in the disulfide (oxidized) form and a mutant version lacking the peroxidatic cysteine, as well as chemically reduced and hyperoxidized PRDX5 proteins. We first analyzed the oxidation state and oligomerization profile by Western blot, mass spectrometry, and SEC-MALS. Using ELISA, we demonstrate that the disulfide bridge between the enzymatic cysteines is required to allow improved TLR4-dependent IL-8 secretion. Moreover, single-molecule force spectroscopy experiments revealed that TLR4 alone is not sufficient to discriminate the different PRDX5 redox forms. Finally, flow cytometry binding assays show that disulfide PRDX5 has a higher propensity to bind to the surface of living TLR4-expressing cells than the mutant protein. Taken together, these results demonstrate the importance of the redox state of PRDX5 cysteine residues on TLR4-induced inflammation.
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17
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Ma Y, Yang X, Wang H, Qin Z, Yi C, Shi C, Luo M, Chen G, Yan J, Liu X, Liu Z. CBS-derived H2S facilitates host colonization of Vibrio cholerae by promoting the iron-dependent catalase activity of KatB. PLoS Pathog 2021; 17:e1009763. [PMID: 34283874 PMCID: PMC8324212 DOI: 10.1371/journal.ppat.1009763] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/30/2021] [Accepted: 06/28/2021] [Indexed: 12/04/2022] Open
Abstract
Sensing and resisting oxidative stress is critical for Vibrio cholerae to survive in either the aquatic environment or the gastrointestinal tract. Previous studies mainly focused on the mechanisms of oxidative stress response regulation that rely on enzymatic antioxidant systems, while functions of non-enzymatic antioxidants are rarely discussed in V. cholerae. For the first time, we investigated the role of hydrogen sulfide (H2S), the simplest thiol compound, in protecting V. cholerae against oxidative stress. We found that degradation of L-cysteine by putative cystathionine β-synthase (CBS) is the major source of endogenous H2S in V. cholerae. Our results indicate that intracellular H2S level has a positive correlation with cbs expression, while the enhanced H2S production can render V. cholerae cells less susceptible to H2O2 in vitro. Using proteome analysis and real-time qPCR assay, we found that cbs expression could stimulate the expression of several enzymatic antioxidants, including reactive oxygen species (ROS) detoxifying enzymes SodB, KatG and AhpC, the DNA protective protein DPS and the protein redox regulator Trx1. Assays of ROS detoxification capacities revealed that CBS-derived H2S could promote catalase activity at the post-translational level, especially for KatB, which serves as an important way that endogenous H2S participates in H2O2 detoxification. The enhancement of catalase activity by H2S is achieved through facilitating the uptake of iron. Adult mice experiments showed that cbs mutant has colonization defect, while either complementation of cbs or exogenous supplement of N-Acetyl-L-Cysteine restores its fitness in the host environment. Herein, we proposed that V. cholerae regulates CBS-dependent H2S production for better survival and proliferation under ROS stress.
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Affiliation(s)
- Yao Ma
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoman Yang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongou Wang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zixin Qin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chunrong Yi
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Changping Shi
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Luo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guozhong Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jin Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhi Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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18
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Thioredoxin Dependent Changes in the Redox States of FurA from Anabaena sp. PCC 7120. Antioxidants (Basel) 2021; 10:antiox10060913. [PMID: 34199999 PMCID: PMC8229018 DOI: 10.3390/antiox10060913] [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: 05/04/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
FurA is a multifunctional regulator in cyanobacteria that contains five cysteines, four of them arranged into two CXXC motifs. Lack of a structural zinc ion enables FurA to develop disulfide reductase activity. In vivo, FurA displays several redox isoforms, and the oxidation state of its cysteines determines its activity as regulator and its ability to bind different metabolites. Because of the relationship between FurA and the control of genes involved in oxidative stress defense and photosynthetic metabolism, we sought to investigate the role of type m thioredoxin TrxA as a potential redox partner mediating dithiol-disulfide exchange reactions necessary to facilitate the interaction of FurA with its different ligands. Both in vitro cross-linking assays and in vivo two-hybrid studies confirmed the interaction between FurA and TrxA. Light to dark transitions resulted in reversible oxidation of a fraction of the regulator present in Anabaena sp. PCC7120. Reconstitution of an electron transport chain using E. coli NADPH-thioredoxin-reductase followed by alkylation of FurA reduced cysteines evidenced the ability of TrxA to reduce FurA. Furthermore, the use of site-directed mutants allowed us to propose a plausible mechanism for FurA reduction. These results point to TrxA as one of the redox partners that modulates FurA performance.
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19
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Liu C, Wu T, Shu X, Li S, Wang DR, Wang N, Zhou R, Yang H, Jiang H, Hendriks IA, Gong P, Zhang L, Nielsen ML, Li K, Wang L, Yang B. Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa. Adv Biol (Weinh) 2021; 5:e2000308. [DOI: 10.1002/adbi.202000308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/03/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Chao Liu
- Beijing Advanced Innovation Center for Big Data‐based Precision Medicine School of Medicine and Engineering Beihang University and Key Laboratory of Big Data‐Based Precision Medicine (Beihang University) Ministry of Industry and Information Technology Beijing 100191 China
| | - Ting Wu
- MOE Laboratory of Biosystem Homeostasis and Protection and Life Sciences Institute Zhejiang University Hangzhou 310058 China
| | - Xin Shu
- MOE Laboratory of Biosystem Homeostasis and Protection and Life Sciences Institute Zhejiang University Hangzhou 310058 China
| | - Shang‐Tong Li
- Tsinghua Institute of Multidisciplinary Biomedical Research Tsinghua University and National Institute of Biological Science (NIBS) Beijing 102206 China
| | - Daniel R. Wang
- Department of Pharmaceutical Chemistry and The Cardiovascular Research Institute University of California San Francisco San Francisco CA 94158 USA
| | - Nanxi Wang
- Department of Pharmaceutical Chemistry and The Cardiovascular Research Institute University of California San Francisco San Francisco CA 94158 USA
| | - Rong Zhou
- Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing 100193 China
| | - Hao Yang
- Beijing Advanced Innovation Center for Big Data‐based Precision Medicine School of Medicine and Engineering Beihang University and Key Laboratory of Big Data‐Based Precision Medicine (Beihang University) Ministry of Industry and Information Technology Beijing 100191 China
| | - Hong Jiang
- Kidney Disease Center The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou 310003 China
| | - Ivo A. Hendriks
- Proteomics Program Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2200 Denmark
| | - Pengyun Gong
- Beijing Advanced Innovation Center for Big Data‐based Precision Medicine School of Medicine and Engineering Beihang University and Key Laboratory of Big Data‐Based Precision Medicine (Beihang University) Ministry of Industry and Information Technology Beijing 100191 China
| | - Long Zhang
- MOE Laboratory of Biosystem Homeostasis and Protection and Life Sciences Institute Zhejiang University Hangzhou 310058 China
| | - Michael L. Nielsen
- Proteomics Program Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2200 Denmark
| | - Kui Li
- Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing 100193 China
| | - Lei Wang
- Department of Pharmaceutical Chemistry and The Cardiovascular Research Institute University of California San Francisco San Francisco CA 94158 USA
| | - Bing Yang
- MOE Laboratory of Biosystem Homeostasis and Protection and Life Sciences Institute Zhejiang University Hangzhou 310058 China
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20
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Kopeckova M, Pavkova I, Link M, Rehulka P, Stulik J. Identification of Bacterial Protein Interaction Partners Points to New Intracellular Functions of Francisella tularensis Glyceraldehyde-3-Phosphate Dehydrogenase. Front Microbiol 2020; 11:576618. [PMID: 33013814 PMCID: PMC7513575 DOI: 10.3389/fmicb.2020.576618] [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: 06/26/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is well known for its involvement in numerous non-metabolic processes inside mammalian cells. Alternative functions of prokaryotic GAPDH are mainly deduced from its extracellular localization ability to bind to selected host proteins. Data on its participation in intracellular bacterial processes are scarce as there has been to date only one study dealing with this issue. We previously have reported several points of evidence that the GAPDH homolog of Francisella tularensis GapA might also exert additional non-enzymatic functions. Following on from our earlier observations we decided to identify GapA's interacting partners within the bacterial proteome to explore its new roles at intracellular level. The quantitative proteomics approach based on stable isotope labeling of amino acids in cell culture (SILAC) in combination with affinity purification mass spectrometry enabled us to identify 18 proteins potentially interacting with GapA. Six of those interactions were further confirmed by alternative methods. Half of the identified proteins were involved in non-metabolic processes. Further analysis together with quantitative label-free comparative analysis of proteomes isolated from the wild-type strain strain with deleted gapA gene suggests that GapA is implicated in DNA repair processes. Absence of GapA promotes secretion of its most potent interaction partner the hypothetical protein with peptidase propeptide domain (PepSY) thereby indicating that it impacts on subcellular distribution of some proteins.
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Affiliation(s)
- Monika Kopeckova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Ivona Pavkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Pavel Rehulka
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Jiri Stulik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
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21
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Abstract
Introduction: Protein thiols are susceptible to oxidation in health and disease. Redox proteomics methods facilitate the identification, quantification, and rationalization of oxidation processes including those involving protein thiols. These residues are crucial to understanding redox homeostasis underpinning normal cell functioning and regulation as well as novel biomarkers of pathology and promising novel drug targets.Areas covered: This article reviews redox proteomic approaches to study of protein thiols in some important human pathologies and assesses the clinical potential of individual Cys residues as novel biomarkers for disease detection and as targets for novel treatments.Expert commentary: Although protein thiols are not as routinely used as redox biomarkers as some other lesions such as carbonylation, there has been growing recent interest in their potential. Driven largely by developments in high-resolution mass spectrometry it is possible now to identify proteins that are redox modified at thiol groups or that interact with regulatory oxidoreductases. Thiols that are specifically susceptible to modification by reactive oxygen species can be routinely identified now and quantitative MS can be used to quantify the proportion of a protein that is redox modified.
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Affiliation(s)
- David Sheehan
- Department of Chemistry, Khalifa University, Abu Dhabi, United Arab Emirates.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Brian McDonagh
- Department of Physiology, School of Medicine, National University of Ireland, Galway, Ireland
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22
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Backes S, Garg SG, Becker L, Peleh V, Glockshuber R, Gould SB, Herrmann JM. Development of the Mitochondrial Intermembrane Space Disulfide Relay Represents a Critical Step in Eukaryotic Evolution. Mol Biol Evol 2019; 36:742-756. [PMID: 30668797 DOI: 10.1093/molbev/msz011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The mitochondrial intermembrane space evolved from the bacterial periplasm. Presumably as a consequence of their common origin, most proteins of these compartments are stabilized by structural disulfide bonds. The molecular machineries that mediate oxidative protein folding in bacteria and mitochondria, however, appear to share no common ancestry. Here we tested whether the enzymes Erv1 and Mia40 of the yeast mitochondrial disulfide relay could be functionally replaced by corresponding components of other compartments. We found that the sulfhydryl oxidase Erv1 could be replaced by the Ero1 oxidase or the protein disulfide isomerase from the endoplasmic reticulum, however at the cost of respiration deficiency. In contrast to Erv1, the mitochondrial oxidoreductase Mia40 proved to be indispensable and could not be replaced by thioredoxin-like enzymes, including the cytoplasmic reductase thioredoxin, the periplasmic dithiol oxidase DsbA, and Pdi1. From our studies we conclude that the profound inertness against glutathione, its slow oxidation kinetics and its high affinity to substrates renders Mia40 a unique and essential component of mitochondrial biogenesis. Evidently, the development of a specific mitochondrial disulfide relay system represented a crucial step in the evolution of the eukaryotic cell.
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Affiliation(s)
- Sandra Backes
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sriram G Garg
- Molecular Evolution, Heinrich-Heine-University of Dusseldorf, Dusseldorf, Germany
| | - Laura Becker
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Valentina Peleh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Rudi Glockshuber
- Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Sven B Gould
- Molecular Evolution, Heinrich-Heine-University of Dusseldorf, Dusseldorf, Germany
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23
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Chasapis CT, Makridakis M, Damdimopoulos AE, Zoidakis J, Lygirou V, Mavroidis M, Vlahou A, Miranda-Vizuete A, Spyrou G, Vlamis-Gardikas A. Implications of the mitochondrial interactome of mammalian thioredoxin 2 for normal cellular function and disease. Free Radic Biol Med 2019; 137:59-73. [PMID: 31018154 DOI: 10.1016/j.freeradbiomed.2019.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/15/2019] [Indexed: 12/23/2022]
Abstract
Multiple thioredoxin isoforms exist in all living cells. To explore the possible functions of mammalian mitochondrial thioredoxin 2 (Trx2), an interactome of mouse Trx2 was initially created using (i) a monothiol mouse Trx2 species for capturing protein partners from different organs and (ii) yeast two hybrid screens on human liver and rat brain cDNA libraries. The resulting interactome consisted of 195 proteins (Trx2 included) plus the mitochondrial 16S RNA. 48 of these proteins were classified as mitochondrial (MitoCarta2.0 human inventory). In a second step, the mouse interactome was combined with the current four-membered mitochondrial sub-network of human Trx2 (BioGRID) to give a 53-membered human Trx2 mitochondrial interactome (52 interactor proteins plus the mitochondrial 16S RNA). Although thioredoxins are thiol-employing disulfide oxidoreductases, approximately half of the detected interactions were not due to covalent disulfide bonds. This finding reinstates the extended role of thioredoxins as moderators of protein function by specific non-covalent, protein-protein interactions. Analysis of the mitochondrial interactome suggested that human Trx2 was involved potentially in mitochondrial integrity, formation of iron sulfur clusters, detoxification of aldehydes, mitoribosome assembly and protein synthesis, protein folding, ADP ribosylation, amino acid and lipid metabolism, glycolysis, the TCA cycle and the electron transport chain. The oxidoreductase functions of Trx2 were verified by its detected interactions with mitochondrial peroxiredoxins and methionine sulfoxide reductase. Parkinson's disease, triosephosphate isomerase deficiency, combined oxidative phosphorylation deficiency, and lactate dehydrogenase b deficiency are some of the diseases where the proposed mitochondrial network of Trx2 may be implicated.
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Affiliation(s)
- Christos T Chasapis
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology, Hellas (FORTH), Platani 26504, Greece
| | | | - Anastassios E Damdimopoulos
- Department of Biosciences and Nutrition, Center for Innovative Medicine (CIMED), Karolinska Institutet, Huddinge, Sweden
| | - Jerome Zoidakis
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Vasiliki Lygirou
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Manolis Mavroidis
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Antonia Vlahou
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Antonio Miranda-Vizuete
- Redox Homeostasis Group, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
| | - Giannis Spyrou
- Department of Clinical and Experimental Medicine, Division of Clinical Chemistry, Linköping University, S-581 85 Linköping, Sweden
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24
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The Chaperone and Redox Properties of CnoX Chaperedoxins Are Tailored to the Proteostatic Needs of Bacterial Species. mBio 2018; 9:mBio.01541-18. [PMID: 30482828 PMCID: PMC6282202 DOI: 10.1128/mbio.01541-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
How proteins are protected from stress-induced aggregation is a crucial question in biology and a long-standing mystery. While a long series of landmark studies have provided important contributions to our current understanding of the proteostasis network, key fundamental questions remain unsolved. In this study, we show that the intrinsic features of the chaperedoxin CnoX, a folding factor that combines chaperone and redox protective function, have been tailored during evolution to fit to the specific needs of their host. Whereas Escherichia coli CnoX needs to be activated by bleach, a powerful oxidant produced by our immune system, its counterpart in Caulobacter crescentus, a bacterium living in bleach-free environments, is a constitutive chaperone. In addition, the redox properties of E. coli and C. crescentus CnoX also differ to best contribute to their respective cellular redox homeostasis. This work demonstrates how proteins from the same family have evolved to meet the needs of their hosts. Hypochlorous acid (bleach), an oxidizing compound produced by neutrophils, turns the Escherichia coli chaperedoxin CnoX into a powerful holdase protecting its substrates from bleach-induced aggregation. CnoX is well conserved in bacteria, even in non-infectious species unlikely to encounter this oxidant, muddying the role of CnoX in these organisms. Here, we found that CnoX in the non-pathogenic aquatic bacterium Caulobacter crescentus functions as a holdase that efficiently protects 50 proteins from heat-induced aggregation. Remarkably, the chaperone activity of Caulobacter CnoX is constitutive. Like E. coli CnoX, Caulobacter CnoX transfers its substrates to DnaK/J/GrpE and GroEL/ES for refolding, indicating conservation of cooperation with GroEL/ES. Interestingly, Caulobacter CnoX exhibits thioredoxin oxidoreductase activity, by which it controls the redox state of 90 proteins. This function, which E. coli CnoX lacks, is likely welcome in a bacterium poorly equipped with antioxidant defenses. Thus, the redox and chaperone properties of CnoX chaperedoxins were fine-tuned during evolution to adapt these proteins to the specific needs of each species.
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25
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Goemans CV, Beaufay F, Wahni K, Van Molle I, Messens J, Collet JF. An essential thioredoxin is involved in the control of the cell cycle in the bacterium Caulobacter crescentus. J Biol Chem 2018; 293:3839-3848. [PMID: 29367337 PMCID: PMC5846133 DOI: 10.1074/jbc.ra117.001042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/23/2018] [Indexed: 11/06/2022] Open
Abstract
Thioredoxins (Trxs) are antioxidant proteins that are conserved among all species. These proteins have been extensively studied and perform reducing reactions on a broad range of substrates. Here, we identified Caulobacter crescentus Trx1 (CCNA_03653; CcTrx1) as an oxidoreductase that is involved in the cell cycle progression of this model bacterium and is required to sustain life. Intriguingly, the abundance of CcTrx1 varies throughout the C. crescentus cell cycle: although the expression of CcTrx1 is induced in stalked cells, right before DNA replication initiation, CcTrx1 is actively degraded by the ClpXP protease in predivisional cells. Importantly, we demonstrated that regulation of the abundance of CcTrx1 is crucial for cell growth and survival as modulating CcTrx1 levels leads to cell death. Finally, we also report a comprehensive biochemical and structural characterization of this unique and essential Trx. The requirement to precisely control the abundance of CcTrx1 for cell survival underlines the importance of redox control for optimal cell cycle progression in C. crescentus.
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Affiliation(s)
- Camille V Goemans
- From WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium,
- the de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
- the Brussels Center for Redox Biology, 1200 Brussels, Belgium
| | - François Beaufay
- the de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Khadija Wahni
- the Brussels Center for Redox Biology, 1200 Brussels, Belgium
- the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium, and
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Inge Van Molle
- the Brussels Center for Redox Biology, 1200 Brussels, Belgium
- the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium, and
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Joris Messens
- the Brussels Center for Redox Biology, 1200 Brussels, Belgium
- the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium, and
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Jean-François Collet
- From WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium,
- the de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
- the Brussels Center for Redox Biology, 1200 Brussels, Belgium
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26
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Vanmarsenille C, Díaz Del Olmo I, Elseviers J, Hassanzadeh Ghassabeh G, Moonens K, Vertommen D, Martel A, Haesebrouck F, Pasmans F, Hernalsteens JP, De Greve H. Nanobodies targeting conserved epitopes on the major outer membrane protein of Campylobacter as potential tools for control of Campylobacter colonization. Vet Res 2017; 48:86. [PMID: 29216932 PMCID: PMC5721652 DOI: 10.1186/s13567-017-0491-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/19/2017] [Indexed: 11/10/2022] Open
Abstract
Campylobacter infections are among the most prevalent foodborne infections in humans, resulting in a massive disease burden worldwide. Broilers have been identified as the major source of campylobacteriosis and reducing Campylobacter loads in the broiler caeca has been proposed as an effective measure to decrease the number of infections in humans. Failure of current methods to control Campylobacter in broilers stresses the urgency to develop novel mitigation measures. We obtained six nanobodies with a broad specificity, that recognize strains belonging to the two most relevant species, Campylobacter jejuni and Campylobacter coli. The target of the nanobodies was identified as the major outer membrane protein, a porin that contributes to bacterial virulence and viability. Multimerization of the nanobodies led to agglutination of C. jejuni cells, which may affect colonization in the chicken gut. These Campylobacter-specific nanobodies may be useful to develop a strategy for preserving chickens from Campylobacter colonization.
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Affiliation(s)
- Charlotte Vanmarsenille
- Structural Molecular Microbiology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Genetische Virologie, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Inés Díaz Del Olmo
- Structural Molecular Microbiology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Genetische Virologie, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jelle Elseviers
- VIB Nanobody Service Facility, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | | | - Kristof Moonens
- Structural Molecular Microbiology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Didier Vertommen
- Faculty of Medicine and de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 74, 1200, Brussels, Belgium
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | | | - Henri De Greve
- Structural Molecular Microbiology, VIB, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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27
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Egea J, Fabregat I, Frapart YM, Ghezzi P, Görlach A, Kietzmann T, Kubaichuk K, Knaus UG, Lopez MG, Olaso-Gonzalez G, Petry A, Schulz R, Vina J, Winyard P, Abbas K, Ademowo OS, Afonso CB, Andreadou I, Antelmann H, Antunes F, Aslan M, Bachschmid MM, Barbosa RM, Belousov V, Berndt C, Bernlohr D, Bertrán E, Bindoli A, Bottari SP, Brito PM, Carrara G, Casas AI, Chatzi A, Chondrogianni N, Conrad M, Cooke MS, Costa JG, Cuadrado A, My-Chan Dang P, De Smet B, Debelec-Butuner B, Dias IHK, Dunn JD, Edson AJ, El Assar M, El-Benna J, Ferdinandy P, Fernandes AS, Fladmark KE, Förstermann U, Giniatullin R, Giricz Z, Görbe A, Griffiths H, Hampl V, Hanf A, Herget J, Hernansanz-Agustín P, Hillion M, Huang J, Ilikay S, Jansen-Dürr P, Jaquet V, Joles JA, Kalyanaraman B, Kaminskyy D, Karbaschi M, Kleanthous M, Klotz LO, Korac B, Korkmaz KS, Koziel R, Kračun D, Krause KH, Křen V, Krieg T, Laranjinha J, Lazou A, Li H, Martínez-Ruiz A, Matsui R, McBean GJ, Meredith SP, Messens J, Miguel V, Mikhed Y, Milisav I, Milković L, Miranda-Vizuete A, Mojović M, Monsalve M, Mouthuy PA, Mulvey J, Münzel T, Muzykantov V, Nguyen ITN, Oelze M, Oliveira NG, Palmeira CM, Papaevgeniou N, Pavićević A, Pedre B, Peyrot F, Phylactides M, Pircalabioru GG, Pitt AR, Poulsen HE, Prieto I, Rigobello MP, Robledinos-Antón N, Rodríguez-Mañas L, Rolo AP, Rousset F, Ruskovska T, Saraiva N, Sasson S, Schröder K, Semen K, Seredenina T, Shakirzyanova A, Smith GL, Soldati T, Sousa BC, Spickett CM, Stancic A, Stasia MJ, Steinbrenner H, Stepanić V, Steven S, Tokatlidis K, Tuncay E, Turan B, Ursini F, Vacek J, Vajnerova O, Valentová K, Van Breusegem F, Varisli L, Veal EA, Yalçın AS, Yelisyeyeva O, Žarković N, Zatloukalová M, Zielonka J, Touyz RM, Papapetropoulos A, Grune T, Lamas S, Schmidt HHHW, Di Lisa F, Daiber A. European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS). Redox Biol 2017; 13:94-162. [PMID: 28577489 PMCID: PMC5458069 DOI: 10.1016/j.redox.2017.05.007] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 12/12/2022] Open
Abstract
The European Cooperation in Science and Technology (COST) provides an ideal framework to establish multi-disciplinary research networks. COST Action BM1203 (EU-ROS) represents a consortium of researchers from different disciplines who are dedicated to providing new insights and tools for better understanding redox biology and medicine and, in the long run, to finding new therapeutic strategies to target dysregulated redox processes in various diseases. This report highlights the major achievements of EU-ROS as well as research updates and new perspectives arising from its members. The EU-ROS consortium comprised more than 140 active members who worked together for four years on the topics briefly described below. The formation of reactive oxygen and nitrogen species (RONS) is an established hallmark of our aerobic environment and metabolism but RONS also act as messengers via redox regulation of essential cellular processes. The fact that many diseases have been found to be associated with oxidative stress established the theory of oxidative stress as a trigger of diseases that can be corrected by antioxidant therapy. However, while experimental studies support this thesis, clinical studies still generate controversial results, due to complex pathophysiology of oxidative stress in humans. For future improvement of antioxidant therapy and better understanding of redox-associated disease progression detailed knowledge on the sources and targets of RONS formation and discrimination of their detrimental or beneficial roles is required. In order to advance this important area of biology and medicine, highly synergistic approaches combining a variety of diverse and contrasting disciplines are needed.
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Affiliation(s)
- Javier Egea
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine. Univerisdad Autonoma de Madrid, Spain
| | - Isabel Fabregat
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | - Yves M Frapart
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | | | - Agnes Görlach
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Kateryna Kubaichuk
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ulla G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Manuela G Lopez
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine. Univerisdad Autonoma de Madrid, Spain
| | | | - Andreas Petry
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - Rainer Schulz
- Institute of Physiology, JLU Giessen, Giessen, Germany
| | - Jose Vina
- Department of Physiology, University of Valencia, Spain
| | - Paul Winyard
- University of Exeter Medical School, St Luke's Campus, Exeter EX1 2LU, UK
| | - Kahina Abbas
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - Opeyemi S Ademowo
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Catarina B Afonso
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Ioanna Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Haike Antelmann
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Fernando Antunes
- Departamento de Química e Bioquímica and Centro de Química e Bioquímica, Faculdade de Ciências, Portugal
| | - Mutay Aslan
- Department of Medical Biochemistry, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Markus M Bachschmid
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Rui M Barbosa
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Vsevolod Belousov
- Molecular technologies laboratory, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - David Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, USA
| | - Esther Bertrán
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | | | - Serge P Bottari
- GETI, Institute for Advanced Biosciences, INSERM U1029, CNRS UMR 5309, Grenoble-Alpes University and Radio-analysis Laboratory, CHU de Grenoble, Grenoble, France
| | - Paula M Brito
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; Faculdade de Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Guia Carrara
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ana I Casas
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Afroditi Chatzi
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - Niki Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Marcus Conrad
- Helmholtz Center Munich, Institute of Developmental Genetics, Neuherberg, Germany
| | - Marcus S Cooke
- Oxidative Stress Group, Dept. Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA
| | - João G Costa
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid. Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Pham My-Chan Dang
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - Barbara De Smet
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy; Pharmahungary Group, Szeged, Hungary
| | - Bilge Debelec-Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir 35100, Turkey
| | - Irundika H K Dias
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Joe Dan Dunn
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - Amanda J Edson
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Mariam El Assar
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain
| | - Jamel El-Benna
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Ana S Fernandes
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Kari E Fladmark
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Ulrich Förstermann
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Rashid Giniatullin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Zoltán Giricz
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Anikó Görbe
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Helen Griffiths
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK; Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Vaclav Hampl
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Alina Hanf
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Jan Herget
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pablo Hernansanz-Agustín
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Melanie Hillion
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Jingjing Huang
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Serap Ilikay
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - Pidder Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Vincent Jaquet
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Jaap A Joles
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | | | | | - Mahsa Karbaschi
- Oxidative Stress Group, Dept. Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Lars-Oliver Klotz
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - Bato Korac
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - Kemal Sami Korkmaz
- Department of Bioengineering, Cancer Biology Laboratory, Faculty of Engineering, Ege University, Bornova, 35100 Izmir, Turkey
| | - Rafal Koziel
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Damir Kračun
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - Karl-Heinz Krause
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Vladimír Křen
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, UK
| | - João Laranjinha
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Antigone Lazou
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Huige Li
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Antonio Martínez-Ruiz
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Reiko Matsui
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Gethin J McBean
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Stuart P Meredith
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Verónica Miguel
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Yuliya Mikhed
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Irina Milisav
- University of Ljubljana, Faculty of Medicine, Institute of Pathophysiology and Faculty of Health Sciences, Ljubljana, Slovenia
| | - Lidija Milković
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Miloš Mojović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - María Monsalve
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Pierre-Alexis Mouthuy
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - John Mulvey
- Department of Medicine, University of Cambridge, UK
| | - Thomas Münzel
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Vladimir Muzykantov
- Department of Pharmacology, Center for Targeted Therapeutics & Translational Nanomedicine, ITMAT/CTSA Translational Research Center University of Pennsylvania The Perelman School of Medicine, Philadelphia, PA, USA
| | - Isabel T N Nguyen
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | - Matthias Oelze
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Nuno G Oliveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos M Palmeira
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - Nikoletta Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Aleksandra Pavićević
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Brandán Pedre
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Fabienne Peyrot
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France; ESPE of Paris, Paris Sorbonne University, Paris, France
| | - Marios Phylactides
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Henrik E Poulsen
- Laboratory of Clinical Pharmacology, Rigshospitalet, University Hospital Copenhagen, Denmark; Department of Clinical Pharmacology, Bispebjerg Frederiksberg Hospital, University Hospital Copenhagen, Denmark; Department Q7642, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Ignacio Prieto
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Maria Pia Rigobello
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Natalia Robledinos-Antón
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid. Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Leocadio Rodríguez-Mañas
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain; Servicio de Geriatría, Hospital Universitario de Getafe, Getafe, Spain
| | - Anabela P Rolo
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - Francis Rousset
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, Stip, Republic of Macedonia
| | - Nuno Saraiva
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Shlomo Sasson
- Institute for Drug Research, Section of Pharmacology, Diabetes Research Unit, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Katrin Schröder
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany
| | - Khrystyna Semen
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Tamara Seredenina
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Anastasia Shakirzyanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Thierry Soldati
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - Bebiana C Sousa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Corinne M Spickett
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Ana Stancic
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - Marie José Stasia
- Université Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, F38000 Grenoble, France; CDiReC, Pôle Biologie, CHU de Grenoble, Grenoble, F-38043, France
| | - Holger Steinbrenner
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - Višnja Stepanić
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Sebastian Steven
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - Erkan Tuncay
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - Belma Turan
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - Fulvio Ursini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | - Olga Vajnerova
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Valentová
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lokman Varisli
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - Elizabeth A Veal
- Institute for Cell and Molecular Biosciences, and Institute for Ageing, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - A Suha Yalçın
- Department of Biochemistry, School of Medicine, Marmara University, İstanbul, Turkey
| | | | - Neven Žarković
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | | | - Rhian M Touyz
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - Andreas Papapetropoulos
- Laboratoty of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Tilman Grune
- German Institute of Human Nutrition, Department of Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Santiago Lamas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Harald H H W Schmidt
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Fabio Di Lisa
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy.
| | - Andreas Daiber
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany.
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Pérez-Pérez ME, Mauriès A, Maes A, Tourasse NJ, Hamon M, Lemaire SD, Marchand CH. The Deep Thioredoxome in Chlamydomonas reinhardtii: New Insights into Redox Regulation. MOLECULAR PLANT 2017; 10:1107-1125. [PMID: 28739495 DOI: 10.1016/j.molp.2017.07.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/04/2017] [Accepted: 07/11/2017] [Indexed: 05/20/2023]
Abstract
Thiol-based redox post-translational modifications have emerged as important mechanisms of signaling and regulation in all organisms, and thioredoxin plays a key role by controlling the thiol-disulfide status of target proteins. Recent redox proteomic studies revealed hundreds of proteins regulated by glutathionylation and nitrosylation in the unicellular green alga Chlamydomonas reinhardtii, while much less is known about the thioredoxin interactome in this organism. By combining qualitative and quantitative proteomic analyses, we have comprehensively investigated the Chlamydomonas thioredoxome and 1188 targets have been identified. They participate in a wide range of metabolic pathways and cellular processes. This study broadens not only the redox regulation to new enzymes involved in well-known thioredoxin-regulated metabolic pathways but also sheds light on cellular processes for which data supporting redox regulation are scarce (aromatic amino acid biosynthesis, nuclear transport, etc). Moreover, we characterized 1052 thioredoxin-dependent regulatory sites and showed that these data constitute a valuable resource for future functional studies in Chlamydomonas. By comparing this thioredoxome with proteomic data for glutathionylation and nitrosylation at the protein and cysteine levels, this work confirms the existence of a complex redox regulation network in Chlamydomonas and provides evidence of a tremendous selectivity of redox post-translational modifications for specific cysteine residues.
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Affiliation(s)
- María Esther Pérez-Pérez
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Adeline Mauriès
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alexandre Maes
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Nicolas J Tourasse
- Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FRC550, CNRS, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Marion Hamon
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France; Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FRC550, CNRS, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Stéphane D Lemaire
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | - Christophe H Marchand
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France; Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FRC550, CNRS, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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