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de Oliveira Silva JV, Meneguello JE, Formagio MD, de Freitas CF, Malacarne LC, Marchiosi R, de Mendonça PDSB, Zanetti Campanerut-Sá PA, Graton Mikcha JM. Multi-targets of antimicrobial photodynamic therapy mediated by erythrosine against Staphylococcus aureus identified by proteomic approach. Photochem Photobiol 2024. [PMID: 38594817 DOI: 10.1111/php.13944] [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: 12/13/2023] [Revised: 02/13/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Staphylococcus aureus is a global challenge to the clinical field and food industry. Therefore, the development of antimicrobial photodynamic therapy (aPDT) has become one of the valuable methods to control this pathogen. The antibacterial activity of photoinactivation by erythrosine (Ery) against S. aureus has been reported, but its modes of action are unclear. This study aimed to employ a proteomic approach to analyze modes of action of Ery-aPDT against S. aureus. We determined the antibacterial effect by Ery-aPDT assays, quantified reactive oxygen species (ROS) and injury to the cell membrane, and determined protein expression using a proteomic approach combined with bioinformatic tools. Ery-aPDT was effective in reducing S. aureus to undetectable levels. In addition, the increment of ROS accompanied the increase in the reduction of cell viability, and damage to cellular membranes was shown by sublethal injury. In proteomic analysis, we found 17 differentially expressed proteins. These proteins revealed changes mainly associated with defense to oxidative stress, energy metabolism, translation, and protein biosynthesis. Thus, these results suggest that the effectiveness of Ery-aPDT is due to multi-targets in the bacterial cell that cause the death of S. aureus.
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Affiliation(s)
| | - Jean Eduardo Meneguello
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Paraná, Brazil
| | - Maíra Dante Formagio
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Paraná, Brazil
| | | | | | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Paraná, Brazil
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Fasnacht M, Polacek N. Oxidative Stress in Bacteria and the Central Dogma of Molecular Biology. Front Mol Biosci 2021; 8:671037. [PMID: 34041267 PMCID: PMC8141631 DOI: 10.3389/fmolb.2021.671037] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Ever since the "great oxidation event," Earth's cellular life forms had to cope with the danger of reactive oxygen species (ROS) affecting the integrity of biomolecules and hampering cellular metabolism circuits. Consequently, increasing ROS levels in the biosphere represented growing stress levels and thus shaped the evolution of species. Whether the ROS were produced endogenously or exogenously, different systems evolved to remove the ROS and repair the damage they inflicted. If ROS outweigh the cell's capacity to remove the threat, we speak of oxidative stress. The injuries through oxidative stress in cells are diverse. This article reviews the damage oxidative stress imposes on the different steps of the central dogma of molecular biology in bacteria, focusing in particular on the RNA machines involved in transcription and translation.
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Affiliation(s)
- Michel Fasnacht
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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Apoorva S, Behera P, Sajjanar B, Mahawar M. Identification of oxidant susceptible proteins in Salmonella Typhimurium. Mol Biol Rep 2020; 47:2231-2242. [PMID: 32076998 DOI: 10.1007/s11033-020-05328-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/13/2020] [Indexed: 11/26/2022]
Abstract
The human gut pathogen, Salmonella Typhimurium (S. Typhimurium) not only survives but also replicates inside the phagocytic cells. Bacterial proteins are the primary targets of phagocyte generated oxidants. Because of the different amino acid composition, some proteins are more prone to oxidation than others. Many oxidant induced modifications to amino acids have been described. Introduction of carbonyl group is one of such modifications, which takes place quite early following exposure of proteins to oxidants and is quite stable. Therefore, carbonyl groups can be exploited to identify oxidant susceptible proteins. Hypochlorous acid (HOCl) is one of the most potent oxidants produced by phagocytes. Incubation of S. Typhimurium with 3 mM HOCl resulted in more than 150 folds loss of bacterial viability. Proteins extracted from HOCl exposed S. Typhimurium cells showed about 60 folds (p < 0.001) more carbonyl levels as compared to unexposed cells. Similarly, 2, 4-Dinitrophenylhydrazine (2, 4-DNPH) derivatized proteins of HOCl treated S. Typhimurium cultures reacted strongly with anti-DNP antibodies as compared to buffer treated counterpart. Next, we have derivatized carbonyl groups on the proteins with biotin hydrazide. The derivatized proteins were then isolated by avidin affinity chromatography. Mass spectrometry based analysis revealed the presence of 204 proteins.
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Affiliation(s)
- Shekhar Apoorva
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., 243122, India
| | - Pranatee Behera
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., 243122, India
| | - Basavaraj Sajjanar
- Division of Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., 243122, India
| | - Manish Mahawar
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., 243122, India.
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Zhao X, Guo X, Tang X, Zhang H, Wang M, Kong Y, Zhang X, Zhao Z, Lv M, Li L. Misregulation of ER-Golgi Vesicle Transport Induces ER Stress and Affects Seed Vigor and Stress Response. FRONTIERS IN PLANT SCIENCE 2018; 9:658. [PMID: 29868102 PMCID: PMC5968616 DOI: 10.3389/fpls.2018.00658] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/30/2018] [Indexed: 05/20/2023]
Abstract
Seeds of higher plants accumulate numerous storage proteins to use as nitrogen resources for early plant development. Seed storage proteins (SSPs) are synthesized as large precursors on the rough endoplasmic reticulum (rER), and are delivered to protein storage vacuoles (PSVs) via vesicle transport, where they are processed to mature forms. We previously identified an Arabidopsis ER-localized tethering complex, MAG2 complex, which might be involved in Golgi to ER retrograde transport. The MAG2 complex is composed of 4 subunits, MAG2, MIP1, MIP2, and MIP3. Mutants with defective alleles for these subunits accumulated SSP precursors inside the ER lumen. Here, we report that the mag2-1 mip3-1 and mip2-1 mip3-1 double mutant have more serious vesicle transport defects than the mag2-1, mip2-1, and mip3-1 single mutants, since they accumulate more SSP precursors than the corresponding single mutants, and ER stress is more severe than the single mutants. The mag2-1 mip3-1 and mip2-1 mip3-1 double mutants show growth and developmental defects rather than the single mutants. Both single and double mutant seeds are found to have lower protein content and decreased germinating vigor than wild type seeds. All the mutants are sensitive to abscisic acid (ABA) and salt stress, and exhibit alteration in ABA signaling pathway. Our study clarified that ER-Golgi vesicle transport affects seed vigor through controlling seed protein quality and content, as well as plant response to environmental stress via influencing ABA signaling pathway.
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Affiliation(s)
- Xiaonan Zhao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Xiufen Guo
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Xiaofei Tang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, China
| | - Hailong Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Mingjing Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Yun Kong
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Xiaomeng Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Zhenjie Zhao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Min Lv
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Lixin Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
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Yutthanasirikul R, Nagano T, Jimbo H, Hihara Y, Kanamori T, Ueda T, Haruyama T, Konno H, Yoshida K, Hisabori T, Nishiyama Y. Oxidation of a Cysteine Residue in Elongation Factor EF-Tu Reversibly Inhibits Translation in the Cyanobacterium Synechocystis sp. PCC 6803. J Biol Chem 2016; 291:5860-5870. [PMID: 26786107 DOI: 10.1074/jbc.m115.706424] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 11/06/2022] Open
Abstract
Translational elongation is susceptible to inactivation by reactive oxygen species (ROS) in the cyanobacterium Synechocystis sp. PCC 6803, and elongation factor G has been identified as a target of oxidation by ROS. In the present study we examined the sensitivity to oxidation by ROS of another elongation factor, EF-Tu. The structure of EF-Tu changes dramatically depending on the bound nucleotide. Therefore, we investigated the sensitivity to oxidation in vitro of GTP- and GDP-bound EF-Tu as well as that of nucleotide-free EF-Tu. Assays of translational activity with a reconstituted translation system from Escherichia coli revealed that GTP-bound and nucleotide-free EF-Tu were sensitive to oxidation by H2O2, whereas GDP-bound EF-Tu was resistant to H2O2. The inactivation of EF-Tu was the result of oxidation of Cys-82, a single cysteine residue, and subsequent formation of both an intermolecular disulfide bond and sulfenic acid. Replacement of Cys-82 with serine rendered EF-Tu resistant to inactivation by H2O2, confirming that Cys-82 was a target of oxidation. Furthermore, oxidized EF-Tu was reduced and reactivated by thioredoxin. Gel-filtration chromatography revealed that some of the oxidized nucleotide-free EF-Tu formed large complexes of >30 molecules. Atomic force microscopy revealed that such large complexes dissociated into several smaller aggregates upon the addition of dithiothreitol. Immunological analysis of the redox state of EF-Tu in vivo showed that levels of oxidized EF-Tu increased under strong light. Thus, resembling elongation factor G, EF-Tu appears to be sensitive to ROS via oxidation of a cysteine residue, and its inactivation might be reversed in a redox-dependent manner.
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Affiliation(s)
- Rayakorn Yutthanasirikul
- From the Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Takanori Nagano
- From the Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Haruhiko Jimbo
- From the Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yukako Hihara
- From the Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Takashi Kanamori
- GeneFrontier Corporation, Todai-Kashiwa Venture Plaza, 5-4-19 Kashiwanoha, Kashiwa 277-0882, Japan,; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan
| | - Takuya Ueda
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan
| | - Takamitsu Haruyama
- Bio-AFM Frontier Research Center, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan, and
| | - Hiroki Konno
- Bio-AFM Frontier Research Center, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan, and
| | - Keisuke Yoshida
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Toru Hisabori
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Yoshitaka Nishiyama
- From the Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan,.
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6
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Leibeling S, Maeß MB, Centler F, Kleinsteuber S, von Bergen M, Thullner M, Harms H, Müller RH. Posttranslational oxidative modification of (R)-2-(2,4-dichlorophenoxy)propionate/α-ketoglutarate-dependent dioxygenases (RdpA) leads to improved degradation of 2,4-dichlorophenoxyacetate (2,4-D). Eng Life Sci 2013. [DOI: 10.1002/elsc.201100093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Sabine Leibeling
- Department of Environmental Microbiology; UFZ-Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Marten B. Maeß
- Department of Environmental Microbiology; UFZ-Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Florian Centler
- Department of Environmental Microbiology; UFZ-Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology; UFZ-Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Martin von Bergen
- Department of Proteomics and Department of Metabolomics; UFZ-Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Martin Thullner
- Department of Environmental Microbiology; UFZ-Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Hauke Harms
- Department of Environmental Microbiology; UFZ-Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Roland H. Müller
- Department of Environmental Microbiology; UFZ-Helmholtz Centre for Environmental Research; Leipzig; Germany
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7
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Suo Y, Huang Y, Liu Y, Shi C, Shi X. The expression of superoxide dismutase (SOD) and a putative ABC transporter permease is inversely correlated during biofilm formation in Listeria monocytogenes 4b G. PLoS One 2012; 7:e48467. [PMID: 23119031 PMCID: PMC3485238 DOI: 10.1371/journal.pone.0048467] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 09/25/2012] [Indexed: 11/19/2022] Open
Abstract
Little is known about the molecular basis of biofilm formation in Listeria monocytogenes. The superoxide dismutase (SOD) of the deletion mutant of lm.G_1771 gene, which encodes for a putative ABC transporter permease, is highly expressed in biofilm. In this study, the sod gene deletion mutant Δsod, and double deletion mutant of the sod and lm. G_1771 genes Δ1771Δsod were used to investigate the role of SOD and its relationship to the expression of the putative ABC transporter permease in biofilm formation. Our results showed that the ability to form a biofilm was significantly reduced in the Δsod mutant and the Δ1771Δsod double mutant. Both Δsod and Δ1771Δsod mutants exhibited slow growth phenotypes and produced more reactive oxygen species (ROS). The growth was inhibited in the mutants by methyl viologen (MV, internal oxygen radical generator) treatment. In addition, the expression of one oxidation resistance gene (kat), two stress regulators encoding genes (perR and sigB), and one DNA repair gene (recA) were analyzed in both the wild-type L. monocytogenes 4b G and the deletion mutants by RT-qPCR. The expression levels of the four genes were increased in the deletion mutants when biofilms were formed. Taken together, our data indicated that SOD played an important role in biofilm formation through coping with the oxidant burden in deficient antioxidant defenses.
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Affiliation(s)
- Yujuan Suo
- MOST-USDA Joint Research Center for Food Safety and Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyan Huang
- MOST-USDA Joint Research Center for Food Safety and Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanhong Liu
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety and Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety and Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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8
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Mohan H, Maheswari KU, Bera AK, Suraishkumar G. Reactive oxygen species mediated modifications in Bacillus subtilis lipid membrane to improve protein productivities. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Maisonneuve E, Ducret A, Khoueiry P, Lignon S, Longhi S, Talla E, Dukan S. Rules governing selective protein carbonylation. PLoS One 2009; 4:e7269. [PMID: 19802390 PMCID: PMC2751825 DOI: 10.1371/journal.pone.0007269] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 07/28/2009] [Indexed: 11/28/2022] Open
Abstract
Background Carbonyl derivatives are mainly formed by direct metal-catalysed oxidation (MCO) attacks on the amino-acid side chains of proline, arginine, lysine and threonine residues. For reasons unknown, only some proteins are prone to carbonylation. Methodology/Principal Findings We used mass spectrometry analysis to identify carbonylated sites in: BSA that had undergone in vitro MCO, and 23 carbonylated proteins in Escherichia coli. The presence of a carbonylated site rendered the neighbouring carbonylatable site more prone to carbonylation. Most carbonylated sites were present within hot spots of carbonylation. These observations led us to suggest rules for identifying sites more prone to carbonylation. We used these rules to design an in silico model (available at http://www.lcb.cnrs-mrs.fr/CSPD/), allowing an effective and accurate prediction of sites and of proteins more prone to carbonylation in the E. coli proteome. Conclusions/Significance We observed that proteins evolve to either selectively maintain or lose predicted hot spots of carbonylation depending on their biological function. As our predictive model also allows efficient detection of carbonylated proteins in Bacillus subtilis, we believe that our model may be extended to direct MCO attacks in all organisms.
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Affiliation(s)
- Etienne Maisonneuve
- Laboratoire de Chimie Bactérienne – Aix Marseille Université - UPR 9043-CNRS, 31, Chemin Joseph Aiguier, Marseille, France
| | - Adrien Ducret
- Laboratoire de Chimie Bactérienne – Aix Marseille Université - UPR 9043-CNRS, 31, Chemin Joseph Aiguier, Marseille, France
| | - Pierre Khoueiry
- Laboratoire de Chimie Bactérienne – Aix Marseille Université - UPR 9043-CNRS, 31, Chemin Joseph Aiguier, Marseille, France
| | - Sabrina Lignon
- Service de micro séquençage et de spectrométrie de masse – CNRS-31, Chemin Joseph Aiguier, Marseille, France
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques, Aix Marseille Université - CNRS, UMR 6098, Marseille, France
| | - Emmanuel Talla
- Laboratoire de Chimie Bactérienne – Aix Marseille Université - UPR 9043-CNRS, 31, Chemin Joseph Aiguier, Marseille, France
- * E-mail: (SD); (ET)
| | - Sam Dukan
- Laboratoire de Chimie Bactérienne – Aix Marseille Université - UPR 9043-CNRS, 31, Chemin Joseph Aiguier, Marseille, France
- * E-mail: (SD); (ET)
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Depke M, Steil L, Domanska G, Völker U, Schütt C, Kiank C. Altered hepatic mRNA expression of immune response and apoptosis-associated genes after acute and chronic psychological stress in mice. Mol Immunol 2009; 46:3018-28. [PMID: 19592098 DOI: 10.1016/j.molimm.2009.06.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 06/16/2009] [Indexed: 01/16/2023]
Abstract
Using a combination of transcriptional profiling and Ingenuity Pathway Analysis (IPA, www.ingenuity.com) we investigated acute and chronic psychological stress induced alterations of hepatic gene expression of BALB/c mice. Already after a 2-h single stress session, up-regulation of several LPS and glucocorticoid-sensitive immune response genes and markers related to oxidative stress and apoptotic processes were observed. Support for the existence of oxidative stress was gained by measuring increased protein carbonylation, but no alterations of immune responsiveness or cell death were measured in mice after acute stress compared to the control group. When animals were repeatedly stressed during 4.5-days, we found reduced transcription of antigen presentation molecules, altered mRNA levels of immune cell signaling mediators and persisting high expression of apoptosis-related genes. These alterations were associated with a measurable immune suppression characterized by a reduced ability to clear experimental Salmonella typhimurium infection from the liver and a heightened hepatocyte apoptosis. Moreover, genes associated with anti-oxidative functions and regenerative processes were induced in the hepatic tissue of chronically stressed mice. These findings indicate that modulation of the immune response and of apoptosis-related genes is initiated already during a single acute stress exposure. However, immune suppression will only manifest in repeatedly stressed mice which additionally show induction of protective and liver regenerative genes to prevent further hepatocyte damage.
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Affiliation(s)
- Maren Depke
- Interfaculty Institute of Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Germany
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11
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Garg N, Manchanda G. ROS generation in plants: Boon or bane? PLANT BIOSYSTEMS - AN INTERNATIONAL JOURNAL DEALING WITH ALL ASPECTS OF PLANT BIOLOGY 2009. [PMID: 0 DOI: 10.1080/11263500802633626] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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12
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The Campylobacter jejuni thiol peroxidases Tpx and Bcp both contribute to aerotolerance and peroxide-mediated stress resistance but have distinct substrate specificities. J Bacteriol 2008; 190:5279-90. [PMID: 18515414 DOI: 10.1128/jb.00100-08] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microaerophilic food-borne pathogen Campylobacter jejuni experiences variable oxygen concentrations during its life cycle, especially during transitions between the external environment and the avian or mammalian gut. Single knockout mutations in either one of two related thiol peroxidase genes, tpx and bcp, resulted in normal microaerobic growth (10% [vol/vol] oxygen) but poorer growth than that of the wild type under high-aeration conditions (21% [vol/vol] oxygen). However, a tpx/bcp double mutant had a severe microaerobic growth defect and did not grow at high aeration in shake flasks. Although the single mutant strains were no more sensitive than the wild-type strains in disc diffusion assays with hydrogen peroxide, organic peroxides, superoxide, or nitrosative stress agents, in all cases the double mutant was hypersensitive. Quantitative cell viability and cellular lipid peroxidation assays indicated some increased sensitivity of the single tpx and bcp mutants to peroxide stress. Protein carbonylation studies revealed that the tpx/bcp double mutant had a higher degree of oxygen- and peroxide-induced oxidative protein damage than did either of the single mutants. An analysis of the peroxidase activity of the purified recombinant enzymes showed that, surprisingly, Tpx reduced only hydrogen peroxide as substrate, whereas Bcp also reduced organic peroxides. Immunoblotting of wild-type cell extracts with Tpx- or Bcp-specific antibodies showed increased abundance of both proteins under high aeration compared to that under microaerobic growth conditions. Taken together, the results suggest that Tpx and Bcp are partially redundant antioxidant enzymes that play an important role in protection of C. jejuni against oxygen-induced oxidative stress.
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13
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Summerfield TC, Sherman LA. Role of sigma factors in controlling global gene expression in light/dark transitions in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 2007; 189:7829-40. [PMID: 17720783 PMCID: PMC2168720 DOI: 10.1128/jb.01036-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report on differential gene expression in the cyanobacterium Synechocystis sp. strain PCC 6803 after light-dark transitions in wild-type, DeltasigB, and DeltasigD strains. We also studied the effect of day length in the presence of glucose on a DeltasigB DeltasigE mutant. Our results indicated that the absence of SigB or SigD predominately altered gene expression in the dark or in the light, respectively. In the light, approximately 350 genes displayed transcript levels in the DeltasigD strain that were different from those of the wild type, with over 200 of these up-regulated in the mutant. In the dark, removal of SigB altered more than 150 genes, and the levels of 136 of these were increased in the mutant compared to those in the wild type. The removal of both SigB and SigE had a major impact on gene expression under mixotrophic growth conditions and resulted in the inability of cells to grow in the presence of glucose with 8-h light and 16-h dark cycles. Our results indicated the importance of group II sigma factors in the global regulation of transcription in this organism and are best explained by using the sigma cycle paradigm with the stochastic release model described previously (R. A. Mooney, S. A. Darst, and R. Landick, Mol. Cell 20:335-345, 2005). We combined our results with the total protein levels of the sigma factors in the light and dark as calculated previously (S. Imamura, S. Yoshihara, S. Nakano, N. Shiozaki, A. Yamada, K. Tanaka, H. Takahashi, M. Asayama, and M. Shirai, J. Mol. Biol. 325:857-872, 2003; S. Imamura, M. Asayama, H. Takahashi, K. Tanaka, H. Takahashi, and M. Shirai, FEBS Lett. 554:357-362, 2003). Thus, we concluded that the control of global transcription is based on the amount of the various sigma factors present and able to bind RNA polymerase.
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Affiliation(s)
- Tina C Summerfield
- Department of Biological Sciences, Purdue University, 201 S. University St., Hansen Hall, West Lafayette, IN 47907, USA
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Berth M, Moser FM, Kolbe M, Bernhardt J. The state of the art in the analysis of two-dimensional gel electrophoresis images. Appl Microbiol Biotechnol 2007; 76:1223-43. [PMID: 17713763 PMCID: PMC2279157 DOI: 10.1007/s00253-007-1128-0] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 07/13/2007] [Accepted: 07/14/2007] [Indexed: 11/21/2022]
Abstract
Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.
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Affiliation(s)
- Matthias Berth
- DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany
| | | | - Markus Kolbe
- DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany
| | - Jörg Bernhardt
- DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany
- Institute of Microbiology, Greifswald University, Jahnstrasse 15, 17487 Greifswald, Germany
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15
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Foster JS, Singh AK, Rothschild LJ, Sherman LA. Growth-phase dependent differential gene expression in Synechocystis sp. strain PCC 6803 and regulation by a group 2 sigma factor. Arch Microbiol 2006; 187:265-79. [PMID: 17160677 DOI: 10.1007/s00203-006-0193-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 10/25/2006] [Accepted: 11/06/2006] [Indexed: 11/27/2022]
Abstract
Cyanobacteria must continually alter their physiological growth state in response to changes in light intensity and their nutritional and physical environment. Under typical laboratory batch growth conditions, cyanobacteria grow exponentially, then transition to a light-limited stage of linear growth before finally reaching a non-growth stationary phase. In this study, we utilized DNA microarrays to profile the expression of genes in the cyanobacterium Synechocystis sp. PCC 6803 to compare exponential and linear growth. We also studied the importance of SigB, a group 2 sigma factor in this cyanobacterium, during the different growth phases. The transcription of approximately 10% of the genes in the wild type were different in the linear, compared to the exponential phase, and our results showed that: (1) many photosynthesis and regulatory genes had lowered transcript levels; (2) individual genes, such as sigH, phrA, and isiA, which encode a group 4 sigma factor, a DNA photolyase, and a Chl-binding protein, respectively, were strongly induced; and, (3) the loss of SigB significantly impacted the differential expression of genes and modulated the changes seen in the wild type in regard to photosynthesis, regulatory and the unknown genes.
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Affiliation(s)
- Jamie S Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Kennedy Space Center, FL 32899, USA
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16
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Westendorf A, Benndorf D, Pribyl T, Harms H, Müller RH. Kinetic Traits and Enzyme Form Patterns of(R)-2-(2,4-Dichlorophenoxy)propionate/α-Ketoglutarate Dioxygenase (RdpA) after Expression in Different Bacterial Strains. Eng Life Sci 2006. [DOI: 10.1002/elsc.200620165] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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17
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Tsilibaris V, Maenhaut-Michel G, Van Melderen L. Biological roles of the Lon ATP-dependent protease. Res Microbiol 2006; 157:701-13. [PMID: 16854568 DOI: 10.1016/j.resmic.2006.05.004] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 05/22/2006] [Accepted: 05/23/2006] [Indexed: 12/24/2022]
Abstract
The Lon ATP-dependent protease plays a major role in protein quality control. An increasing number of regulatory proteins, however, are being identified as Lon substrates, thus indicating that in addition to its housekeeping function, Lon plays an important role in regulating many biological processes in bacteria. This review presents and discusses the involvement of Lon in different aspects of bacterial physiology, including cell differentiation, sporulation, pathogenicity and survival under starvation conditions.
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Affiliation(s)
- Virginie Tsilibaris
- Laboratoire de Génétique des Procaryotes, IBMM, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
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18
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Temple A, Yen TY, Gronert S. Identification of specific protein carbonylation sites in model oxidations of human serum albumin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1172-80. [PMID: 16750385 DOI: 10.1016/j.jasms.2006.04.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 04/10/2006] [Accepted: 04/10/2006] [Indexed: 05/10/2023]
Abstract
Human serum albumin (HSA) was subjected to oxidative stress and the locations of the resulting protein carbonyls were determined using mass spectrometry in conjunction with a hydrazide labeling scheme. To model oxidative stress, HSA samples were subjected to metal-catalyzed oxidation (MCO) conditions or treated with hypochlorous acid (HOCl). Oxidation led to the conversion of lysine residues to 2-aminoadipic semi-aldehyde residues, which were subsequently labeled with biotin hydrazide. Analysis of the tryptic peptides from the samples indicates that the oxidations are highly selective. Under MCO conditions, only two of the 59 lysine residues appeared to be modified (Lys-97 and Lys-186). With HOCl, five different lysine modification sites were identified (Lys-130, Lys-257, Lys-438, Lys-499, and Lys-598). These results strongly suggest that the preferred site of modification is dependent on the nature of the oxidant and that the process relies on specific structural motifs in the protein to direct the oxidation. The high selectivity seen here provides insights into the factors that in vivo drive the selective carbonylation of specific proteins in systems under oxidative stress.
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Affiliation(s)
- Ani Temple
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
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19
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Hochgräfe F, Mostertz J, Albrecht D, Hecker M. Fluorescence thiol modification assay: oxidatively modified proteins inBacillus subtilis. Mol Microbiol 2005; 58:409-25. [PMID: 16194229 DOI: 10.1111/j.1365-2958.2005.04845.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Oxidatively modified thiol groups of cysteine residues are known to modulate the activity of a growing number of proteins. In this study, we developed a fluorescence-based thiol modification assay and combined it with two-dimensional gel electrophoresis and mass spectrometry to monitor the in vivo thiol state of cytoplasmic proteins. For the Gram-positive model organism Bacillus subtilis our results show that protein thiols of growing cells are mainly present in the reduced state. Only a few proteins were found to be thiol-modified, e.g. enzymes that include oxidized thiols in their catalytic cycle. To detect proteins that are particularly sensitive to oxidative stress we exposed growing B. subtilis cells to diamide, hydrogen peroxide or to the superoxide generating agent paraquat. Diamide mediated a significant increase of oxidized thiols in a variety of metabolic enzymes, whereas treatment with paraquat affected only a few proteins. Exposure to hydrogen peroxide forced the oxidation especially of proteins with active site cysteines, e.g. of cysteine-based peroxidases and glutamine amidotransferase-like proteins. Moreover, high levels of hydrogen peroxide were observed to influence the isoelectric point of proteins of this group indicating the generation of irreversibly oxidated thiols. From the overlapping set of oxidatively modified proteins, also enzymes necessary for methionine biosynthesis were identified, e.g. cobalamin-independent methionine synthase MetE. Growth experiments revealed a methionine limitation after diamide and hydrogen peroxide stress, which suggests a thiol-oxidation-dependent inactivation of MetE. Finally, evidence is presented that the antibiotic nitrofurantoin mediates the formation of oxidized thiols in B. subtilis.
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Affiliation(s)
- Falko Hochgräfe
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
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20
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Job C, Rajjou L, Lovigny Y, Belghazi M, Job D. Patterns of protein oxidation in Arabidopsis seeds and during germination. PLANT PHYSIOLOGY 2005; 138:790-802. [PMID: 15908592 PMCID: PMC1150397 DOI: 10.1104/pp.105.062778] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Increased cellular levels of reactive oxygen species are known to occur during seed development and germination, but the consequences in terms of protein degradation are poorly characterized. In this work, protein carbonylation, which is an irreversible oxidation process leading to a loss of function of the modified proteins, has been analyzed by a proteomic approach during the first stages of Arabidopsis (Arabidopsis thaliana) seed germination. In the dry mature seeds, the legumin-type globulins (12S cruciferins) were the major targets. However, the acidic alpha-cruciferin subunits were carbonylated to a much higher extent than the basic (beta) ones, consistent with a model in which the beta-subunits are buried within the cruciferin molecules and the alpha-subunits are more exposed to the outside. During imbibition, various carbonylated proteins accumulated. This oxidation damage was not evenly distributed among seed proteins and targeted specific proteins as glycolytic enzymes, mitochondrial ATP synthase, chloroplastic ribulose bisphosphate carboxylase large chain, aldose reductase, methionine synthase, translation factors, and several molecular chaperones. Although accumulation of carbonylated proteins is usually considered in the context of aging in a variety of model systems, this was clearly not the case for the Arabidopsis seeds since they germinated at a high rate and yielded vigorous plantlets. The results indicate that the observed specific changes in protein carbonylation patterns are probably required for counteracting and/or utilizing the production of reactive oxygen species caused by recovery of metabolic activity in the germinating seeds.
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Affiliation(s)
- Claudette Job
- Centre National de la Recherche Scientifique/Bayer CropScience Joint Laboratory, Unité Mixte de Recherche 2847, Bayer CropScience, Lyon, France
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Hecker M, Völker U. Towards a comprehensive understanding ofBacillus subtiliscell physiology by physiological proteomics. Proteomics 2004; 4:3727-50. [PMID: 15540212 DOI: 10.1002/pmic.200401017] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Using Bacillus subtilis as a model system for functional genomics, this review will provide insights how proteomics can be used to bring the virtual life of genes to the real life of proteins. Physiological proteomics will generate a new and broad understanding of cellular physiology because the majority of proteins synthesized in the cell can be visualized. From a physiological point of view two major proteome fractions can be distinguished: proteomes of growing cells and proteomes of nongrowing cells. In the main analytical window almost 50% of the vegetative proteome expressed in growing cells of B. subtilis were identified. This proteomic view of growing cells can be employed for analyzing the regulation of entire metabolic pathways and thus opens the chance for a comprehensive understanding of metabolism and growth processes of bacteria. Proteomics, on the other hand, is also a useful tool for analyzing the adaptational network of nongrowing cells that consists of several partially overlapping regulation groups induced by stress/starvation stimuli. Furthermore, proteomic signatures for environmental stimuli can not only be applied to predict the physiological state of cells, but also offer various industrial applications from fermentation monitoring up to the analysis of the mode of action of drugs. Even if DNA array technologies currently provide a better overview of the gene expression profile than proteome approaches, the latter address biological problems in which they can not be replaced by mRNA profiling procedures. This proteomics of the second generation is a powerful tool for analyzing global control of protein stability, the protein interaction network, protein secretion or post-translational modifications of proteins on the way towards the elucidation of the mystery of life.
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Affiliation(s)
- Michael Hecker
- Institute for Microbiology, Erst-Moritz-Arndt-University, Greifswald, Germany.
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