1
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Sengupta S, Nath R, Bhuyan R, Bhattacharjee A. Variation in glucose metabolism under acidified sodium nitrite mediated nitrosative stress in Saccharomyces cerevisiae. J Appl Microbiol 2022; 133:1660-1675. [PMID: 35702895 DOI: 10.1111/jam.15669] [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: 03/25/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
AIMS The work aimed to understand the important changes during glucose metabolism in Saccharomyces cerevisiae under acidified sodium nitrite (ac.NaNO2 ) mediated nitrosative stress. METHODS AND RESULTS Confocal microscopy and fluorescence-activated cell sorting analysis were performed to investigate the generation of reactive nitrogen and oxygen species, and redox homeostasis under nitrosative stress was also characterized. Quantitative PCR analysis revealed that the expression of ADH genes was upregulated under such condition, whereas the ACO2 gene was downregulated. Some of the enzymes of the tricarboxylic acid cycle were partially inhibited, whereas malate metabolism and alcoholic fermentation were increased under nitrosative stress. Kinetics of ethanol production was also characterized. A network analysis was conducted to validate our findings. In the presence of ac.NaNO2 , in vitro protein tyrosine nitration formation was checked by western blotting using pure alcohol dehydrogenase and aconitase. CONCLUSIONS Alcoholic fermentation rate was increased under stress condition and this altered metabolism might be conjoined with the defence machinery to overcome the nitrosative stress. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first work of this kind where the role of metabolism under nitrosative stress has been characterized in S. cerevisiae and it will provide a base to develop an alternative method of industrial ethanol production.
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Affiliation(s)
- Swarnab Sengupta
- Department of Microbiology, University of North Bengal, Raja Rammohunpur, West Bengal, India
| | - Rohan Nath
- Department of Microbiology, University of North Bengal, Raja Rammohunpur, West Bengal, India
| | - Rajabrata Bhuyan
- Department of Bio-Science and Biotechnology, Banasthali Vidyapith (Deemed) University, Banasthali, Rajasthan, India
| | - Arindam Bhattacharjee
- Department of Microbiology, University of North Bengal, Raja Rammohunpur, West Bengal, India
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2
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Sengupta S, Nath R, Bhattacharjee A. Characterizing the effect of S-nitrosoglutathione on Saccharomyces cerevisiae: Upregulation of alcohol dehydrogenase and inactivation of aconitase. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Nitrite reduction in fermented meat products and its impact on aroma. ADVANCES IN FOOD AND NUTRITION RESEARCH 2021; 95:131-181. [PMID: 33745511 DOI: 10.1016/bs.afnr.2020.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fermented meat products are important not only for their sensory characteristics, nutrient content and cultural heritage, but also for their stability and convenience. The aroma of fermented meat products is unique and its formation mechanisms are not completely understood; however, the presence of nitrite and nitrate is essential for the development of cured aroma. The use of nitrite and nitrate as curing agents in meat products is based on its preservation activity. Even though their presence has been associated with several risks due to the formation of nitrosamines, their use is guarantee due to their antimicrobial action against Clostridium botulinum. Recent trends and recommendations by international associations are directed to use nitrite but at the minimum concentration necessary to provide the antimicrobial activity against Clostridium botulinum. This chapter discuss the actual limits of nitrite and nitrite content and their role as curing agents in meat products with special impact on dry fermented products. Regulatory considerations, antimicrobial mechanisms and actual trends regarding nitrite reduction and its effect on sensory and aroma properties are also considered.
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4
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Nilewski S, Varatnitskaya M, Masuch T, Kusnezowa A, Gellert M, Baumann AF, Lupilov N, Kusnezow W, Koch MH, Eisenacher M, Berkmen M, Lillig CH, Leichert LI. Functional metagenomics of the thioredoxin superfamily. J Biol Chem 2021; 296:100247. [PMID: 33361108 PMCID: PMC7949104 DOI: 10.1074/jbc.ra120.016350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/06/2022] Open
Abstract
Environmental sequence data of microbial communities now makes up the majority of public genomic information. The assignment of a function to sequences from these metagenomic sources is challenging because organisms associated with the data are often uncharacterized and not cultivable. To overcome these challenges, we created a rationally designed expression library of metagenomic proteins covering the sequence space of the thioredoxin superfamily. This library of 100 individual proteins represents more than 22,000 thioredoxins found in the Global Ocean Sampling data set. We screened this library for the functional rescue of Escherichia coli mutants lacking the thioredoxin-type reductase (ΔtrxA), isomerase (ΔdsbC), or oxidase (ΔdsbA). We were able to assign functions to more than a quarter of our representative proteins. The in vivo function of a given representative could not be predicted by phylogenetic relation but did correlate with the predicted isoelectric surface potential of the protein. Selected proteins were then purified, and we determined their activity using a standard insulin reduction assay and measured their redox potential. An unexpected gel shift of protein E5 during the redox potential determination revealed a redox cycle distinct from that of typical thioredoxin-superfamily oxidoreductases. Instead of the intramolecular disulfide bond formation typical for thioredoxins, this protein forms an intermolecular disulfide between the attacking cysteines of two separate subunits during its catalytic cycle. Our functional metagenomic approach proved not only useful to assign in vivo functions to representatives of thousands of proteins but also uncovered a novel reaction mechanism in a seemingly well-known protein superfamily.
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Affiliation(s)
- Sebastian Nilewski
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Marharyta Varatnitskaya
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Thorsten Masuch
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany; Protein Expression and Modification Division, New England Biolabs, Ipswich, Massachusetts, USA
| | - Anna Kusnezowa
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Manuela Gellert
- Institute for Medical Biochemistry and Molecular Biology, Universität Greifswald, Greifswald, Germany
| | - Anne F Baumann
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Natalie Lupilov
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Witali Kusnezow
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | | | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Mehmet Berkmen
- Protein Expression and Modification Division, New England Biolabs, Ipswich, Massachusetts, USA
| | - Christopher H Lillig
- Institute for Medical Biochemistry and Molecular Biology, Universität Greifswald, Greifswald, Germany
| | - Lars I Leichert
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.
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5
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Gibhardt CS, Cappello S, Bhardwaj R, Schober R, Kirsch SA, Bonilla Del Rio Z, Gahbauer S, Bochicchio A, Sumanska M, Ickes C, Stejerean-Todoran I, Mitkovski M, Alansary D, Zhang X, Revazian A, Fahrner M, Lunz V, Frischauf I, Luo T, Ezerina D, Messens J, Belousov VV, Hoth M, Böckmann RA, Hediger MA, Schindl R, Bogeski I. Oxidative Stress-Induced STIM2 Cysteine Modifications Suppress Store-Operated Calcium Entry. Cell Rep 2020; 33:108292. [PMID: 33086068 DOI: 10.1016/j.celrep.2020.108292] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/28/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Store-operated calcium entry (SOCE) through STIM-gated ORAI channels governs vital cellular functions. In this context, SOCE controls cellular redox signaling and is itself regulated by redox modifications. However, the molecular mechanisms underlying this calcium-redox interplay and the functional outcomes are not fully understood. Here, we examine the role of STIM2 in SOCE redox regulation. Redox proteomics identify cysteine 313 as the main redox sensor of STIM2 in vitro and in vivo. Oxidative stress suppresses SOCE and calcium currents in cells overexpressing STIM2 and ORAI1, an effect that is abolished by mutation of cysteine 313. FLIM and FRET microscopy, together with MD simulations, indicate that oxidative modifications of cysteine 313 alter STIM2 activation dynamics and thereby hinder STIM2-mediated gating of ORAI1. In summary, this study establishes STIM2-controlled redox regulation of SOCE as a mechanism that affects several calcium-regulated physiological processes, as well as stress-induced pathologies.
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Affiliation(s)
- Christine Silvia Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Sabrina Cappello
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Rajesh Bhardwaj
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Bern, Switzerland
| | - Romana Schober
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria; Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Sonja Agnes Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Germany
| | - Zuriñe Bonilla Del Rio
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Stefan Gahbauer
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Germany
| | - Anna Bochicchio
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Germany
| | - Magdalena Sumanska
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Christian Ickes
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Ioana Stejerean-Todoran
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Miso Mitkovski
- Light Microscopy Facility, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Dalia Alansary
- Biophysics, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Xin Zhang
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Aram Revazian
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Marc Fahrner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
| | - Victoria Lunz
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
| | - Irene Frischauf
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
| | - Ting Luo
- VIB-VUB Center for Structural Biology, Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daria Ezerina
- VIB-VUB Center for Structural Biology, Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Vsevolod Vadimovich Belousov
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany; Pirogov Russian National Research Medical University, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia
| | - Markus Hoth
- Biophysics, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Rainer Arnold Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Germany
| | | | - Rainer Schindl
- Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany.
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6
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Varatnitskaya M, Degrossoli A, Leichert LI. Redox regulation in host-pathogen interactions: thiol switches and beyond. Biol Chem 2020; 402:299-316. [PMID: 33021957 DOI: 10.1515/hsz-2020-0264] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/29/2020] [Indexed: 12/23/2022]
Abstract
Our organism is exposed to pathogens on a daily basis. Owing to this age-old interaction, both pathogen and host evolved strategies to cope with these encounters. Here, we focus on the consequences of the direct encounter of cells of the innate immune system with bacteria. First, we will discuss the bacterial strategies to counteract powerful reactive species. Our emphasis lies on the effects of hypochlorous acid (HOCl), arguably the most powerful oxidant produced inside the phagolysosome of professional phagocytes. We will highlight individual examples of proteins in gram-negative bacteria activated by HOCl via thiol-disulfide switches, methionine sulfoxidation, and N-chlorination of basic amino acid side chains. Second, we will discuss the effects of HOCl on proteins of the host. Recent studies have shown that both host and bacteria address failing protein homeostasis by activation of chaperone-like holdases through N-chlorination. After discussing the role of individual proteins in the HOCl-defense, we will turn our attention to the examination of effects on host and pathogen on a systemic level. Recent studies using genetically encoded redox probes and redox proteomics highlight differences in redox homeostasis in host and pathogen and give first hints at potential cellular HOCl signaling beyond thiol-disulfide switch mechanisms.
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Affiliation(s)
- Marharyta Varatnitskaya
- Institute for Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Adriana Degrossoli
- Faculty of Health Science - Health Science Department, Federal University of Lavras, Lavras, Brazil
| | - Lars I Leichert
- Institute for Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr University Bochum, Bochum, Germany
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7
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Loescher CM, Breitkreuz M, Li Y, Nickel A, Unger A, Dietl A, Schmidt A, Mohamed BA, Kötter S, Schmitt JP, Krüger M, Krüger M, Toischer K, Maack C, Leichert LI, Hamdani N, Linke WA. Regulation of titin-based cardiac stiffness by unfolded domain oxidation (UnDOx). Proc Natl Acad Sci U S A 2020; 117:24545-24556. [PMID: 32929035 PMCID: PMC7533878 DOI: 10.1073/pnas.2004900117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The relationship between oxidative stress and cardiac stiffness is thought to involve modifications to the giant muscle protein titin, which in turn can determine the progression of heart disease. In vitro studies have shown that S-glutathionylation and disulfide bonding of titin fragments could alter the elastic properties of titin; however, whether and where titin becomes oxidized in vivo is less certain. Here we demonstrate, using multiple models of oxidative stress in conjunction with mechanical loading, that immunoglobulin domains preferentially from the distal titin spring region become oxidized in vivo through the mechanism of unfolded domain oxidation (UnDOx). Via oxidation type-specific modification of titin, UnDOx modulates human cardiomyocyte passive force bidirectionally. UnDOx also enhances titin phosphorylation and, importantly, promotes nonconstitutive folding and aggregation of unfolded domains. We propose a mechanism whereby UnDOx enables the controlled homotypic interactions within the distal titin spring to stabilize this segment and regulate myocardial passive stiffness.
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Affiliation(s)
| | - Martin Breitkreuz
- Institute of Physiology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Yong Li
- Institute of Physiology II, University of Munster, 48149 Munster, Germany
| | - Alexander Nickel
- Comprehensive Heart Failure Center Wuerzburg, University Clinic Wuerzburg, 97078 Wuerzburg, Germany
| | - Andreas Unger
- Institute of Physiology II, University of Munster, 48149 Munster, Germany
| | - Alexander Dietl
- Department of Internal Medicine II, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Andreas Schmidt
- Institute for Genetics, University of Cologne, 50931 Cologne, Germany
| | - Belal A Mohamed
- Department of Cardiology and Pneumology, University Medicine Goettingen, 37075 Goettingen, Germany
| | - Sebastian Kötter
- Department of Cardiovascular Physiology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Joachim P Schmitt
- Department of Pharmacology and Clinical Pharmacology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Marcus Krüger
- Institute for Genetics, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine and Excellence Cluster "Cellular Stress Responses in Aging-Associated Diseases" (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Martina Krüger
- Department of Cardiovascular Physiology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Karl Toischer
- Department of Cardiology and Pneumology, University Medicine Goettingen, 37075 Goettingen, Germany
| | - Christoph Maack
- Comprehensive Heart Failure Center Wuerzburg, University Clinic Wuerzburg, 97078 Wuerzburg, Germany
| | - Lars I Leichert
- Institute for Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Nazha Hamdani
- Institute of Physiology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wolfgang A Linke
- Institute of Physiology II, University of Munster, 48149 Munster, Germany;
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8
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Irons JL, Hodge-Hanson K, Downs DM. RidA Proteins Protect against Metabolic Damage by Reactive Intermediates. Microbiol Mol Biol Rev 2020; 84:e00024-20. [PMID: 32669283 PMCID: PMC7373157 DOI: 10.1128/mmbr.00024-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Rid (YjgF/YER057c/UK114) protein superfamily was first defined by sequence homology with available protein sequences from bacteria, archaea, and eukaryotes (L. Parsons, N. Bonander, E. Eisenstein, M. Gilson, et al., Biochemistry 42:80-89, 2003, https://doi.org/10.1021/bi020541w). The archetypal subfamily, RidA (reactive intermediate deaminase A), is found in all domains of life, with the vast majority of free-living organisms carrying at least one RidA homolog. In over 2 decades, close to 100 reports have implicated Rid family members in cellular processes in prokaryotes, yeast, plants, and mammals. Functional roles have been proposed for Rid enzymes in amino acid biosynthesis, plant root development and nutrient acquisition, cellular respiration, and carcinogenesis. Despite the wealth of literature and over a dozen high-resolution structures of different RidA enzymes, their biochemical function remained elusive for decades. The function of the RidA protein was elucidated in a bacterial model system despite (i) a minimal phenotype of ridA mutants, (ii) the enzyme catalyzing a reaction believed to occur spontaneously, and (iii) confusing literature on the pleiotropic effects of RidA homologs in prokaryotes and eukaryotes. Subsequent work provided the physiological framework to support the RidA paradigm in Salmonella enterica by linking the phenotypes of mutants lacking ridA to the accumulation of the reactive metabolite 2-aminoacrylate (2AA), which damaged metabolic enzymes. Conservation of enamine/imine deaminase activity of RidA enzymes from all domains raises the likelihood that, despite the diverse phenotypes, the consequences when RidA is absent are due to accumulated 2AA (or a similar reactive enamine) and the diversity of metabolic phenotypes can be attributed to differences in metabolic network architecture. The discovery of the RidA paradigm in S. enterica laid a foundation for assessing the role of Rid enzymes in diverse organisms and contributed fundamental lessons on metabolic network evolution and diversity in microbes. This review describes the studies that defined the conserved function of RidA, the paradigm of enamine stress in S. enterica, and emerging studies that explore how this paradigm differs in other organisms. We focus primarily on the RidA subfamily, while remarking on our current understanding of the other Rid subfamilies. Finally, we describe the current status of the field and pose questions that will drive future studies on this widely conserved protein family to provide fundamental new metabolic information.
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Affiliation(s)
- Jessica L Irons
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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9
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Abstract
Neutrophils kill invading microbes and therefore represent the first line of defense of the innate immune response. Activated neutrophils assemble NADPH oxidase to convert substantial amounts of molecular oxygen into superoxide, which, after dismutation into peroxide, serves as the substrate for the generation of the potent antimicrobial hypochlorous acid (HOCl) in the phagosomal space. In this minireview, we explore the most recent insights into physiological consequences of HOCl stress. Not surprisingly, Gram-negative bacteria have evolved diverse posttranslational defense mechanisms to protect their proteins, the main targets of HOCl, from HOCl-mediated damage. We discuss the idea that oxidation of conserved cysteine residues and partial unfolding of its structure convert the heat shock protein Hsp33 into a highly active chaperone holdase that binds unfolded proteins and prevents their aggregation. We examine two novel members of the Escherichia coli chaperone holdase family, RidA and CnoX, whose thiol-independent activation mechanism differs from that of Hsp33 and requires N-chlorination of positively charged amino acids during HOCl exposure. Furthermore, we summarize the latest findings with respect to another bacterial defense strategy employed in response to HOCl stress, which involves the accumulation of the universally conserved biopolymer inorganic polyphosphate. We then discuss sophisticated adaptive strategies that bacteria have developed to enhance their survival during HOCl stress. Understanding bacterial defense and survival strategies against one of the most powerful neutrophilic oxidants may provide novel insights into treatment options that potentially compromise the ability of pathogens to resist HOCl stress and therefore may increase the efficacy of the innate immune response.
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10
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Sengupta S, Deb M, Nath R, Prasad Saha S, Bhattacharjee A. Optimization of Ethanol Production using Nitrosative Stress Exposed S.cerevisiae. Cell Biochem Biophys 2019; 78:101-110. [PMID: 31875278 DOI: 10.1007/s12013-019-00897-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/12/2019] [Indexed: 11/28/2022]
Abstract
S.cerevisiae is an industrially important organism known for its ability to produce ethanol as the demand for ethanol is increasing day by day all over the world, the need to find better and alternative ways to increase ethanol production is also rising. In this work we have proposed such alternative but effective method for producing ethanol by S.cerevisiae. Here, we are reporting for the first time the effect of nitrosative stress on ethanol production. Under in vivo condition, nitrosative stress is marked by the modification of macromolecules in the presence of reactive nitrogen species (RNS). Our result showed that treated cells were more capable for ethanol production compared with untreated cells. Our result also showed enhanced alcohol dehydrogenase activity under stressed condition. Further ethanol production was also optimized by using Response Surface Methodology (RSM) with stressed cells. Further, production of ethanol with immobilized beads of stress affected Saccharomyces cerevisiae was also determined. Overall, the obtained data showed that under nitrosative stress, the maximum ethanol production is 34.4 g/l after 24 h and such higher production was observed even after several cycles of fermentation. This is the first report of this kind showing the relation between nitrosative stress and ethanol production in Saccharomyces cerevisiae which may have important industrial application.
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Affiliation(s)
- Swarnab Sengupta
- Department of Microbiology, University of North Bengal, Siliguri, India
| | - Minakshi Deb
- Department of Microbiology, University of North Bengal, Siliguri, India
| | - Rohan Nath
- Department of Microbiology, University of North Bengal, Siliguri, India
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11
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Hong LTT, Hachiya T, Hase S, Shiwa Y, Yoshikawa H, Sakakibara Y, Nguyen SLT, Kimura K. Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene. J Biosci Bioeng 2019; 128:690-696. [PMID: 31272833 DOI: 10.1016/j.jbiosc.2019.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/21/2019] [Accepted: 05/27/2019] [Indexed: 02/06/2023]
Abstract
Poly-γ-glutamic acid (γPGA) production by Bacillus subtilis is regulated by the quorum sensing system where DegQ transmits the cell density signal to a DNA-binding protein DegU. A mutation suppressing the γPGA-negative phenotype of degQ gene knock-out mutant (ΔdegQ) was identified through whole genome sequencing. The mutation conferred an amino acid substitution of Ser103 to phenylalanine (S103F) in yabJ that belongs to the highly conserved YjgF/YER057c/UK114 family. Genetic experiments including LacZ-fusion assay of γPGA synthetic operon confirmed that the suppressor mutation (yabJS103F) was responsible for the recovery of γPGA production. The yabJ itself was not essential for the γPGA production and the mutant allele enabled γPGA production of the ΔdegQ strain even in the presence of wild type yabJ. Thus, yabJS103F was a dominant positive allele. degU-lacZ fusion gene was hyper-expressed in cells carrying the yabJS103F, but disruption of yabJ did not affect the transcription level of the degU-lacZ. These observations suggested that YabJ acquired a function to stimulate expression of degU by the S103F mutation which is involved in the regulation of γPGA synthesis.
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Affiliation(s)
- Le Thi Thu Hong
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Tsuyoshi Hachiya
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Sumitaka Hase
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan; Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Yasubumi Sakakibara
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Sy Le Thanh Nguyen
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Keitarou Kimura
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan.
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12
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Reichmann D, Voth W, Jakob U. Maintaining a Healthy Proteome during Oxidative Stress. Mol Cell 2019; 69:203-213. [PMID: 29351842 DOI: 10.1016/j.molcel.2017.12.021] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/11/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]
Abstract
Some of the most challenging stress conditions that organisms encounter during their lifetime involve the transient accumulation of reactive oxygen and chlorine species. Extremely reactive to amino acid side chains, these oxidants cause widespread protein unfolding and aggregation. It is therefore not surprising that cells draw on a variety of different strategies to counteract the damage and maintain a healthy proteome. Orchestrated largely by direct changes in the thiol oxidation status of key proteins, the response strategies involve all layers of protein protection. Reprogramming of basic biological functions helps decrease nascent protein synthesis and restore redox homeostasis. Mobilization of oxidative stress-activated chaperones and production of stress-resistant non-proteinaceous chaperones prevent irreversible protein aggregation. Finally, redox-controlled increase in proteasome activity removes any irreversibly damaged proteins. Together, these systems pave the way to restore protein homeostasis and enable organisms to survive stress conditions that are inevitable when living an aerobic lifestyle.
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Affiliation(s)
- Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Wilhelm Voth
- Department of Molecular, Cellular, and Developmental Biology and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1048, USA.
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13
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Xie K, Bunse C, Marcus K, Leichert LI. Quantifying changes in the bacterial thiol redox proteome during host-pathogen interaction. Redox Biol 2018; 21:101087. [PMID: 30682706 PMCID: PMC6351232 DOI: 10.1016/j.redox.2018.101087] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022] Open
Abstract
Phagocyte-derived production of a complex mixture of different oxidants is a major mechanism of the host defense against microbial intruders. On the protein level, a major target of these oxidants is the thiol group of the amino acid cysteine in proteins. Oxidation of thiol groups is a widespread regulatory post-translational protein modification. It is used by bacteria to respond to and to overcome oxidative stress. Numerous redox proteomic studies have shown that protein thiols in bacteria, such as Escherichia coli react towards a number of oxidants in specific ways. However, our knowledge about protein thiols in bacteria exposed to the complex mixture of oxidants encountered in the phagolysosome is still limited. In this study, we used a quantitative redox proteomic method (OxICAT) to assess the in vivo thiol oxidation status of phagocytized E. coli. The majority (65.5%) of identified proteins harbored thiols that were significantly oxidized (> 30%) upon phagocytosis. A substantial number of these proteins are from major metabolic pathways or are involved in cell detoxification and stress response, suggesting a systemic breakdown of the bacterial cysteine proteome in phagocytized bacteria. 16 of the oxidized proteins provide E. coli with a significant growth advantage in the presence of H2O2, when compared to deletion mutants lacking these proteins, and 11 were shown to be essential under these conditions.
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Affiliation(s)
- Kaibo Xie
- Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, 44780 Bochum, Germany
| | - Christina Bunse
- Ruhr University Bochum, Medizinisches Proteom-Center, 44801 Bochum, Germany
| | - Katrin Marcus
- Ruhr University Bochum, Medizinisches Proteom-Center, 44801 Bochum, Germany
| | - Lars I Leichert
- Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, 44780 Bochum, Germany.
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14
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Antimicrobial Efficacy and Safety of a Novel Gas Plasma-Activated Catheter Lock Solution. Antimicrob Agents Chemother 2018; 62:AAC.00744-18. [PMID: 29844050 DOI: 10.1128/aac.00744-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/23/2018] [Indexed: 02/05/2023] Open
Abstract
Antimicrobial lock solutions are important for prevention of microbial colonization and infection of long-term central venous catheters. We investigated the efficacy and safety of a novel antibiotic-free lock solution formed from gas plasma-activated disinfectant (PAD). Using a luminal biofilm model, viable cells of methicillin-resistant Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa, and Candida albicans in mature biofilms were reduced by 6 to 8 orders of magnitude with a PAD lock for 60 min. Subsequent 24-h incubation of PAD-treated samples resulted in no detectable regrowth of viable bacteria or fungi. As a comparison, the use of a minocycline-EDTA-ethanol lock solution for 60 min led to regrowth of bacteria and fungi, up to 107 to 109 CFU/ml, in 24 h. The PAD lock solution had minimal impact on human umbilical vein endothelial cell viability, whereas the minocycline-EDTA-ethanol solution elicited cell death in nearly half of human endothelial cells. Additionally, PAD treatment caused little topological change to catheter materials. In conclusion, PAD represents a novel antibiotic-free, noncytotoxic lock solution that elicits rapid and broad-spectrum eradication of biofilm-laden microbes and shows promise for the prevention and treatment of intravascular catheter infections.
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Abstract
Cysteine thiols are involved in a diverse set of biological transformations, including nucleophilic and redox catalysis, metal coordination and formation of both dynamic and structural disulfides. Often posttranslationally modified, cysteines are also frequently alkylated by electrophilic compounds, including electrophilic metabolites, drugs, and natural products, and are attractive sites for covalent probe and drug development. Quantitative proteomics combined with activity-based protein profiling has been applied to annotate cysteine reactivity, susceptibility to posttranslational modifications, and accessibility to chemical probes, uncovering thousands of functional and small-molecule targetable cysteines across a diverse set of proteins, proteome-wide in an unbiased manner. Reactive cysteines have been targeted by high-throughput screening and fragment-based ligand discovery efforts. New cysteine-reactive electrophiles and compound libraries have been synthesized to enable inhibitor discovery broadly and to minimize nonspecific toxicity and off-target activity of compounds. With the recent blockbuster success of several covalent inhibitors, and the development of new chemical proteomic strategies to broadly identify reactive, ligandable and posttranslationally modified cysteines, cysteine profiling is poised to enable the development of new potent and selective chemical probes and even, in some cases, new drugs.
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16
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Voth W, Jakob U. Stress-Activated Chaperones: A First Line of Defense. Trends Biochem Sci 2017; 42:899-913. [PMID: 28893460 DOI: 10.1016/j.tibs.2017.08.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 10/18/2022]
Abstract
Proteins are constantly challenged by environmental stress conditions that threaten their structure and function. Especially problematic are oxidative, acid, and severe heat stress which induce very rapid and widespread protein unfolding and generate conditions that make canonical chaperones and/or transcriptional responses inadequate to protect the proteome. We review here recent advances in identifying and characterizing stress-activated chaperones which are inactive under non-stress conditions but become potent chaperones under specific protein-unfolding stress conditions. We discuss the post-translational mechanisms by which these chaperones sense stress, and consider the role that intrinsic disorder plays in their regulation and function. We examine their physiological roles under both non-stress and stress conditions, their integration into the cellular proteostasis network, and their potential as novel therapeutic targets.
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Affiliation(s)
- Wilhelm Voth
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular Biology, Universitätsmedizin Göttingen, 37073 Göttingen, Germany
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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17
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Lindemann C, Thomanek N, Hundt F, Lerari T, Meyer HE, Wolters D, Marcus K. Strategies in relative and absolute quantitative mass spectrometry based proteomics. Biol Chem 2017; 398:687-699. [DOI: 10.1515/hsz-2017-0104] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/28/2017] [Indexed: 11/15/2022]
Abstract
Abstract
Quantitative mass spectrometry approaches are used for absolute and relative quantification in global proteome studies. To date, relative and absolute quantification techniques are available that differ in quantification accuracy, proteome coverage, complexity and robustness. This review focuses on most common relative or absolute quantification strategies exemplified by three experimental studies. A label-free relative quantification approach was performed for the investigation of the membrane proteome of sensory cilia to the depth of olfactory receptors in Mus musculus. A SILAC-based relative quantification approach was successfully applied for the identification of core components and transient interactors of the peroxisomal importomer in Saccharomyces cerevisiae. Furthermore, AQUA using stable isotopes was exemplified to unraveling the prenylome influenced by novel prenyltransferase inhibitors. Characteristic enrichment and fragmentation strategies for a robust quantification of the prenylome are also summarized.
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Borisov VB, Forte E, Siletsky SA, Arese M, Davletshin AI, Sarti P, Giuffrè A. Cytochrome bd protects bacteria against oxidative and nitrosative stress: A potential target for next-generation antimicrobial agents. BIOCHEMISTRY (MOSCOW) 2015; 80:565-75. [DOI: 10.1134/s0006297915050077] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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20
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Dahl JU, Gray MJ, Jakob U. Protein quality control under oxidative stress conditions. J Mol Biol 2015; 427:1549-63. [PMID: 25698115 PMCID: PMC4357566 DOI: 10.1016/j.jmb.2015.02.014] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 02/11/2015] [Accepted: 02/11/2015] [Indexed: 12/22/2022]
Abstract
Accumulation of reactive oxygen and chlorine species (RO/CS) is generally regarded to be a toxic and highly undesirable event, which serves as contributing factor in aging and many age-related diseases. However, it is also put to excellent use during host defense, when high levels of RO/CS are produced to kill invading microorganisms and regulate bacterial colonization. Biochemical and cell biological studies of how bacteria and other microorganisms deal with RO/CS have now provided important new insights into the physiological consequences of oxidative stress, the major targets that need protection, and the cellular strategies employed by organisms to mitigate the damage. This review examines the redox-regulated mechanisms by which cells maintain a functional proteome during oxidative stress. We will discuss the well-characterized redox-regulated chaperone Hsp33, and we will review recent discoveries demonstrating that oxidative stress-specific activation of chaperone function is a much more widespread phenomenon than previously anticipated. New members of this group include the cytosolic ATPase Get3 in yeast, the Escherichia coli protein RidA, and the mammalian protein α2-macroglobulin. We will conclude our review with recent evidence showing that inorganic polyphosphate (polyP), whose accumulation significantly increases bacterial oxidative stress resistance, works by a protein-like chaperone mechanism. Understanding the relationship between oxidative and proteotoxic stresses will improve our understanding of both host-microbe interactions and how mammalian cells combat the damaging side effects of uncontrolled RO/CS production, a hallmark of inflammation.
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Affiliation(s)
- Jan-Ulrik Dahl
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Michael J Gray
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA.
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Boronat S, García-Santamarina S, Hidalgo E. Gel-free proteomic methodologies to study reversible cysteine oxidation and irreversible protein carbonyl formation. Free Radic Res 2015; 49:494-510. [PMID: 25782062 DOI: 10.3109/10715762.2015.1009053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Oxidative modifications in proteins have been traditionally considered as hallmarks of damage by oxidative stress and aging. However, oxidants can generate a huge variety of reversible and irreversible modifications in amino acid side chains as well as in the protein backbones, and these post-translational modifications can contribute to the activation of signal transduction pathways, and also mediate the toxicity of oxidants. Among the reversible modifications, the most relevant ones are those arising from cysteine oxidation. Thus, formation of sulfenic acid or disulfide bonds is known to occur in many enzymes as part of their catalytic cycles, and it also participates in the activation of signaling cascades. Furthermore, these reversible modifications have been usually attributed with a protective role, since they may prevent the formation of irreversible damage by scavenging reactive oxygen species. Among irreversible modifications, protein carbonyl formation has been linked to damage and death, since it cannot be repaired and can lead to protein loss-of-function and to the formation of protein aggregates. This review is aimed at researchers interested on the biological consequences of oxidative stress, both at the level of signaling and toxicity. Here we are providing a concise overview on current mass-spectrometry-based methodologies to detect reversible cysteine oxidation and irreversible protein carbonyl formation in proteomes. We do not pretend to impose any of the different methodologies, but rather to provide an objective catwalk on published gel-free approaches to detect those two types of modifications, from a biologist's point of view.
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Affiliation(s)
- S Boronat
- Departament de Ciències Experimentals i de la Salut, Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , C/Dr. Aiguader 88, E-08003 Barcelona , Spain
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22
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Dávila Costa JS, Leichert L, Alvarez HM, Herrero OM. Label-free and redox proteomic analyses of the triacylglycerol-accumulating Rhodococcus jostii RHA1. Microbiology (Reading) 2015; 161:593-610. [DOI: 10.1099/mic.0.000028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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23
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Schoenebeck B, May C, Güldner C, Respondek G, Mollenhauer B, Hoeglinger G, Meyer HE, Marcus K. Improved preparation of nasal lavage fluid (NLF) as a noninvasive sample for proteomic biomarker discovery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:741-5. [PMID: 25680929 DOI: 10.1016/j.bbapap.2015.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED Nasal lavage fluid (NLF) becomes more and more important as a noninvasive patient sample serving as a new opportunity to discover new biomarkers in diverse human diseases comprising mainly respiratory disorders. This was supported by the observation that the protein profile of NLF differs from conventional samples of i.e. whole blood, hence being capable to complement or even expand the so far biomarker index. Since sample acquisition and processing are the most crucial steps for a profound and sensitive identification we present here a modified protocol of NLF generation and measurement. We show that mild washing steps for sample generation followed by column-mediated concentration and acetone precipitation are appropriate steps to minimize serum leakage by concomitantly highlighting proteins which represent typical components of NLF. This is shown by separation of proteins via 2D-PAGE followed by LC-MS/MS as well as Gel-LC-MS/MS measurements of cut and digested protein spots/bands. SIGNIFICANCE For a better understanding of the molecular mechanisms underlying respiratory diseases NLF samples are favored sources for protein research. NLF acquisition and sample processing were impaired so far by the problem of blood serum leakage and high salt content. Here, we present a modified protocol of NLF generation leading to the display of typical inventory of NLF proteins combined with reduced salt and serum contaminants. By this, both assay reproducibility and the detection of up- or down-regulated proteins reliably can be discovered in the case of biomarker screenings in a disease versus control design. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Bodo Schoenebeck
- Abteilung für Neuroanatomie und Molekulare Hirnforschung, Medizinische Fakultaet, Ruhr-Universitaet Bochum, 44801 Bochum, Germany
| | - Caroline May
- Abteilung für Medizinische Proteomik/Bioanalytik, Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, 44801 Bochum, Germany
| | - Christian Güldner
- Department of Otolaryngology, Phillips Universität, Marburg, Germany
| | - Gesine Respondek
- Department of Neurology, Technische Universität München, Munich, Germany and German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | | | - Guenter Hoeglinger
- Lehrstuhl für Translationale Neurodegeneration, Technische Universität München, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen, 81377 München, Germany
| | - Helmut E Meyer
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany
| | - Katrin Marcus
- Abteilung für Funktionelle Proteomik, Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, 44801 Bochum, Germany.
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Müller A, Langklotz S, Lupilova N, Kuhlmann K, Bandow JE, Leichert LIO. Activation of RidA chaperone function by N-chlorination. Nat Commun 2014; 5:5804. [PMID: 25517874 PMCID: PMC4284807 DOI: 10.1038/ncomms6804] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 11/07/2014] [Indexed: 12/25/2022] Open
Abstract
Escherichia coli RidA is a member of a structurally conserved, yet functionally highly diverse protein family involved in translation inhibition (human), Hsp90-like chaperone activity (fruit fly) and enamine/imine deamination (Salmonella enterica). Here, we show that E. coli RidA modified with HOCl acts as a highly effective chaperone. Although activation of RidA is reversed by treatment with DTT, ascorbic acid, the thioredoxin system and glutathione, it is independent of cysteine modification. Instead, treatment with HOCl or chloramines decreases the amino group content of RidA by reversibly N-chlorinating positively charged residues. N-chlorination increases hydrophobicity of RidA and promotes binding to a wide spectrum of unfolded cytosolic proteins. Deletion of ridA results in an HOCl-sensitive phenotype. HOCl-mediated N-chlorination thus is a cysteine-independent post-translational modification that reversibly turns RidA into an effective chaperone holdase, which plays a crucial role in the protection of cytosolic proteins during oxidative stress. Hypochlorous acid generated by neutrophils acts as a potent antibacterial agent. Müller et al. now show that this oxidant directly activates a protective counter-response in E. coli by N-chlorinating the protein RidA and converting it into an effective protein chaperone.
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Affiliation(s)
- Alexandra Müller
- Institute of Biochemistry and Pathobiochemistry-Microbial Biochemistry, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Sina Langklotz
- Biology of Microorganisms, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Nataliya Lupilova
- Institute of Biochemistry and Pathobiochemistry-Microbial Biochemistry, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Katja Kuhlmann
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Julia Elisabeth Bandow
- Biology of Microorganisms, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Lars Ingo Ole Leichert
- Institute of Biochemistry and Pathobiochemistry-Microbial Biochemistry, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
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Stern AM, Zhu J. An introduction to nitric oxide sensing and response in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2014; 87:187-220. [PMID: 24581392 DOI: 10.1016/b978-0-12-800261-2.00005-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nitric oxide (NO) is a radical gas that has been intensively studied for its role as a bacteriostatic agent. NO reacts in complex ways with biological molecules, especially metal centers and other radicals, to generate other bioactive compounds that inhibit enzymes, oxidize macromolecules, and arrest bacterial growth. Bacteria encounter not only NO derived from the host during infection but also NO derived from other bacteria and inorganic sources. The transcriptional responses used by bacteria to respond to NO are diverse but usually involve an iron-containing transcription factor that binds NO and alters its affinity for either DNA or factors involved in transcription, leading to the production of enzymatic tolerance systems. Some of these systems, such as flavohemoglobin and flavorubredoxin, directly remove NO. Some do not but are still important for NO tolerance through other mechanisms. The targets of NO that are protected by these systems include many metabolic pathways such as the tricarboxylic acid cycle and branched chain amino acid synthesis. This chapter discusses these topics and others and serves as a general introduction to microbial NO biology.
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