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Sastre S, Manta B, Semelak JA, Estrin D, Trujillo M, Radi R, Zeida A. Catalytic Mechanism of Mycobacterium tuberculosis Methionine Sulfoxide Reductase A. Biochemistry 2024; 63:533-544. [PMID: 38286790 DOI: 10.1021/acs.biochem.3c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The oxidation of Met to methionine sulfoxide (MetSO) by oxidants such as hydrogen peroxide, hypochlorite, or peroxynitrite has profound effects on protein function. This modification can be reversed by methionine sulfoxide reductases (msr). In the context of pathogen infection, the reduction of oxidized proteins gains significance due to microbial oxidative damage generated by the immune system. For example, Mycobacterium tuberculosis (Mt) utilizes msrs (MtmsrA and MtmsrB) as part of the repair response to the host-induced oxidative stress. The absence of these enzymes makes Mycobacteria prone to increased susceptibility to cell death, pointing them out as potential therapeutic targets. This study provides a detailed characterization of the catalytic mechanism of MtmsrA using a comprehensive approach, including experimental techniques and theoretical methodologies. Confirming a ping-pong type enzymatic mechanism, we elucidate the catalytic parameters for sulfoxide and thioredoxin substrates (kcat/KM = 2656 ± 525 M-1 s-1 and 1.7 ± 0.8 × 106 M-1 s-1, respectively). Notably, the entropic nature of the activation process thermodynamics, representing ∼85% of the activation free energy at room temperature, is underscored. Furthermore, the current study questions the plausibility of a sulfurane intermediate, which may be a transition-state-like structure, suggesting the involvement of a conserved histidine residue as an acid-base catalyst in the MetSO reduction mechanism. This mechanistic insight not only advances our understanding of Mt antioxidant enzymes but also holds implications for future drug discovery and biotechnological applications.
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Affiliation(s)
- Santiago Sastre
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Departamento de Biofísica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Programa de Doctorado en Química, Facultad de Química, Universidad de la República, Gral Flores 2124, CP 11800 Montevideo, Uruguay
| | - Bruno Manta
- Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Cátedra de Fisiopatología, Facultad de Odontología, Universidad de la República, Gral Las Heras 1925, CP 11600 Montevideo, Uruguay
| | - Jonathan A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Ciudad Universitaria, Intendente Güiraldes 2160, CP C1428EGA Buenos Aires, Argentina
| | - Dario Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Ciudad Universitaria, Intendente Güiraldes 2160, CP C1428EGA Buenos Aires, Argentina
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
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Barrero-Canosa J, Wang L, Oyugi A, Klaes S, Fischer P, Adrian L, Szewzyk U, Cooper M. Characterization of phage vB_EcoS-EE09 infecting E. coli DSM613 Isolated from Wastewater Treatment Plant Effluent and Comparative Proteomics of the Infected and Non-Infected Host. Microorganisms 2023; 11:2688. [PMID: 38004701 PMCID: PMC10673088 DOI: 10.3390/microorganisms11112688] [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: 10/05/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Phages influence microbial communities, can be applied in phage therapy, or may serve as bioindicators, e.g., in (waste)water management. We here characterized the Escherichia phage vB_EcoS-EE09 isolated from an urban wastewater treatment plant effluent. Phage vB_EcoS-EE09 belongs to the genus Dhillonvirus, class Caudoviricetes. It has an icosahedral capsid with a long non-contractile tail and a dsDNA genome with an approximate size of 44 kb and a 54.6% GC content. Phage vB_EcoS-EE09 infected 12 out of the 17 E. coli strains tested. We identified 16 structural phage proteins, including the major capsid protein, in cell-free lysates by protein mass spectrometry. Comparative proteomics of protein extracts of infected E. coli cells revealed that proteins involved in amino acid and protein metabolism were more abundant in infected compared to non-infected cells. Among the proteins involved in the stress response, 74% were less abundant in the infected cultures compared to the non-infected controls, with six proteins showing significant less abundance. Repressing the expression of these proteins may be a phage strategy to evade host defense mechanisms. Our results contribute to diversifying phage collections, identifying structural proteins to enable better reliability in annotating taxonomically related phage genomes, and understanding phage-host interactions at the protein level.
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Affiliation(s)
- Jimena Barrero-Canosa
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Luyao Wang
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Angelah Oyugi
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Simon Klaes
- Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (S.K.)
- Helmholtz Centre for Environmental Research GmbH—UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Pascal Fischer
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Lorenz Adrian
- Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (S.K.)
- Helmholtz Centre for Environmental Research GmbH—UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Ulrich Szewzyk
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Myriel Cooper
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
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3
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Chen L, Liu R, Li S, Wu M, Yu H, Ge Q. Metabolism of hydrogen peroxide by Lactobacillus plantarum NJAU-01: A proteomics study. Food Microbiol 2023; 112:104246. [PMID: 36906310 DOI: 10.1016/j.fm.2023.104246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/08/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
This study aimed to investigate the time-course effect of Lactobacillus plantarum NJAU-01 in scavenging exogenous hydrogen peroxide (H2O2). The results showed that L. plantarum NJAU-01 at 107 CFU/mL was able to eliminate a maximum of 4 mM H2O2 within a prolonged lag phase and resume to proliferate during the following culture. Redox state in the start-lag phase (0 h, without the addition of H2O2), indicated by glutathione and protein sulfhydryl, was impaired in the lag phase (3 h and 12 h) and then gradually recovered during subsequent growing stages (20 h and 30 h). By using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and proteomics analysis, a total of 163 proteins such as PhoP family transcriptional regulator, glutamine synthetase, peptide methionine sulfoxide reductase, thioredoxin reductase, ribosomal proteins, acetolactate synthase, ATP binding subunit ClpX, phosphoglycerate kinase, UvrABC system protein A and UvrABC system protein B were identified as differential proteins across the entire growth phase. Those proteins were mainly involved in H2O2 sensing, protein synthesis, repairing proteins and DNA lesions, amino sugar and nucleotide sugar metabolism. Our data suggest that biomolecules of L. plantarum NJAU-01 are oxidized to passively consume H2O2 and are restored by the enhanced protein and/or gene repair systems.
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Affiliation(s)
- Lei Chen
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Rui Liu
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China.
| | - Suyun Li
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Mangang Wu
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Hai Yu
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Qingfeng Ge
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China.
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Vincent MS, Ezraty B. Methionine oxidation in bacteria: A reversible post-translational modification. Mol Microbiol 2023; 119:143-150. [PMID: 36350090 DOI: 10.1111/mmi.15000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Methionine is a sulfur-containing residue found in most proteins which are particularly susceptible to oxidation. Although methionine oxidation causes protein damage, it can in some cases activate protein function. Enzymatic systems reducing oxidized methionine have evolved in most bacterial species and methionine oxidation proves to be a reversible post-translational modification regulating protein activity. In this review, we inspect recent examples of methionine oxidation provoking protein loss and gain of function. We further speculate on the role of methionine oxidation as a multilayer endogenous antioxidant system and consider its potential consequences for bacterial virulence.
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Affiliation(s)
- Maxence S Vincent
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
| | - Benjamin Ezraty
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
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Chen Y, He X, Chen Q, He Y, Chen F, Yang C, Wang L. Nanomaterials against intracellular bacterial infection: from drug delivery to intrinsic biofunction. Front Bioeng Biotechnol 2023; 11:1197974. [PMID: 37180049 PMCID: PMC10174311 DOI: 10.3389/fbioe.2023.1197974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
Fighting intracellular bacteria with strong antibiotics evading remains a long-standing challenge. Responding to and regulating the infectious microenvironment is crucial for treating intracellular infections. Sophisticated nanomaterials with unique physicochemical properties exhibit great potential for precise drug delivery towards infection sites, along with modulating infectious microenvironment via their instinct bioactivity. In this review, we first identify the key characters and therapeutic targets of intracellular infection microenvironment. Next, we illustrate how the nanomaterials physicochemical properties, such as size, charge, shape and functionalization affect the interaction between nanomaterials, cells and bacteria. We also introduce the recent progress of nanomaterial-based targeted delivery and controlled release of antibiotics in intracellular infection microenvironment. Notably, we highlight the nanomaterials with unique intrinsic properties, such as metal toxicity and enzyme-like activity for the treatment of intracellular bacteria. Finally, we discuss the opportunities and challenges of bioactive nanomaterials in addressing intracellular infections.
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Affiliation(s)
- Yinglu Chen
- Department of Orthopedics, Academy of Orthopedics-Guangdong Province, Orthopedic Hospital of Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoheng He
- Department of Applied Chemistry, Xi’an University of Technology, Xi’an, China
| | - Qiuhong Chen
- Department of Orthopedics, Academy of Orthopedics-Guangdong Province, Orthopedic Hospital of Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Yi He
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Fangman Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, Macau SAR, China
| | - Chao Yang
- Department of Orthopedics, Academy of Orthopedics-Guangdong Province, Orthopedic Hospital of Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Liang Wang, ; Chao Yang,
| | - Liang Wang
- Department of Orthopedics, Academy of Orthopedics-Guangdong Province, Orthopedic Hospital of Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Liang Wang, ; Chao Yang,
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6
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Gutschmann B, Maldonado Simões M, Schiewe T, Schröter ES, Münzberg M, Neubauer P, Bockisch A, Riedel SL. Continuous feeding strategy for polyhydroxyalkanoate production from solid waste animal fat at laboratory- and pilot-scale. Microb Biotechnol 2022; 16:295-306. [PMID: 35921398 PMCID: PMC9871520 DOI: 10.1111/1751-7915.14104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 01/27/2023] Open
Abstract
Bioconversion of waste animal fat (WAF) to polyhydroxyalkanoates (PHAs) is an approach to lower the production costs of these plastic alternatives. However, the solid nature of WAF requires a tailor-made process development. In this study, a double-jacket feeding system was built to thermally liquefy the WAF to employ a continuous feeding strategy. During laboratory-scale cultivations with Ralstonia eutropha Re2058/pCB113, 70% more PHA (45 gPHA L-1 ) and a 75% higher space-time yield (0.63 gPHA L-1 h-1 ) were achieved compared to previously reported fermentations with solid WAF. During the development process, growth and PHA formation were monitored in real-time by in-line photon density wave spectroscopy. The process robustness was further evaluated during scale-down fermentations employing an oscillating aeration, which did not alter the PHA yield although cells encountered periods of oxygen limitation. Flow cytometry with propidium iodide staining showed that more than two-thirds of the cells were viable at the end of the cultivation and viability was even little higher in the scale-down cultivations. Application of this feeding system at 150-L pilot-scale cultivation yielded in 31.5 gPHA L-1 , which is a promising result for the further scale-up to industrial scale.
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Affiliation(s)
- Björn Gutschmann
- Technische Universität BerlinChair of Bioprocess EngineeringBerlinGermany
| | | | | | - Edith S. Schröter
- Technische Universität BerlinChair of Bioprocess EngineeringBerlinGermany
| | | | - Peter Neubauer
- Technische Universität BerlinChair of Bioprocess EngineeringBerlinGermany
| | - Anika Bockisch
- Technische Universität BerlinChair of Bioprocess EngineeringBerlinGermany,Bio‐PAT e.VBerlinGermany
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7
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The Potential of a Protein Model Synthesized Absent of Methionine. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123679. [PMID: 35744804 PMCID: PMC9230714 DOI: 10.3390/molecules27123679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/20/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022]
Abstract
Methionine is an amino acid long thought to be essential, but only in the case of protein synthesis initiation. In more recent years, methionine has been found to play an important role in antioxidant defense, stability, and modulation of cell and protein activity. Though these findings have expanded the previously held sentiment of methionine having a singular purpose within cells and proteins, the essential nature of methionine can still be challenged. Many of the features that give methionine its newfound functions are shared by the other sulfur-containing amino acid: cysteine. While the antioxidant, stabilizing, and cell/protein modulatory functions of cysteine have already been well established, recent findings have shown a similar hydrophobicity to methionine which suggests cysteine may be able to replace methionine in all functions outside of protein synthesis initiation with little effect on cell and protein function. Furthermore, a number of novel mechanisms for alternative initiation of protein synthesis have been identified that suggest a potential to bypass the traditional methionine-dependent initiation during times of stress. In this review, these findings are discussed with a number of examples that demonstrate a potential model for synthesizing a protein in the absence of methionine.
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8
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Wu M, Shan W, Zhao GP, Lyu LD. The H2O2 Concentration-Dependent Kinetics of Gene Expression: Linking the Intensity of Oxidative Stress and Mycobacterial Physiological Adaptation. Emerg Microbes Infect 2022; 11:573-584. [PMID: 35076334 PMCID: PMC8856045 DOI: 10.1080/22221751.2022.2034484] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Defence against oxidative stress is crucial for Mycobacterium tuberculosis to survive and replicate within macrophages. Mycobacteria have evolved multilayer antioxidant systems, including scavenging enzymes, iron homeostasis, repair pathways, and metabolic adaptation, for coping with oxidative stress. How these systems are coordinated to enable the physiological adaptation to different intensities of oxidative stress, however, remains unclear. To address this, we investigated the expression kinetics of the well-characterized antioxidant genes at bacteriostatic H2O2 concentrations ranging from 1 mM to 10 mM employing Mycolicibacterium smegmatis as a model. Our results showed that most of the selected genes were expressed in a H2O2 concentration-dependent manner, whereas a subset exhibited sustained induction or repression without dose–effect, reflecting H2O2 concentration-dependent physiological adaptations. Through analyzing the dynamics of the coordinated gene expression, we demonstrated that the expressions of the H2O2 scavenging enzymes, DNA damage response, and Fe–S cluster repair function were strikingly correlated to the intensity of oxidative stress. The sustained induction of mbtB, irtA, and dnaE2 indicated that mycobacteria might deploy increased iron acquisition and error-prone lesion bypass function as fundamental strategies to counteract oxidative damages, which are distinct from the defence tactics of Escherichia coli characterized by shrinking the iron pool and delaying the DNA repair. Moreover, the distinct gene expression kinetics among the tricarboxylic acid cycle, glyoxylate shunt, and methylcitrate cycle suggested that mycobacteria could dynamically redirect its metabolic fluxes according to the intensity of oxidative stress. This work defines the H2O2 concentration-dependent gene expression kinetics and provides unique insights into mycobacterial antioxidant defence strategies.
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Affiliation(s)
- Mengying Wu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, 200032 Shanghai, China
| | - Wenyan Shan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, 200032 Shanghai, China
| | - Guo-Ping Zhao
- Department of Microbiology, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, 200032 Shanghai, China
- Shanghai Clinical Research Center for Infectious Disease (Tuberculosis), Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, 200433 Shanghai, China
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9
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dos Santos CI, Campos CDL, Nunes-Neto WR, do Carmo MS, Nogueira FAB, Ferreira RM, Costa EPS, Gonzaga LF, Araújo JMM, Monteiro JM, Monteiro CRAV, Platner FS, Figueiredo IFS, Holanda RA, Monteiro SG, Fernandes ES, Monteiro AS, Monteiro-Neto V. Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti- Candida Activity. J Fungi (Basel) 2021; 7:jof7100794. [PMID: 34682216 PMCID: PMC8537286 DOI: 10.3390/jof7100794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/10/2021] [Accepted: 09/20/2021] [Indexed: 01/20/2023] Open
Abstract
Limosilactobacillus fermentum (ATCC 23271) was originally isolated from the human intestine and has displayed antimicrobial activity, primarily against Candida species. Complete genome sequencing and comparative analyses were performed to elucidate the genetic basis underlying its probiotic potential. The ATCC 23271 genome was found to contain 2,193,335 bp, with 2123 protein-coding sequences. Phylogenetic analysis revealed that the ATCC 23271 strain shares 941 gene clusters with six other probiotic strains of L. fermentum. Putative genes known to confer probiotic properties have been identified in the genome, including genes related to adhesion, tolerance to acidic pH and bile salts, tolerance to oxidative stress, and metabolism and transport of sugars and other compounds. A search for bacteriocin genes revealed a sequence 48% similar to that of enterolysin A, a protein from Enterococcus faecalis. However, in vitro assays confirmed that the strain has inhibitory activity on the growth of Candida species and also interferes with their adhesion to HeLa cells. In silico analyses demonstrated a high probability of the protein with antimicrobial activity. Our data reveal the genome features of L. fermentum ATCC 23271, which may provide insight into its future use given the functional benefits, especially against Candida infections.
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Affiliation(s)
- Camilla I. dos Santos
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, BIONORTE, São Luís 65055-310, MA, Brazil; (C.I.d.S.); (W.R.N.-N.); (E.P.S.C.)
| | - Carmem D. L. Campos
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (C.D.L.C.); (R.M.F.); (L.F.G.); (J.M.M.A.); (J.M.M.); (R.A.H.); (A.S.M.)
| | - Wallace R. Nunes-Neto
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, BIONORTE, São Luís 65055-310, MA, Brazil; (C.I.d.S.); (W.R.N.-N.); (E.P.S.C.)
| | - Monique S. do Carmo
- Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, MA, Brazil; (M.S.d.C.); (F.A.B.N.); (C.R.A.V.M.); (S.G.M.)
| | - Flávio A. B. Nogueira
- Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, MA, Brazil; (M.S.d.C.); (F.A.B.N.); (C.R.A.V.M.); (S.G.M.)
| | - Rômulo M. Ferreira
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (C.D.L.C.); (R.M.F.); (L.F.G.); (J.M.M.A.); (J.M.M.); (R.A.H.); (A.S.M.)
| | - Ennio P. S. Costa
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, BIONORTE, São Luís 65055-310, MA, Brazil; (C.I.d.S.); (W.R.N.-N.); (E.P.S.C.)
| | - Laoane F. Gonzaga
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (C.D.L.C.); (R.M.F.); (L.F.G.); (J.M.M.A.); (J.M.M.); (R.A.H.); (A.S.M.)
| | - Jéssica M. M. Araújo
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (C.D.L.C.); (R.M.F.); (L.F.G.); (J.M.M.A.); (J.M.M.); (R.A.H.); (A.S.M.)
| | - Joveliane M. Monteiro
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (C.D.L.C.); (R.M.F.); (L.F.G.); (J.M.M.A.); (J.M.M.); (R.A.H.); (A.S.M.)
| | - Cinara Regina A. V. Monteiro
- Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, MA, Brazil; (M.S.d.C.); (F.A.B.N.); (C.R.A.V.M.); (S.G.M.)
| | - Fernanda S. Platner
- Faculdades Pequeno Príncipe, FPP, Curitiba 80230-020, PR, Brazil; (F.S.P.); (I.F.S.F.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, IPPPP, Curitiba 80250-060, PR, Brazil
| | - Isabella F. S. Figueiredo
- Faculdades Pequeno Príncipe, FPP, Curitiba 80230-020, PR, Brazil; (F.S.P.); (I.F.S.F.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, IPPPP, Curitiba 80250-060, PR, Brazil
| | - Rodrigo A. Holanda
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (C.D.L.C.); (R.M.F.); (L.F.G.); (J.M.M.A.); (J.M.M.); (R.A.H.); (A.S.M.)
| | - Silvio G. Monteiro
- Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, MA, Brazil; (M.S.d.C.); (F.A.B.N.); (C.R.A.V.M.); (S.G.M.)
| | - Elizabeth S. Fernandes
- Faculdades Pequeno Príncipe, FPP, Curitiba 80230-020, PR, Brazil; (F.S.P.); (I.F.S.F.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, IPPPP, Curitiba 80250-060, PR, Brazil
| | - Andrea S. Monteiro
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (C.D.L.C.); (R.M.F.); (L.F.G.); (J.M.M.A.); (J.M.M.); (R.A.H.); (A.S.M.)
| | - Valério Monteiro-Neto
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, BIONORTE, São Luís 65055-310, MA, Brazil; (C.I.d.S.); (W.R.N.-N.); (E.P.S.C.)
- Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, MA, Brazil; (M.S.d.C.); (F.A.B.N.); (C.R.A.V.M.); (S.G.M.)
- Correspondence: ; Tel.: +55-98-3272-9591
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10
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Gutschmann B, Bock MCE, Jahns S, Neubauer P, Brigham CJ, Riedel SL. Untargeted metabolomics analysis of Ralstonia eutropha during plant oil cultivations reveals the presence of a fucose salvage pathway. Sci Rep 2021; 11:14267. [PMID: 34253787 PMCID: PMC8275744 DOI: 10.1038/s41598-021-93720-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Process engineering of biotechnological productions can benefit greatly from comprehensive analysis of microbial physiology and metabolism. Ralstonia eutropha (syn. Cupriavidus necator) is one of the best studied organisms for the synthesis of biodegradable polyhydroxyalkanoate (PHA). A comprehensive metabolomic study during bioreactor cultivations with the wild-type (H16) and an engineered (Re2058/pCB113) R. eutropha strain for short- and or medium-chain-length PHA synthesis has been carried out. PHA production from plant oil was triggered through nitrogen limitation. Sample quenching allowed to conserve the metabolic states of the cells for subsequent untargeted metabolomic analysis, which consisted of GC-MS and LC-MS analysis. Multivariate data analysis resulted in identification of significant changes in concentrations of oxidative stress-related metabolites and a subsequent accumulation of antioxidative compounds. Moreover, metabolites involved in the de novo synthesis of GDP-L-fucose as well as the fucose salvage pathway were identified. The related formation of fucose-containing exopolysaccharides potentially supports the emulsion-based growth of R. eutropha on plant oils.
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Affiliation(s)
- Björn Gutschmann
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Martina C. E. Bock
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Stefan Jahns
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Christopher J. Brigham
- grid.422596.e0000 0001 0639 028XSchool of Engineering, Wentworth Institute of Technology, Boston, MA USA
| | - Sebastian L. Riedel
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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11
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Iwadate Y, Ramezanifard R, Golubeva YA, Fenlon LA, Slauch JM. PaeA (YtfL) protects from cadaverine and putrescine stress in Salmonella Typhimurium and E. coli. Mol Microbiol 2021; 115:1379-1394. [PMID: 33481283 PMCID: PMC10923242 DOI: 10.1111/mmi.14686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Salmonella and E. coli synthesize, import, and export cadaverine, putrescine, and spermidine to maintain physiological levels and provide pH homeostasis. Both low and high intracellular levels of polyamines confer pleiotropic phenotypes or lethality. Here, we demonstrate that the previously uncharacterized inner membrane protein PaeA (YtfL) is required for reducing cytoplasmic cadaverine and putrescine concentrations. We identified paeA as a gene involved in stationary phase survival when cells were initially grown in acidic medium, in which they produce cadaverine. The paeA mutant is also sensitive to putrescine, but not to spermidine or spermine. Sensitivity to external cadaverine in stationary phase is only observed at pH > 8, suggesting that the polyamines need to be deprotonated to passively diffuse into the cell cytoplasm. In the absence of PaeA, intracellular polyamine levels increase and the cells lose viability. Degradation or modification of the polyamines is not relevant. Ectopic expression of the known cadaverine exporter, CadB, in stationary phase partially suppresses the paeA phenotype, and overexpression of PaeA in exponential phase partially complements a cadB mutant grown in acidic medium. These data support the hypothesis that PaeA is a cadaverine/putrescine exporter, reducing potentially toxic levels under certain stress conditions.
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Affiliation(s)
- Yumi Iwadate
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Rouhallah Ramezanifard
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Yekaterina A. Golubeva
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Luke A. Fenlon
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
- Current address: Department of Internal Medicine, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, Utah 84132
| | - James M. Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
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12
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Porrini C, Ramarao N, Tran SL. Dr. NO and Mr. Toxic - the versatile role of nitric oxide. Biol Chem 2021; 401:547-572. [PMID: 31811798 DOI: 10.1515/hsz-2019-0368] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/04/2019] [Indexed: 12/25/2022]
Abstract
Nitric oxide (NO) is present in various organisms from humans, to plants, fungus and bacteria. NO is a fundamental signaling molecule implicated in major cellular functions. The role of NO ranges from an essential molecule to a potent mediator of cellular damages. The ability of NO to react with a broad range of biomolecules allows on one hand its regulation and a gradient concentration and on the other hand to exert physiological as well as pathological functions. In humans, NO is implicated in cardiovascular homeostasis, neurotransmission and immunity. However, NO can also contribute to cardiovascular diseases (CVDs) or septic shock. For certain denitrifying bacteria, NO is part of their metabolism as a required intermediate of the nitrogen cycle. However, for other bacteria, NO is toxic and harmful. To survive, those bacteria have developed processes to resist this toxic effect and persist inside their host. NO also contributes to maintain the host/microbiota homeostasis. But little is known about the impact of NO produced during prolonged inflammation on microbiota integrity, and some pathogenic bacteria take advantage of the NO response to colonize the gut over the microbiota. Taken together, depending on the environmental context (prolonged production, gradient concentration, presence of partners for interaction, presence of oxygen, etc.), NO will exert its beneficial or detrimental function. In this review, we highlight the dual role of NO for humans, pathogenic bacteria and microbiota, and the mechanisms used by each organism to produce, use or resist NO.
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Affiliation(s)
- Constance Porrini
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Nalini Ramarao
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Seav-Ly Tran
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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13
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Nair SS, Chauhan TKS, Kumawat M, Sarkhel R, Apoorva S, Shome A, Athira V, Kumar B, Abhishek, Mahawar M. Deletion of both methionine sulfoxide reductase A and methionine sulfoxide reductase C genes renders Salmonella Typhimurium highly susceptible to hypochlorite stress and poultry macrophages. Mol Biol Rep 2021; 48:3195-3203. [PMID: 33954903 DOI: 10.1007/s11033-021-06381-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/24/2021] [Indexed: 10/21/2022]
Abstract
Salmonella Typhimurium survives and replicates inside the oxidative environment of phagocytic cells. Proteins, because of their composition and location, are the foremost targets of host inflammatory response. Among others, Met-residues are highly prone to oxidation. Methionine sulfoxide reductase (Msr), with the help of thioredoxin-thioredoxin reductase, can repair oxidized methionine (Met-SO) residues to Met. There are four methionine sulfoxide reductases localized in the cytosol of S. Typhimurium, MsrA, MsrB, MsrC and BisC. MsrA repairs both protein-bound and free 'S' Met-SO, MsrB repairs protein-bound 'R' Met-SO, MsrC repairs free 'R' Met-SO and BisC repairs free 'S' Met-SO. To assess the role(s) of various Msrs in Salmonella, few studies have been conducted by utilizing ΔmsrA, ΔmsrB, ΔmsrC, ΔmsrAΔmsrB, ΔmsrBΔmsrC and ΔbisC mutant strains of S. Typhimurium. Out of the above-mentioned mutants, ΔmsrA and ΔmsrC were found to play important role in the stress survival of this bacterium; however, the combined roles of these two genes have not been determined. In the current study, we have generated msrAmsrC double gene deletion strain (ΔmsrAΔmsrC) of S. Typhimurium and evaluated the effect of gene deletions on the survival of Salmonella against hypochlorite stress and intramacrophage replication. In in vitro growth curve analysis, ΔmsrAΔmsrC mutant strain showed a longer lag phase during the initial stages of the growth; however, it attained similar growth as the wild type strain of S. Typhimurium after 5 h. The ΔmsrAΔmsrC mutant strain has been highly (~ 3000 folds more) sensitive (p < 0.001) to hypochlorite stress. Further, ΔmsrA and ΔmsrAΔmsrC mutant strains showed more than 8 and 26 folds more susceptibility to poultry macrophages, respectively. Our data suggest that the deletion of both msrA and msrC genes severely affect the oxidative stress survival and intramacrophage proliferation of S. Typhimurium.
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Affiliation(s)
- Sonu S Nair
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India
| | | | - Manoj Kumawat
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India
| | - Ratanti Sarkhel
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India
| | - Shekhar Apoorva
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India
| | - Arijit Shome
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India
| | - V Athira
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India
| | - Bablu Kumar
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India
| | - Abhishek
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India.
| | - Manish Mahawar
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, 243 122, India.
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14
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Felix L, Mylonakis E, Fuchs BB. Thioredoxin Reductase Is a Valid Target for Antimicrobial Therapeutic Development Against Gram-Positive Bacteria. Front Microbiol 2021; 12:663481. [PMID: 33936021 PMCID: PMC8085250 DOI: 10.3389/fmicb.2021.663481] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022] Open
Abstract
There is a drought of new antibacterial compounds that exploit novel targets. Thioredoxin reductase (TrxR) from the Gram-positive bacterial antioxidant thioredoxin system has emerged from multiple screening efforts as a potential target for auranofin, ebselen, shikonin, and allicin. Auranofin serves as the most encouraging proof of concept drug, demonstrating TrxR inhibition can result in bactericidal effects and inhibit Gram-positive bacteria in both planktonic and biofilm states. Minimal inhibitory concentrations are on par or lower than gold standard medications, even among drug resistant isolates. Importantly, existing drug resistance mechanisms that challenge treatment of infections like Staphylococcus aureus do not confer resistance to TrxR targeting compounds. The observed inhibition by multiple compounds and inability to generate a bacterial genetic mutant demonstrate TrxR appears to play an essential role in Gram-positive bacteria. These findings suggest TrxR can be exploited further for drug development. Examining the interaction between TrxR and these proof of concept compounds illustrates that compounds representing a new antimicrobial class can be developed to directly interact and inhibit the validated target.
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Affiliation(s)
- LewisOscar Felix
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, United States
| | - Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, United States
| | - Beth Burgwyn Fuchs
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, United States
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15
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Arias DG, Cabeza MS, Echarren ML, Faral-Tello P, Iglesias AA, Robello C, Guerrero SA. On the functionality of a methionine sulfoxide reductase B from Trypanosoma cruzi. Free Radic Biol Med 2020; 158:96-114. [PMID: 32682073 DOI: 10.1016/j.freeradbiomed.2020.06.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 06/20/2020] [Accepted: 06/26/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Methionine is an amino acid susceptible to be oxidized to give a racemic mixture of R and S forms of methionine sulfoxide (MetSO). This posttranslational modification has been reported to occur in vivo under either normal or stress conditions. The reduction of MetSO to methionine is catalyzed by methionine sulfoxide reductases (MSRs), thiol-dependent enzymes present in almost all organisms. These enzymes can reduce specifically one or another of the isomers of MetSO (free and protein-bound). This redox modification could change the structure and function of many proteins, either concerned in redox or other metabolic pathways. The study of antioxidant systems in Trypanosoma cruzi has been mainly focused on the involvement of trypanothione, a specific redox component for these organisms. Though, little information is available concerning mechanisms for repairing oxidized methionine residues in proteins, which would be relevant for the survival of these pathogens in the different stages of their life cycle. METHODS We report an in vitro functional and in vivo cellular characterization of methionine sulfoxide reductase B (MSRB, specific for protein-bound MetSO R-enantiomer) from T. cruzi strain Dm28c. RESULTS MSRB exhibited both cytosolic and mitochondrial localization in epimastigote cells. From assays involving parasites overexpressing MSRB, we observed the contribution of this protein to increase the general resistance against oxidative damage, the infectivity of trypomastigote cells, and intracellular replication of the amastigote stage. Also, we report that epimastigotes overexpressing MSRB exhibit inhibition of the metacyclogenesis process; this suggesting the involvement of the proteins as negative modulators in this cellular differentiation. CONCLUSIONS AND GENERAL SIGNIFICANCE This report contributes to novel insights concerning redox metabolism in T. cruzi. Results herein presented support the importance of enzymatic steps involved in the metabolism of L-Met and in repairing oxidized macromolecules in this parasite.
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Affiliation(s)
- Diego G Arias
- Laboratorio de Enzimología Molecular - Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas - Universidad Nacional del Litoral, Santa Fe, Argentina.
| | - Matías S Cabeza
- Laboratorio de Enzimología Molecular - Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas - Universidad Nacional del Litoral, Santa Fe, Argentina
| | - María L Echarren
- Laboratorio de Enzimología Molecular - Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina
| | - Paula Faral-Tello
- Laboratorio de Interacción Hospedero-Patógeno, UBM, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular - Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas - Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Carlos Robello
- Laboratorio de Interacción Hospedero-Patógeno, UBM, Instituto Pasteur de Montevideo, Montevideo, Uruguay; Departamento de Bioquímica - Facultad de Medicina - Universidad de la República, Montevideo, Uruguay
| | - Sergio A Guerrero
- Laboratorio de Enzimología Molecular - Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas - Universidad Nacional del Litoral, Santa Fe, Argentina
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16
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Zhai Z, Yang Y, Wang H, Wang G, Ren F, Li Z, Hao Y. Global transcriptomic analysis of Lactobacillus plantarum CAUH2 in response to hydrogen peroxide stress. Food Microbiol 2020; 87:103389. [DOI: 10.1016/j.fm.2019.103389] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/27/2019] [Accepted: 11/20/2019] [Indexed: 12/25/2022]
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17
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Mih N, Monk JM, Fang X, Catoiu E, Heckmann D, Yang L, Palsson BO. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinformatics 2020; 21:162. [PMID: 32349661 PMCID: PMC7191737 DOI: 10.1186/s12859-020-3505-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/17/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the two leads to the formation of a structural systems biology framework, which we have used to analyze differences between the reactive oxygen species (ROS) sensitivity of the proteomes of sequenced strains of E. coli. As proteins are one of the main targets of oxidative damage, understanding how the genetic changes of different strains of a species relates to its oxidative environment can reveal hypotheses as to why these variations arise and suggest directions of future experimental work. RESULTS Creating a reference structural proteome for E. coli allows us to comprehensively map genetic changes in 1764 different strains to their locations on 4118 3D protein structures. We use metabolic modeling to predict basal ROS production levels (ROStype) for 695 of these strains, finding that strains with both higher and lower basal levels tend to enrich their proteomes with antioxidative properties, and speculate as to why that is. We computationally assess a strain's sensitivity to an oxidative environment, based on known chemical mechanisms of oxidative damage to protein groups, defined by their localization and functionality. Two general groups - metalloproteins and periplasmic proteins - show enrichment of their antioxidative properties between the 695 strains with a predicted ROStype as well as 116 strains with an assigned pathotype. Specifically, proteins that a) utilize a molybdenum ion as a cofactor and b) are involved in the biogenesis of fimbriae show intriguing protective properties to resist oxidative damage. Overall, these findings indicate that a strain's sensitivity to oxidative damage can be elucidated from the structural proteome, though future experimental work is needed to validate our model assumptions and findings. CONCLUSION We thus demonstrate that structural systems biology enables a proteome-wide, computational assessment of changes to atomic-level physicochemical properties and of oxidative damage mechanisms for multiple strains in a species. This integrative approach opens new avenues to study adaptation to a particular environment based on physiological properties predicted from sequence alone.
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Affiliation(s)
- Nathan Mih
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Jonathan M. Monk
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Xin Fang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Edward Catoiu
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - David Heckmann
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Laurence Yang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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18
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Ouyang X, Li X, Liu J, Liu Y, Xie Y, Du Z, Xie H, Chen B, Lu W, Chen D. Structure–activity relationship and mechanism of four monostilbenes with respect to ferroptosis inhibition. RSC Adv 2020; 10:31171-31179. [PMID: 35520676 PMCID: PMC9056428 DOI: 10.1039/d0ra04896h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/08/2020] [Indexed: 12/20/2022] Open
Abstract
Erastin-treated bone marrow-derived mesenchymal stem cells (bmMSCs) were prepared and used to compare the ferroptosis inhibitory bioactivities of four monostilbenes, including rhapontigenin (1a), isorhapontigenin (1b), piceatannol-3′-O-glucoside (1c), and rhapontin (1d). Their relative levels were 1c ≈ 1b > 1a ≈ 1d in 4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-undecanoic acid (C11-BODIPY), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and flow cytometric assays. The comparison highlighted two 4′-OH-containing monostilbenes (1c and 1b) in ferroptosis inhibitory bioactivity. Similar structure–activity relationships were also observed in antioxidant assays, including 1,1-diphenyl-2-picryl-hydrazl radical (DPPH˙)-trapping, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide radical (PTIO˙)-trapping, and Fe3+-reducing assays. UPLC-ESI-Q-TOF-MS analysis of the DPPH˙-trapping reaction of the monostilbenes revealed that they can inhibit ferroptosis in erastin-treated bmMSCs through a hydrogen donation-based antioxidant pathway. After hydrogen donation, these monostilbenes usually produce the corresponding stable dimers; additionally, the hydrogen donation potential was enhanced by the 4′-OH. The enhancement by 4′-OH can be attributed to the transannular resonance effect. This effect can be used to predict the inhibition potential of other π–π conjugative phenolics. Erastin-treated bone marrow-derived mesenchymal stem cells (bmMSCs) were prepared and used to compare the ferroptosis inhibitory bioactivities of four monostilbenes, including rhapontigenin (1a), isorhapontigenin (1b), piceatannol-3′-O-glucoside (1c), and rhapontin (1d).![]()
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Affiliation(s)
- Xiaojian Ouyang
- School of Chinese Herbal Medicine
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
| | - Xican Li
- School of Chinese Herbal Medicine
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
| | - Jie Liu
- School of Basic Medical Science
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
- The Research Center of Basic Integrative Medicine
| | - Yangping Liu
- School of Basic Medical Science
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
- The Research Center of Basic Integrative Medicine
| | - Yulu Xie
- School of Chinese Herbal Medicine
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
| | - Zhongcun Du
- School of Chinese Herbal Medicine
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
| | - Hong Xie
- School of Chinese Herbal Medicine
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
| | - Ban Chen
- School of Chinese Herbal Medicine
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
| | - Wenbiao Lu
- School of Chinese Herbal Medicine
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
| | - Dongfeng Chen
- School of Basic Medical Science
- Guangzhou University of Chinese Medicine
- Guangzhou 510006
- China
- The Research Center of Basic Integrative Medicine
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19
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Lai L, Sun J, Tarafdar S, Liu C, Murphy E, Kim G, Levine RL. Loss of methionine sulfoxide reductases increases resistance to oxidative stress. Free Radic Biol Med 2019; 145:374-384. [PMID: 31606431 PMCID: PMC6891793 DOI: 10.1016/j.freeradbiomed.2019.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022]
Abstract
Oxidation of methionine residues to methionine sulfoxide scavenges reactive species, thus protecting against oxidative stress. Reduction of the sulfoxide back to methionine by methionine sulfoxide reductases creates a cycle with catalytic efficiency. Protection by the methionine sulfoxide reductases is well documented in cultured cells, from microorganisms to mammals. However, knocking out one or two of the 4 mammalian reductases had little effect in mice that were not stressed. We hypothesized that the minimal effect is due to redundancy provided by the 4 reductases. We tested the hypothesis by creating a transgenic mouse line lacking all 4 reductases and predicted that this mouse would be exceptionally sensitive to oxidative stress. The mutant mice were phenotypically normal at birth, exhibited normal post-natal growth, and were fertile. Surprisingly, rather than being more sensitive to oxidative stress, they were more resistant to both cardiac ischemia-reperfusion injury and to parenteral paraquat, a redox-cycling agent. Resistance was not a result of hormetic induction of the antioxidant transcription factor Nrf2 nor activation of Akt. The mechanism of protection may be novel.
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Affiliation(s)
- Lo Lai
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, United States
| | - Junhui Sun
- Laboratory of Cardiac Physiology, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, United States
| | - Sreya Tarafdar
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, United States
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, United States
| | - Elizabeth Murphy
- Laboratory of Cardiac Physiology, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, United States
| | - Geumsoo Kim
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, United States
| | - Rodney L Levine
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, United States.
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20
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Mobeen F, Sharma V, Prakash T. Functional signature analysis of extreme Prakriti endophenotypes in gut microbiome of western Indian rural population. Bioinformation 2019; 15:490-505. [PMID: 31485135 PMCID: PMC6704335 DOI: 10.6026/97320630015490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/30/2019] [Indexed: 12/27/2022] Open
Abstract
Ayurveda is practiced in India from ancient times and stratifies the individuals based on their Prakriti constitution. Advancements in modern science have led to the association of Prakriti with molecular, biochemical, genomic and other entities. We have recently explored the gut microbiome composition and microbial signatures in healthy extreme Prakriti endo-phenotypes. However, their functional potentials are still lacking. The present study includes 63 females (29 Vata, 11 Pitta, and 23 Kapha) and 50 males (13 Vata, 18 Pitta, and 19 Kapha) samples. The predictive functional profiling and organism level functional traits of the human gut microbiome have been carried out in Prakriti groups using imputed metagenomic approach. A higher functional level redundancy is found than the taxonomy across the Prakriti groups, however the dominant taxa contributing to the functional profiles are found to be different. A high number of functional signatures specific to the Prakriti groups were identified in female datasets. Some of the functional signatures were found to be gender specific. For example, a higher abundance of microbes contributing potential pathogenic and stress tolerance related functions was found in Kapha in female and Pitta in male. The functional signatures correlated well with phenotypes and disease predisposition of Prakriti groups.
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Affiliation(s)
- Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| | - Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
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21
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Kappler U, Nasreen M, McEwan A. New insights into the molecular physiology of sulfoxide reduction in bacteria. Adv Microb Physiol 2019; 75:1-51. [PMID: 31655735 DOI: 10.1016/bs.ampbs.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sulfoxides occur in biology as products of the S-oxygenation of small molecules as well as in peptides and proteins and their formation is often associated with oxidative stress and can affect biological function. In bacteria, sulfoxide damage can be reversed by different types of enzymes. Thioredoxin-dependent peptide methionine sulfoxide reductases (MSR proteins) repair oxidized methionine residues and are found in all Domains of life. In bacteria MSR proteins are often found in the cytoplasm but in some bacteria, including pathogenic Neisseria, Streptococci, and Haemophilus they are extracytoplasmic. Mutants lacking MSR proteins are often sensitive to oxidative stress and in pathogens exhibit decreased virulence as indicated by reduced survival in host cell or animal model systems. Molybdenum enzymes are also known to reduce S-oxides and traditionally their physiological role was considered to be in anaerobic respiration using dimethylsulfoxide (DMSO) as an electron acceptor. However, it now appears that some enzymes (MtsZ) of the DMSO reductase family of Mo enzymes use methionine sulfoxide as preferred physiological substrate and thus may be involved in scavenging/recycling of this amino acid. Similarly, an enzyme (MsrP/YedY) of the sulfite oxidase family of Mo enzymes has been shown to be involved in repair of methionine sulfoxides in periplasmic proteins. Again, some mutants deficient in Mo-dependent sulfoxide reductases exhibit reduced virulence, and there is evidence that these Mo enzymes and some MSR systems are induced by hypochlorite produced by the innate immune system. This review describes recent advances in the understanding of the molecular microbiology of MSR systems and the broadening of the role of Mo-dependent sulfoxide reductase to encompass functions beyond anaerobic respiration.
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Affiliation(s)
- Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Marufa Nasreen
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alastair McEwan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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22
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Ding X, Liu K, Lu Y, Gong G. Morphological, transcriptional, and metabolic analyses of osmotic-adapted mechanisms of the halophilic Aspergillus montevidensis ZYD4 under hypersaline conditions. Appl Microbiol Biotechnol 2019; 103:3829-3846. [PMID: 30859256 DOI: 10.1007/s00253-019-09705-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 11/30/2022]
Abstract
Halophilic fungi in hypersaline habitats require multiple cellular responses for high-salinity adaptation. However, the exact mechanisms behind these adaptation processes remain to be slightly known. The current study is aimed at elucidating the morphological, transcriptomic, and metabolomic changes of the halophilic fungus Aspergillus montevidensis ZYD4 under hypersaline conditions. Under these conditions, the fungus promoted conidia formation and suppressed cleistothecium development. Furthermore, the fungus differentially expressed genes (P < 0.0001) that controlled ion transport, amino acid transport and metabolism, soluble sugar accumulation, fatty acid β-oxidation, saturated fatty acid synthesis, electron transfer, and oxidative stress tolerance. Additionally, the hypersalinized mycelia widely accumulated metabolites, including amino acids, soluble sugars, saturated fatty acids, and other carbon- and nitrogen-containing compounds. The addition of metabolites-such as neohesperidin, biuret, aspartic acid, alanine, proline, and ornithine-significantly promoted the growth (P ≤ 0.05) and the morphological adaptations of A. montevidensis ZYD4 grown in hypersaline environments. Our study demonstrated that morphological shifts, ion equilibrium, carbon and nitrogen metabolism for solute accumulation, and energy production are vital to halophilic fungi so that they can build tolerance to high-salinity environments.
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Affiliation(s)
- Xiaowei Ding
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.,School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China
| | - Kaihui Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China. .,School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China.
| | - Yuxin Lu
- School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China
| | - Guoli Gong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
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23
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Piacenza L, Trujillo M, Radi R. Reactive species and pathogen antioxidant networks during phagocytosis. J Exp Med 2019; 216:501-516. [PMID: 30792185 PMCID: PMC6400530 DOI: 10.1084/jem.20181886] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/04/2019] [Accepted: 02/04/2019] [Indexed: 11/23/2022] Open
Abstract
This review discusses the generation of phagosomal cytotoxic reactive species by activated macrophages and neutrophils for the control of intracellular pathogens, and the mechanisms by which microbes combat host-derived oxidants via antioxidant networks that mitigate the redox-dependent control of infection. The generation of phagosomal cytotoxic reactive species (i.e., free radicals and oxidants) by activated macrophages and neutrophils is a crucial process for the control of intracellular pathogens. The chemical nature of these species, the reactions they are involved in, and the subsequent effects are multifaceted and depend on several host- and pathogen-derived factors that influence their production rates and catabolism inside the phagosome. Pathogens rely on an intricate and synergistic antioxidant armamentarium that ensures their own survival by detoxifying reactive species. In this review, we discuss the generation, kinetics, and toxicity of reactive species generated in phagocytes, with a focus on the response of macrophages to internalized pathogens and concentrating on Mycobacterium tuberculosis and Trypanosoma cruzi as examples of bacterial and parasitic infection, respectively. The ability of pathogens to deal with host-derived reactive species largely depends on the competence of their antioxidant networks at the onset of invasion, which in turn can tilt the balance toward pathogen survival, proliferation, and virulence over redox-dependent control of infection.
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Affiliation(s)
- Lucía Piacenza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay .,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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24
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Mehta M, Singh A. Mycobacterium tuberculosis WhiB3 maintains redox homeostasis and survival in response to reactive oxygen and nitrogen species. Free Radic Biol Med 2019; 131:50-58. [PMID: 30500421 PMCID: PMC6635127 DOI: 10.1016/j.freeradbiomed.2018.11.032] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/30/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (Mtb) survives under oxidatively and nitosatively hostile niches inside host phagocytes. In other bacteria, adaptation to these stresses is dependent upon the redox sensitive two component systems (e.g., ArcAB) and transcription factors (e.g., FNR/SoxR). However, these factors are absent in Mtb. Therefore, it is not completely understood how Mtb maintains survival and redox balance in response to reactive oxygen species (ROS) and reactive nitrogen species (RNS). Here, we present evidences that a 4Fe-4S-cofactor containing redox-sensitive transcription factor (WhiB3) is exploited by Mtb to adapt under ROS and RNS stress. We show that MtbΔwhiB3 is acutely sensitive to oxidants and to nitrosative agents. Using a genetic biosensor of cytoplasmic redox state (Mrx1-roGFP2) of Mtb, we show that WhiB3 facilitates recovery from ROS (cumene hydroperoxide and hydrogen peroxide) and RNS (acidified nitrite and peroxynitrite). Also, MtbΔwhiB3 displayed reduced survival inside RAW 264.7 macrophages. Consistent with the role of WhiB3 in modulating host-pathogen interaction, we discovered that WhiB3 coordinates the formation of early human granulomas during interaction of Mtb with human peripheral blood mononuclear cells (PBMCs). Altogether, our study provides empirical proof that WhiB3 is required to mitigate redox stress induced by ROS and RNS, which may be important to activate host/bacterial pathways required for the granuloma development and maintenance.
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Affiliation(s)
- Mansi Mehta
- Microbiology and Cell Biology, Centre for Infectious Disease Research (CIDR), Indian Institute of Science (IISc), CV Raman Av, Bangalore 12, India
| | - Amit Singh
- Microbiology and Cell Biology, Centre for Infectious Disease Research (CIDR), Indian Institute of Science (IISc), CV Raman Av, Bangalore 12, India.
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25
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Tarafdar S, Kim G, Levine RL. Drosophila methionine sulfoxide reductase A (MSRA) lacks methionine oxidase activity. Free Radic Biol Med 2019; 131:154-161. [PMID: 30529269 PMCID: PMC7409368 DOI: 10.1016/j.freeradbiomed.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 11/19/2022]
Abstract
Mouse, human, and E. coli methionine sulfoxide reductase A (MSRA) stereospecifically catalyze both the reduction of S-methionine sulfoxide to methionine and the oxidation of methionine to S-methionine sulfoxide. Calmodulin has 9 methionine residues, but only Met77 is oxidized by MSRA, and this is completely reversed when MSRA operates in the reductase direction. Given the powerful genetic tools available for Drosophila, we selected this model organism to identify the in vivo calmodulin targets regulated by redox modulation of Met77. The active site sequences of mammalian and Drosophila MSRA are identical, and both contain two cysteine residues in their carboxy terminal domains. We produced recombinant Drosophila MSRA and studied its biochemical and biophysical properties. The enzyme is active as a methionine sulfoxide reductase, but it cannot function as a methionine oxidase. The first step in the mammalian oxidase reaction is formation of a sulfenic acid at the active site, and the second step is the reaction of the sulfenic acid with a carboxy terminal domain cysteine to form a disulfide bond. The third step regenerates the active site through a disulfide exchange reaction with a second carboxy terminal domain cysteine. Drosophila MSRA carries out the first and second steps, but it cannot regenerate the active site in the third step. Thus, unlike the E. coli and mammalian enzymes, Drosophila MSRA catalyzes only the reduction of methionine sulfoxide and not the oxidation of methionine.
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Affiliation(s)
- Sreya Tarafdar
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, United States.
| | - Geumsoo Kim
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, United States.
| | - Rodney L Levine
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, United States.
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26
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The Oxidized Protein Repair Enzymes Methionine Sulfoxide Reductases and Their Roles in Protecting against Oxidative Stress, in Ageing and in Regulating Protein Function. Antioxidants (Basel) 2018; 7:antiox7120191. [PMID: 30545068 PMCID: PMC6316033 DOI: 10.3390/antiox7120191] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 12/31/2022] Open
Abstract
Cysteine and methionine residues are the amino acids most sensitive to oxidation by reactive oxygen species. However, in contrast to other amino acids, certain cysteine and methionine oxidation products can be reduced within proteins by dedicated enzymatic repair systems. Oxidation of cysteine first results in either the formation of a disulfide bridge or a sulfenic acid. Sulfenic acid can be converted to disulfide or sulfenamide or further oxidized to sulfinic acid. Disulfide can be easily reversed by different enzymatic systems such as the thioredoxin/thioredoxin reductase and the glutaredoxin/glutathione/glutathione reductase systems. Methionine side chains can also be oxidized by reactive oxygen species. Methionine oxidation, by the addition of an extra oxygen atom, leads to the generation of methionine sulfoxide. Enzymatically catalyzed reduction of methionine sulfoxide is achieved by either methionine sulfoxide reductase A or methionine sulfoxide reductase B, also referred as to the methionine sulfoxide reductases system. This oxidized protein repair system is further described in this review article in terms of its discovery and biologically relevant characteristics, and its important physiological roles in protecting against oxidative stress, in ageing and in regulating protein function.
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27
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Drzeżdżon J, Jacewicz D, Chmurzyński L. The impact of environmental contamination on the generation of reactive oxygen and nitrogen species - Consequences for plants and humans. ENVIRONMENT INTERNATIONAL 2018; 119:133-151. [PMID: 29957355 DOI: 10.1016/j.envint.2018.06.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/15/2018] [Accepted: 06/16/2018] [Indexed: 05/23/2023]
Abstract
Environmental contaminants, such as heavy metals, nanomaterials, and pesticides, induce the formation of reactive oxygen and nitrogen species (RONS). Plants interact closely with the atmosphere, water, and soil, and consequently RONS intensely affect their biochemistry. For the past 30 years researchers have thoroughly examined the role of RONS in plant organisms and oxidative modifications to cellular components. Hydrogen peroxide, superoxide anion, nitrogen(II) oxide, and hydroxyl radicals have been found to take part in many metabolic pathways. In this review the various aspects of the oxidative stress induced by environmental contamination are described based on an analysis of literature. The review reinforces the contention that RONS play a dual role, that is, both a deleterious and a beneficial one, in plants. Environmental contamination affects human health, also, and so we have additionally described the impact of RONS on the coupled human - environment system.
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Affiliation(s)
- Joanna Drzeżdżon
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Dagmara Jacewicz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Lech Chmurzyński
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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28
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Singh VK, Singh K, Baum K. The Role of Methionine Sulfoxide Reductases in Oxidative Stress Tolerance and Virulence of Staphylococcus aureus and Other Bacteria. Antioxidants (Basel) 2018; 7:antiox7100128. [PMID: 30274148 PMCID: PMC6210949 DOI: 10.3390/antiox7100128] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/19/2018] [Accepted: 09/26/2018] [Indexed: 11/18/2022] Open
Abstract
Methionine sulfoxide reductases (MSRA1 and MSRB) are proteins overproduced in Staphylococcus aureus during exposure with cell wall-active antibiotics. Later studies identified the presence of two additional MSRA proteins (MSRA2 and MSRA3) in S. aureus. These MSR proteins have been characterized in many other bacteria as well. This review provides the current knowledge about the conditions and regulatory network that mimic the expression of these MSR encoding genes and their role in defense from oxidative stress and virulence.
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Affiliation(s)
- Vineet K Singh
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, MO 63501, USA.
| | | | - Kyle Baum
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, MO 63501, USA.
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29
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Xie XL, Yang H, Chen LN, Wei Y, Zhang SH. ANXC7 Is a Mitochondrion-Localized Annexin Involved in Controlling Conidium Development and Oxidative Resistance in the Thermophilic Fungus Thermomyces lanuginosus. Front Microbiol 2018; 9:1770. [PMID: 30271384 PMCID: PMC6142879 DOI: 10.3389/fmicb.2018.01770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/16/2018] [Indexed: 01/23/2023] Open
Abstract
Annexins (ANXs) are widely expressed and structurally related proteins which play multiple biological roles in animals, plants, and fungi. Although ANXs have been localized to the cytosol and the cell membrane and the molecular basis of the four annexin repeats is well established, the in vivo roles of these proteins are still far from clear, particularly with regard to the filamentous fungi. Thermomyces lanuginosus, a thermophilic fungus, is widely used in the fermentation industry; however, the role of ANX in this organism is unknown. In this study, a single ANX homologue (ANXC7) was identified and characterized in T. lanuginosus. The expression pattern indicated that ANXC7 is closely associated to conidium development, and it accumulated in the mitochondria of the forming conidia. The deletion of ANXC7 (ΔANXC7) resulted in no obvious phenotype related to colony growth on solid CM medium. However, when ΔANXC7 was grown in CM liquid culture, the mycelium masses appeared to be larger and looser compared to the wild-type. Additionally, the dry weight of the mutant mycelia was significantly increased. Under conditions that compromise cell-wall integrity, ΔANXC7 was less vulnerable than the wild-type with regard to such damage. Moreover, based on a surface hydrophobicity test, the ΔANXC7 strain was clearly less hydrophobic. The growth of ΔANXC7 was inhibited when grown under selected stress conditions, particularly with regard to salt stress; however, the oxidative resistance to exogenous H2O2 in ΔANXC7 was increased, and endogenous H2O2 levels within the ΔANXC7 were lower than in the wild-type, thereby suggesting that the ANXC7 specifically controls oxidative resistance. Based on microscopic observation, 4-day-conidia were more prevalent than 5-day conidia on the conidiophore stalk of ΔANXC7, even though the ΔANXC7 demonstrated an increased production of conidia during these days, indicating precocious conidial maturation and shedding from the conidiophore stalk in this strain. Taken together, our data indicate that ANXC7 localizes to the mitochondria and is involved in controlling conidium development and oxidative resistance in T. lanuginosus.
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Affiliation(s)
- Xiang-Li Xie
- College of Plant Sciences, Jilin University, Changchun, China
| | - Huan Yang
- College of Plant Sciences, Jilin University, Changchun, China
| | - Li-Na Chen
- College of Plant Sciences, Jilin University, Changchun, China
| | - Yi Wei
- College of Plant Sciences, Jilin University, Changchun, China
| | - Shi-Hong Zhang
- College of Plant Sciences, Jilin University, Changchun, China
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30
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Synergistic antibacterial activity of silver with antibiotics correlating with the upregulation of the ROS production. Sci Rep 2018; 8:11131. [PMID: 30042429 PMCID: PMC6057937 DOI: 10.1038/s41598-018-29313-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/20/2018] [Indexed: 11/08/2022] Open
Abstract
Thiol-dependent enzymes, including the thioredoxin (Trx) and glutathione (GSH) systems, have recently been found as promising bactericidal targets in multidrug-resistant (MDR) bacteria. We previously discovered that silver acted synergistically with ebselen in the inhibition of the Trx system and also resulted in a fast depletion of GSH in Gram-negative bacteria. Silver has been found by others to improve the sensitivity of bacteria to certain conventional antibiotics. Here, we found that the synergistic antibacterial effects of silver with four conventional antibiotics was correlated with the blockage of bacterial Trx system by silver. The synergistic antibacterial effect came along with the production of reactive oxygen species. All these results suggested that silver primarily enhanced the bactericidal activities of conventional antibiotics towards Gram-negative strains through the upregulation of ROS production.
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31
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Shen Y, Zhang X, Zhang Y, Li H, Dai L, Peng X, Peng Z, Xie Y. A fluorescent sensor for fast detection of peroxynitrite by removing of C=N in a benzothiazole derivative. Anal Chim Acta 2018. [DOI: 10.1016/j.aca.2018.01.046] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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32
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Laloo AE, Wei J, Wang D, Narayanasamy S, Vanwonterghem I, Waite D, Steen J, Kaysen A, Heintz-Buschart A, Wang Q, Schulz B, Nouwens A, Wilmes P, Hugenholtz P, Yuan Z, Bond PL. Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5386-5397. [PMID: 29620869 DOI: 10.1021/acs.est.7b04273] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA.
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Affiliation(s)
- Andrew E Laloo
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Justin Wei
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Dongbo Wang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education , Hunan University , Changsa 410082 , China
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - David Waite
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Jason Steen
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Anne Kaysen
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Qilin Wang
- Griffith School of Engineering & Centre for Clean Environment and Energy , Griffith University , Nathan , QLD 4111 , Australia
| | - Benjamin Schulz
- School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Philip L Bond
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
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Lupoli TJ, Vaubourgeix J, Burns-Huang K, Gold B. Targeting the Proteostasis Network for Mycobacterial Drug Discovery. ACS Infect Dis 2018; 4:478-498. [PMID: 29465983 PMCID: PMC5902792 DOI: 10.1021/acsinfecdis.7b00231] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the world's deadliest infectious diseases and urgently requires new antibiotics to treat drug-resistant strains and to decrease the duration of therapy. During infection, Mtb encounters numerous stresses associated with host immunity, including hypoxia, reactive oxygen and nitrogen species, mild acidity, nutrient starvation, and metal sequestration and intoxication. The Mtb proteostasis network, composed of chaperones, proteases, and a eukaryotic-like proteasome, provides protection from stresses and chemistries of host immunity by maintaining the integrity of the mycobacterial proteome. In this Review, we explore the proteostasis network as a noncanonical target for antibacterial drug discovery.
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Affiliation(s)
- Tania J. Lupoli
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Kristin Burns-Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
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Lim JM, Lim JC, Kim G, Levine RL. Myristoylated methionine sulfoxide reductase A is a late endosomal protein. J Biol Chem 2018; 293:7355-7366. [PMID: 29593096 DOI: 10.1074/jbc.ra117.000473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/19/2018] [Indexed: 12/11/2022] Open
Abstract
Methionine residues in proteins provide antioxidant defense by reacting with oxidizing species, which oxidize methionine to methionine sulfoxide. Reduction of the sulfoxide back to methionine is catalyzed by methionine sulfoxide reductases, essential for protection against oxidative stress. The nonmyristoylated form of methionine sulfoxide reductase A (MSRA) is present in mitochondria, whereas the myristoylated form has been previously reported to be cytosolic. Despite the importance of MSRA in antioxidant defense, its in vivo binding partners and substrates have not been identified. Starting with a protein array, and followed by immunoprecipitation experiments, colocalization studies, and subcellular fractionation, we identified the late endosomal protein, StAR-related lipid transfer domain-containing 3 (STARD3), as a binding partner of myristoylated MSRA, but not of nonmyristoylated MSRA. STARD3 is known to have both membrane-binding and cytosolic domains that are important in STARD3-mediated transport of cholesterol from the endoplasmic reticulum to the endosome. We found that the STARD3 cytosolic domain localizes MSRA to the late endosome. We propose that the previous conclusion that myristoylated MSRA is strictly a cytosolic protein is artifactual and likely due to vigorous overexpression of MSRA. We conclude that myristoylated MSRA is a late endosomal protein that may play a role in lipid metabolism or may protect endosomal proteins from oxidative damage.
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Affiliation(s)
- Jung Mi Lim
- Laboratory of Biochemistry, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Jung Chae Lim
- Laboratory of Biochemistry, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Geumsoo Kim
- Laboratory of Biochemistry, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Rodney L Levine
- Laboratory of Biochemistry, NHLBI, National Institutes of Health, Bethesda, Maryland 20892.
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Reyes AM, Pedre B, De Armas MI, Tossounian MA, Radi R, Messens J, Trujillo M. Chemistry and Redox Biology of Mycothiol. Antioxid Redox Signal 2018; 28:487-504. [PMID: 28372502 DOI: 10.1089/ars.2017.7074] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
SIGNIFICANCE Mycothiol (MSH, AcCys-GlcN-Ins) is the main low-molecular weight (LMW) thiol of most Actinomycetes, including the human pathogen Mycobacterium tuberculosis that affects millions of people worldwide. Strains with decreased MSH content show increased susceptibilities to hydroperoxides and electrophilic compounds. In M. tuberculosis, MSH modulates the response to several antituberculosis drugs. Enzymatic routes involving MSH could provide clues for specific drug design. Recent Advances: Physicochemical data argue against a rapid, nonenzymatic reaction of MSH with oxidants, disulfides, or electrophiles. Moreover, exposure of the bacteria to high concentrations of two-electron oxidants resulted in protein mycothiolation. The recently described glutaredoxin-like protein mycoredoxin-1 (Mrx-1) provides a route for catalytic reduction of mycothiolated proteins, protecting critical cysteines from irreversible oxidation. The description of MSH/Mrx-1-dependent activities of peroxidases helped to explain the higher susceptibility to oxidants observed in Actinomycetes lacking MSH. Moreover, the first mycothiol-S-transferase, member of the DinB superfamily of proteins, was described. In Corynebacterium, both the MSH/Mrx-1 and the thioredoxin pathways reduce methionine sulfoxide reductase A. A novel tool for in vivo imaging of the MSH/mycothiol disulfide (MSSM) status allows following changes in the mycothiol redox state during macrophage infection and its relationship with antibiotic sensitivity. CRITICAL ISSUES Redundancy of MSH with other LMW thiols is starting to be unraveled and could help to rationalize the differences in the reported importance of MSH synthesis observed in vitro versus in animal infection models. FUTURE DIRECTIONS Future work should be directed to establish the structural bases of the specificity of MSH-dependent enzymes, thus facilitating drug developments. Antioxid. Redox Signal. 28, 487-504.
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Affiliation(s)
- Aníbal M Reyes
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Brandán Pedre
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - María Inés De Armas
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Maria-Armineh Tossounian
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - Rafael Radi
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Joris Messens
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - Madia Trujillo
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
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Ferrer-Sueta G, Campolo N, Trujillo M, Bartesaghi S, Carballal S, Romero N, Alvarez B, Radi R. Biochemistry of Peroxynitrite and Protein Tyrosine Nitration. Chem Rev 2018; 118:1338-1408. [DOI: 10.1021/acs.chemrev.7b00568] [Citation(s) in RCA: 292] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Gerardo Ferrer-Sueta
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Nicolás Campolo
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Silvina Bartesaghi
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sebastián Carballal
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Romero
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Methionine in Proteins: It's Not Just for Protein Initiation Anymore. Neurochem Res 2018; 44:247-257. [PMID: 29327308 DOI: 10.1007/s11064-017-2460-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/19/2017] [Accepted: 12/26/2017] [Indexed: 12/21/2022]
Abstract
Methionine in proteins is often thought to be a generic hydrophobic residue, functionally replaceable with another hydrophobic residue such as valine or leucine. This is not the case, and the reason is that methionine contains sulfur that confers special properties on methionine. The sulfur can be oxidized, converting methionine to methionine sulfoxide, and ubiquitous methionine sulfoxide reductases can reduce the sulfoxide back to methionine. This redox cycle enables methionine residues to provide a catalytically efficient antioxidant defense by reacting with oxidizing species. The cycle also constitutes a reversible post-translational covalent modification analogous to phosphorylation. As with phosphorylation, enzymatically-mediated oxidation and reduction of specific methionine residues functions as a regulatory process in the cell. Methionine residues also form bonds with aromatic residues that contribute significantly to protein stability. Given these important functions, alteration of the methionine-methionine sulfoxide balance in proteins has been correlated with disease processes, including cardiovascular and neurodegenerative diseases. Methionine isn't just for protein initiation.
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Iwadate Y, Kato JI. Involvement of the ytfK gene from the PhoB regulon in stationary-phase H 2 O 2 stress tolerance in Escherichia coli. Microbiology (Reading) 2017; 163:1912-1923. [DOI: 10.1099/mic.0.000534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yumi Iwadate
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Jun-ichi Kato
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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Ehrlichia chaffeensis and Its Invasin EtpE Block Reactive Oxygen Species Generation by Macrophages in a DNase X-Dependent Manner. mBio 2017; 8:mBio.01551-17. [PMID: 29162709 PMCID: PMC5698551 DOI: 10.1128/mbio.01551-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The obligatory intracellular pathogen Ehrlichia chaffeensis lacks most genes that confer resistance to oxidative stress but can block reactive oxygen species (ROS) generation by host monocytes-macrophages. Bacterial and host molecules responsible for this inhibition have not been identified. To infect host cells, Ehrlichia uses the C terminus of its surface invasin, entry-triggering protein of Ehrlichia (EtpE; EtpE-C), which directly binds the mammalian cell surface receptor glycosylphosphatidylinositol-anchored protein DNase X. We investigated whether EtpE-C binding to DNase X blocks ROS production by mouse bone marrow-derived macrophages (BMDMs). On the basis of a luminol-dependent chemiluminescence assay, E. chaffeensis inhibited phorbol myristate acetate (PMA)-induced ROS generation by BMDMs from wild-type, but not DNase X−/−, mice. EtpE-C is critical for inhibition, as recombinant EtpE-C (rEtpE-C)-coated latex beads, but not recombinant N-terminal EtpE-coated or uncoated beads, inhibited PMA-induced ROS generation by BMDMs from wild-type mice. DNase X is required for this inhibition, as none of these beads inhibited PMA-induced ROS generation by BMDMs from DNase X−/− mice. Previous studies showed that E. chaffeensis does not block ROS generation in neutrophils, a cell type that is a potent ROS generator but is not infected by E. chaffeensis. Human and mouse peripheral blood neutrophils did not express DNase X. Our findings point to a unique survival mechanism of ROS-sensitive obligate intramonocytic bacteria that involves invasin EtpE binding to DNase X on the host cell surface. This is the first report of bacterial invasin having such a subversive activity on ROS generation. Ehrlichia chaffeensis preferentially infects monocytes-macrophages and causes a life-threatening emerging tick-transmitted infectious disease called human monocytic ehrlichiosis. Ehrlichial infection, and hence the disease, depends on the ability of this bacterium to avoid or overcome powerful microbicidal mechanisms of host monocytes-macrophages, one of which is the generation of ROS. Our findings reveal that an ehrlichial surface invasin, EtpE, not only triggers bacterial entry but also blocks ROS generation by host macrophages through its host cell receptor, DNase X. As ROS sensitivity is an Achilles’ heel of this group of pathogens, understanding the mechanism by which E. chaffeensis rapidly blocks ROS generation suggests a new approach for developing effective anti-infective measures. The discovery of a ROS-blocking pathway is also important, as modulation of ROS generation is important in a variety of ailments and biological processes.
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Liu Y, Chong L, Li X, Tang P, Liu P, Hou C, Zhang X, Li R. Astragaloside IV rescues MPP +-induced mitochondrial dysfunction through upregulation of methionine sulfoxide reductase A. Exp Ther Med 2017; 14:2650-2656. [PMID: 28962208 DOI: 10.3892/etm.2017.4834] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 04/28/2017] [Indexed: 12/21/2022] Open
Abstract
Methionine sulfoxide reductase (Msr) repairs oxidatively damaged proteins through acting as an antioxidant. Oxidative stress has been postulated to cause the mitochondrial dysfunction that is associated with aging and certain diseases, including Parkinson's disease (PD). The present study investigated the protective effects of astragaloside IV (AS-IV) on 1-methyl-4-phenylpyridinium (MPP+)-induced mitochondrial dysfunction through MsrA in PC12 cells. This revealed that oxidative stress reduced the expression of MsrA following MPP+ treatment. AS-IV was demonstrated to protect PC12 cells from MPP+-induced oxidative damage through upregulating MsrA. MsrA expression was dependent on the Sirt1-FOXO3a signaling pathway. In addition, knockdown of MsrA reduced the protective effects of AS-IV, indicating that the antioxidant effects of AS-UV occurred through MsrA. These results suggest that AS-IV exerts antioxidant effects and regulates mitochondrial function. Thus, AS-IV may serve as an effective therapeutic agent for aging and PD.
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Affiliation(s)
- Yue Liu
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Li Chong
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Xiaoqing Li
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Peng Tang
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Peng Liu
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Chen Hou
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Xin Zhang
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Rui Li
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
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Li H, Li X, Wu X, Shi W, Ma H. Observation of the Generation of ONOO– in Mitochondria under Various Stimuli with a Sensitive Fluorescence Probe. Anal Chem 2017; 89:5519-5525. [DOI: 10.1021/acs.analchem.7b00503] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hongyu Li
- Key
Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education
Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohua Li
- Key
Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education
Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaofeng Wu
- Key
Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education
Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Wen Shi
- Key
Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education
Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Huimin Ma
- Key
Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education
Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Batthyány C, Bartesaghi S, Mastrogiovanni M, Lima A, Demicheli V, Radi R. Tyrosine-Nitrated Proteins: Proteomic and Bioanalytical Aspects. Antioxid Redox Signal 2017; 26:313-328. [PMID: 27324931 PMCID: PMC5326983 DOI: 10.1089/ars.2016.6787] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
SIGNIFICANCE "Nitroproteomic" is under active development, as 3-nitrotyrosine in proteins constitutes a footprint left by the reactions of nitric oxide-derived oxidants that are usually associated to oxidative stress conditions. Moreover, protein tyrosine nitration can cause structural and functional changes, which may be of pathophysiological relevance for human disease conditions. Biological protein tyrosine nitration is a free radical process involving the intermediacy of tyrosyl radicals; in spite of being a nonenzymatic process, nitration is selectively directed toward a limited subset of tyrosine residues. Precise identification and quantitation of 3-nitrotyrosine in proteins has represented a "tour de force" for researchers. Recent Advances: A small number of proteins are preferential targets of nitration (usually less than 100 proteins per proteome), contrasting with the large number of proteins modified by other post-translational modifications such as phosphorylation, acetylation, and, notably, S-nitrosation. Proteomic approaches have revealed key features of tyrosine nitration both in vivo and in vitro, including selectivity, site specificity, and effects in protein structure and function. CRITICAL ISSUES Identification of 3-nitrotyrosine-containing proteins and mapping nitrated residues is challenging, due to low abundance of this oxidative modification in biological samples and its unfriendly behavior in mass spectrometry (MS)-based technologies, that is, MALDI, electrospray ionization, and collision-induced dissociation. FUTURE DIRECTIONS The use of (i) classical two-dimensional electrophoresis with immunochemical detection of nitrated proteins followed by protein ID by regular MS/MS in combination with (ii) immuno-enrichment of tyrosine-nitrated peptides and (iii) identification of nitrated peptides by a MIDAS™ experiment is arising as a potent methodology to unambiguously map and quantitate tyrosine-nitrated proteins in vivo. Antioxid. Redox Signal. 26, 313-328.
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Affiliation(s)
- Carlos Batthyány
- 1 Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay .,2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Silvina Bartesaghi
- 3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay .,4 Departamento de Educación Médica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Analía Lima
- 1 Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Verónica Demicheli
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
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Pang M, Lin X, Liu J, Guo C, Gao S, Du H, Lu C, Liu Y. Identification of Aeromonas hydrophila Genes Preferentially Expressed after Phagocytosis by Tetrahymena and Involvement of Methionine Sulfoxide Reductases. Front Cell Infect Microbiol 2016; 6:199. [PMID: 28083518 PMCID: PMC5183988 DOI: 10.3389/fcimb.2016.00199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 12/13/2016] [Indexed: 01/03/2023] Open
Abstract
Free-living protozoa affect the survival and virulence evolution of pathogens in the environment. In this study, we explored the fate of Aeromonas hydrophila when co-cultured with the bacteriovorous ciliate Tetrahymena thermophila and investigated bacterial gene expression associated with the co-culture. Virulent A. hydrophila strains were found to have ability to evade digestion in the vacuoles of this protozoan. In A. hydrophila, a total of 116 genes were identified as up-regulated following co-culture with T. thermophila by selective capture of transcribed sequences (SCOTS) and comparative dot-blot analysis. A large proportion of these genes (42/116) play a role in metabolism, and some of the genes have previously been characterized as required for bacterial survival and replication within macrophages. Then, we inactivated the genes encoding methionine sulfoxide reductases, msrA, and msrB, in A. hydrophila. Compared to the wild-type, the mutants ΔmsrA and ΔmsrAB displayed significantly reduced resistance to predation by T. thermophila, and 50% lethal dose (LD50) determinations in zebrafish demonstrated that both mutants were highly attenuated. This study forms a solid foundation for the study of mechanisms and implications of bacterial defenses.
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Affiliation(s)
- Maoda Pang
- Department of Preventive Veterinary, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Xiaoqin Lin
- Department of Preventive Veterinary, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Jin Liu
- Department of Preventive Veterinary, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Changming Guo
- Department of Preventive Veterinary, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Shanshan Gao
- Department of Preventive Veterinary, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Hechao Du
- Department of Preventive Veterinary, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Chengping Lu
- Department of Preventive Veterinary, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Yongjie Liu
- Department of Preventive Veterinary, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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Chaudhry V, Patil PB. Genomic investigation reveals evolution and lifestyle adaptation of endophytic Staphylococcus epidermidis. Sci Rep 2016; 6:19263. [PMID: 26758912 PMCID: PMC4713051 DOI: 10.1038/srep19263] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/10/2015] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus epidermidis is a major human associated bacterium and also an emerging nosocomial pathogen. There are reports of its association to rodents, sheep and plants. However, comparative and evolutionary studies of ecologically diverse strains of S. epidermidis are lacking. Here, we report the whole genome sequences of four S. epidermidis strains isolated from surface sterilized rice seeds along with genome sequence of type strain. Phylogenomic analysis of rice endophytic S. epidermidis (RESE) with “type strain” unequivocally established their species identity. Whole genome based tree of 93 strains of S. epidermidis revealed RESE as distinct sub-lineage which is more related to rodent sub-lineage than to majority of human lineage strains. Furthermore, comparative genomics revealed 20% variable gene-pool in S. epidermidis, suggesting that genomes of ecologically diverse strains are under flux. Interestingly, we were also able to map several genomic regions that are under flux and gave rise to RESE strains. The largest of these genomic regions encodes a cluster of genes unique to RESE that are known to be required for survival and stress tolerance, apart from those required for adaptation to plant habitat. The genomes and genes of RESE represent distinct ecological resource/sequences and provided first evolutionary insights into adaptation of S. epidermidis to plants.
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Affiliation(s)
- Vasvi Chaudhry
- CSIR- Institute of Microbial Technology, Sector 39A, Chandigarh-160036 (India)
| | - Prabhu B Patil
- CSIR- Institute of Microbial Technology, Sector 39A, Chandigarh-160036 (India)
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E1 of α-ketoglutarate dehydrogenase defends Mycobacterium tuberculosis against glutamate anaplerosis and nitroxidative stress. Proc Natl Acad Sci U S A 2015; 112:E5834-43. [PMID: 26430237 DOI: 10.1073/pnas.1510932112] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes of central carbon metabolism (CCM) in Mycobacterium tuberculosis (Mtb) make an important contribution to the pathogen's virulence. Evidence is emerging that some of these enzymes are not simply playing the metabolic roles for which they are annotated, but can protect the pathogen via additional functions. Here, we found that deficiency of 2-hydroxy-3-oxoadipate synthase (HOAS), the E1 component of the α-ketoglutarate (α-KG) dehydrogenase complex (KDHC), did not lead to general metabolic perturbation or growth impairment of Mtb, but only to the specific inability to cope with glutamate anaplerosis and nitroxidative stress. In the former role, HOAS acts to prevent accumulation of aldehydes, including growth-inhibitory succinate semialdehyde (SSA). In the latter role, HOAS can participate in an alternative four-component peroxidase system, HOAS/dihydrolipoyl acetyl transferase (DlaT)/alkylhydroperoxide reductase colorless subunit gene (ahpC)-neighboring subunit (AhpD)/AhpC, using α-KG as a previously undescribed source of electrons for reductase action. Thus, instead of a canonical role in CCM, the E1 component of Mtb's KDHC serves key roles in situational defense that contribute to its requirement for virulence in the host. We also show that pyruvate decarboxylase (AceE), the E1 component of pyruvate dehydrogenase (PDHC), can participate in AceE/DlaT/AhpD/AhpC, using pyruvate as a source of electrons for reductase action. Identification of these systems leads us to suggest that Mtb can recruit components of its CCM for reactive nitrogen defense using central carbon metabolites.
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Arts IS, Gennaris A, Collet JF. Reducing systems protecting the bacterial cell envelope from oxidative damage. FEBS Lett 2015; 589:1559-68. [DOI: 10.1016/j.febslet.2015.04.057] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 04/29/2015] [Indexed: 02/07/2023]
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Tarrago L, Péterfi Z, Lee BC, Michel T, Gladyshev VN. Monitoring methionine sulfoxide with stereospecific mechanism-based fluorescent sensors. Nat Chem Biol 2015; 11:332-8. [PMID: 25799144 PMCID: PMC4402147 DOI: 10.1038/nchembio.1787] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 02/27/2015] [Indexed: 11/16/2022]
Abstract
Methionine can be reversibly oxidized to methionine sulfoxide (MetO) under physiological and pathophysiological conditions, but its use as a redox marker suffers from the lack of tools to detect and quantify MetO within cells. In this work, we created a pair of complementary stereospecific genetically encoded mechanism-based ratiometric fluorescent sensors of MetO by inserting a circularly permuted yellow fluorescent protein between yeast methionine sulfoxide reductases and thioredoxins. The two sensors, respectively named MetSOx and MetROx for their ability to detect S and R forms of MetO, were used for targeted analysis of protein oxidation, regulation and repair as well as for monitoring MetO in bacterial and mammalian cells, analyzing compartment-specific changes in MetO and examining responses to physiological stimuli.
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Affiliation(s)
- Lionel Tarrago
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zalán Péterfi
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Byung Cheon Lee
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- College of Life Sciences and Biotechnology, Korea University, Seoul, 136-712, South Korea
| | - Thomas Michel
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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48
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Regulation of thrombosis and vascular function by protein methionine oxidation. Blood 2015; 125:3851-9. [PMID: 25900980 DOI: 10.1182/blood-2015-01-544676] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/14/2015] [Indexed: 02/07/2023] Open
Abstract
Redox biology is fundamental to both normal cellular homeostasis and pathological states associated with excessive oxidative stress. Reactive oxygen species function not only as signaling molecules but also as redox regulators of protein function. In the vascular system, redox reactions help regulate key physiologic responses such as cell adhesion, vasoconstriction, platelet aggregation, angiogenesis, inflammatory gene expression, and apoptosis. During pathologic states, altered redox balance can cause vascular cell dysfunction and affect the equilibrium between procoagulant and anticoagulant systems, contributing to thrombotic vascular disease. This review focuses on the emerging role of a specific reversible redox reaction, protein methionine oxidation, in vascular disease and thrombosis. A growing number of cardiovascular and hemostatic proteins are recognized to undergo reversible methionine oxidation, in which methionine residues are posttranslationally oxidized to methionine sulfoxide. Protein methionine oxidation can be reversed by the action of stereospecific enzymes known as methionine sulfoxide reductases. Calcium/calmodulin-dependent protein kinase II is a prototypical methionine redox sensor that responds to changes in the intracellular redox state via reversible oxidation of tandem methionine residues in its regulatory domain. Several other proteins with oxidation-sensitive methionine residues, including apolipoprotein A-I, thrombomodulin, and von Willebrand factor, may contribute to vascular disease and thrombosis.
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49
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Mata-Pérez C, Sánchez-Calvo B, Begara-Morales JC, Luque F, Jiménez-Ruiz J, Padilla MN, Fierro-Risco J, Valderrama R, Fernández-Ocaña A, Corpas FJ, Barroso JB. Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2015; 6:122. [PMID: 25852698 PMCID: PMC4362301 DOI: 10.3389/fpls.2015.00122] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/14/2015] [Indexed: 05/20/2023]
Abstract
Linolenic acid (Ln) released from chloroplast membrane galactolipids is a precursor of the phytohormone jasmonic acid (JA). The involvement of this hormone in different plant biological processes, such as responses to biotic stress conditions, has been extensively studied. However, the role of Ln in the regulation of gene expression during abiotic stress situations mediated by cellular redox changes and/or by oxidative stress processes remains poorly understood. An RNA-seq approach has increased our knowledge of the interplay among Ln, oxidative stress and ROS signaling that mediates abiotic stress conditions. Transcriptome analysis with the aid of RNA-seq in the absence of oxidative stress revealed that the incubation of Arabidopsis thaliana cell suspension cultures (ACSC) with Ln resulted in the modulation of 7525 genes, of which 3034 genes had a 2-fold-change, being 533 up- and 2501 down-regulated genes, respectively. Thus, RNA-seq data analysis showed that an important set of these genes were associated with the jasmonic acid biosynthetic pathway including lypoxygenases (LOXs) and Allene oxide cyclases (AOCs). In addition, several transcription factor families involved in the response to biotic stress conditions (pathogen attacks or herbivore feeding), such as WRKY, JAZ, MYC, and LRR were also modified in response to Ln. However, this study also shows that Ln has the capacity to modulate the expression of genes involved in the response to abiotic stress conditions, particularly those mediated by ROS signaling. In this regard, we were able to identify new targets such as galactinol synthase 1 (GOLS1), methionine sulfoxide reductase (MSR) and alkenal reductase in ACSC. It is therefore possible to suggest that, in the absence of any oxidative stress, Ln is capable of modulating new sets of genes involved in the signaling mechanism mediated by additional abiotic stresses (salinity, UV and high light intensity) and especially in stresses mediated by ROS.
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Affiliation(s)
- Capilla Mata-Pérez
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Beatriz Sánchez-Calvo
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Juan C. Begara-Morales
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Francisco Luque
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of JaénJaén, Spain
| | - Jaime Jiménez-Ruiz
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - María N. Padilla
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Jesús Fierro-Risco
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Raquel Valderrama
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Ana Fernández-Ocaña
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Francisco J. Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Juan B. Barroso
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of JaénJaén, Spain
- *Correspondence: Juan B. Barroso, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of Jaén, Campus Las Lagunillas s/n, Jaén 23071, Spain e-mail:
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MacMicking JD. Cell-autonomous effector mechanisms against mycobacterium tuberculosis. Cold Spring Harb Perspect Med 2014; 4:cshperspect.a018507. [PMID: 25081628 DOI: 10.1101/cshperspect.a018507] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Few pathogens run the gauntlet of sterilizing immunity like Mycobacterium tuberculosis (Mtb). This organism infects mononuclear phagocytes and is also ingested by neutrophils, both of which possess an arsenal of cell-intrinsic effector mechanisms capable of eliminating it. Here Mtb encounters acid, oxidants, nitrosylating agents, and redox congeners, often exuberantly delivered under low oxygen tension. Further pressure is applied by withholding divalent Fe²⁺, Mn²⁺, Cu²⁺, and Zn²⁺, as well as by metabolic privation in the form of carbon needed for anaplerosis and aromatic amino acids for growth. Finally, host E3 ligases ubiquinate, cationic peptides disrupt, and lysosomal enzymes digest Mtb as part of the autophagic response to this particular pathogen. It is a testament to the evolutionary fitness of Mtb that sterilization is rarely complete, although sufficient to ensure most people infected with this airborne bacterium remain disease-free.
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Affiliation(s)
- John D MacMicking
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06510
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