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Watanabe A, Koyano F, Imai K, Hizukuri Y, Ogiwara S, Ito T, Miyamoto J, Shibuya C, Kimura M, Toriumi K, Motono C, Arai M, Tanaka K, Akiyama Y, Yamano K, Matsuda N. The origin of esterase activity of Parkinson's disease causative factor DJ-1 implied by evolutionary trace analysis of its prokaryotic homolog HchA. J Biol Chem 2024; 300:107476. [PMID: 38879013 DOI: 10.1016/j.jbc.2024.107476] [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: 03/31/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 07/14/2024] Open
Abstract
DJ-1, a causative gene for hereditary recessive Parkinsonism, is evolutionarily conserved across eukaryotes and prokaryotes. Structural analyses of DJ-1 and its homologs suggested the 106th Cys is a nucleophilic cysteine functioning as the catalytic center of hydratase or hydrolase activity. Indeed, DJ-1 and its homologs can convert highly electrophilic α-oxoaldehydes such as methylglyoxal into α-hydroxy acids as hydratase in vitro, and oxidation-dependent ester hydrolase (esterase) activity has also been reported for DJ-1. The mechanism underlying such plural activities, however, has not been fully characterized. To address this knowledge gap, we conducted a series of biochemical assays assessing the enzymatic activity of DJ-1 and its homologs. We found no evidence for esterase activity in any of the Escherichia coli DJ-1 homologs. Furthermore, contrary to previous reports, we found that oxidation inactivated rather than facilitated DJ-1 esterase activity. The E. coli DJ-1 homolog HchA possesses phenylglyoxalase and methylglyoxalase activities but lacks esterase activity. Since evolutionary trace analysis identified the 186th H as a candidate residue involved in functional differentiation between HchA and DJ-1, we focused on H186 of HchA and found that an esterase activity was acquired by H186A mutation. Introduction of reverse mutations into the equivalent position in DJ-1 (A107H) selectively eliminated its esterase activity without compromising α-oxoaldehyde hydratase activity. The obtained results suggest that differences in the amino acid sequences near the active site contributed to acquisition of esterase activity in vitro and provide an important clue to the origin and significance of DJ-1 esterase activity.
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Affiliation(s)
- Aiko Watanabe
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Fumika Koyano
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo, Japan; Global Research and Development Center for Business by Quantum-AI Technology (G-QuAT), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Yohei Hizukuri
- Laboratory of Biological Membrane System, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shizuka Ogiwara
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan; Schizophrenia Research Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Tomoya Ito
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Jun Miyamoto
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Chihiro Shibuya
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Mayumi Kimura
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Kazuya Toriumi
- Schizophrenia Research Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Chie Motono
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Waseda University, Shinjuku, Tokyo, Japan
| | - Makoto Arai
- Schizophrenia Research Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Yoshinori Akiyama
- Laboratory of Biological Membrane System, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Koji Yamano
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Noriyuki Matsuda
- Division of Advanced Pathophysiological Science, Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan.
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Bouillet S, Bauer TS, Gottesman S. RpoS and the bacterial general stress response. Microbiol Mol Biol Rev 2024; 88:e0015122. [PMID: 38411096 PMCID: PMC10966952 DOI: 10.1128/mmbr.00151-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Taran S. Bauer
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
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Boteva E, Doychev K, Kirilov K, Handzhiyski Y, Tsekovska R, Gatev E, Mironova R. Deglycation activity of the Escherichia coli glycolytic enzyme phosphoglucose isomerase. Int J Biol Macromol 2024; 257:128541. [PMID: 38056730 DOI: 10.1016/j.ijbiomac.2023.128541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Glycation is a spontaneous chemical reaction, which affects the structure and function of proteins under normal physiological conditions. Therefore, organisms have evolved diverse mechanisms to combat glycation. In this study, we show that the Escherichia coli glycolytic enzyme phosphoglucose isomerase (Pgi) exhibits deglycation activity. We found that E. coli Pgi catalyzes the breakdown of glucose 6-phosphate (G6P)-derived Amadori products (APs) in chicken lysozyme. The affinity of Pgi to the glycated lysozyme (Km, 1.1 mM) was ten times lower than the affinity to its native substrate, fructose 6-phosphate (Km, 0.1 mM). However, the high kinetic constants of the enzyme with the glycated lysozyme (kcat, 396 s-1 and kcat/Km, 3.6 × 105 M-1 s-1) indicated that the Pgi amadoriase activity may have physiological implications. Indeed, when using total E. coli protein (20 mg/mL) as a substrate in the deglycation reaction, we observed a release of G6P from the bacterial protein at a Pgi specific activity of 33 μmol/min/mg. Further, we detected 11.4 % lower APs concentration in protein extracts from Pgi-proficient vs. deficient cells (p = 0.0006) under conditions where the G6P concentration in Pgi-proficient cells was four times higher than in Pgi-deficient cells (p = 0.0001). Altogether, these data point to physiological relevance of the Pgi deglycation activity.
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Affiliation(s)
- Elitsa Boteva
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Konstantin Doychev
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Kiril Kirilov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Yordan Handzhiyski
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Rositsa Tsekovska
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Evan Gatev
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Roumyana Mironova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
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Zhou Y, Cheng Y, Ma T, Wang J, Li S, Wang J, Han L, Hou X, Ma X, Jiang S, Li P, Lv J, Han B, Da R. Transcriptomic and phenotype analysis revealed the role of rpoS in stress resistance and virulence of a novel ST3355 ESBL-producing hypervirulent Klebsiella pneumoniae isolate. Front Cell Infect Microbiol 2023; 13:1259472. [PMID: 37937207 PMCID: PMC10627032 DOI: 10.3389/fcimb.2023.1259472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction An extended-spectrum beta-lactamase (ESBL)-hypervirulent Klebsiella pneumoniae (HvKP) strain HKE9 was isolated from the blood in an outpatient. Methods The effect of the global regulatory factor RpoS on antimicrobial resistance, pathogenicity, and environmental adaptability was elucidated. Results HKE9 is a novel ST3355 (K20/O2a) hypervirulent strain with a positive string test and resistant to cephems except cefotetan. It has a genome size of 5.6M, including two plasmids. CTX-M-15 was found in plasmid 2, and only ompk37 was found in the chromosome. HKE9 could produce bacterial siderophores, and genes of enterobactin, yersiniabactin, aerobactin, and salmochelin have been retrieved in the genome. As a global regulatory factor, knockout of rpoS did not change antimicrobial resistance or hemolytic phenotype while increasing the virulence to Galleria mellonella larvae and showing higher viscosity. Moreover, rpoS knockout can increase bacterial competitiveness and cell adhesion ability. Interestingly, HKE9-M-rpoS decreased resistance to acidic pH, high osmotic pressure, heat shock, and ultraviolet and became sensitive to disinfectants (H2O2, alcohol, and sodium hypochlorite). Although there were 13 Type 6 secretion system (T6SS) core genes divided into two segments with tle1 between segments in the chromosome, transcriptomic analysis showed that rpoS negatively regulated T4SS located on plasmid 2, type 1, and type 3 fimbriae and positively regulate genes responsible for acidic response, hyperosmotic pressure, heat shock, oxidative stress, alcohol and hypochlorous acid metabolism, and quorum sensing. Discussion Here, this novel ST3355 ESBL-HvKP strain HKE9 may spread via various clonal types. The important regulation effect of rpoS is the enhanced tolerance and resistance to environmental stress and disinfectants, which may be at the cost of reducing virulence and regulated by T4SS.
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Affiliation(s)
- Yi Zhou
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Yue Cheng
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Tianyou Ma
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Jun Wang
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
- Department of Microbiology Laboratory, Tongchuan Center for Disease Control and Prevention, Tongchuan, Shaanxi, China
| | - Shaoru Li
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Jingdan Wang
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Lei Han
- School of Basic Medicine, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Xinyao Hou
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Xinxin Ma
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Sijin Jiang
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Pu Li
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Jia Lv
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Bei Han
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Rong Da
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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Sun ME, Zheng Q. The Tale of DJ-1 (PARK7): A Swiss Army Knife in Biomedical and Psychological Research. Int J Mol Sci 2023; 24:ijms24087409. [PMID: 37108572 PMCID: PMC10138432 DOI: 10.3390/ijms24087409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
DJ-1 (also known as PARK7) is a multifunctional enzyme in human beings that is highly conserved and that has also been discovered in diverse species (ranging from prokaryotes to eukaryotes). Its complex enzymatic and non-enzymatic activities (such as anti-oxidation, anti-glycation, and protein quality control), as well as its role as a transcriptional coactivator, enable DJ-1 to serve as an essential regulator in multiple cellular processes (e.g., epigenetic regulations) and make it a promising therapeutic target for diverse diseases (especially cancer and Parkinson's disease). Due to its nature as a Swiss army knife enzyme with various functions, DJ-1 has attracted a large amount of research interest, from different perspectives. In this review, we give a brief summary of the recent advances with respect to DJ-1 research in biomedicine and psychology, as well as the progress made in attempts to develop DJ-1 into a druggable target for therapy.
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Affiliation(s)
- Mo E Sun
- Department of Psychology, Duquesne University, Pittsburgh, PA 15282, USA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
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Prasad M, Kataria P, Ningaraju S, Buddidathi R, Bankapalli K, Swetha C, Susarla G, Venkatesan R, D'Silva P, Shivaprasad PV. Double DJ-1 domain containing Arabidopsis DJ-1D is a robust macromolecule deglycase. THE NEW PHYTOLOGIST 2022; 236:1061-1074. [PMID: 35976797 DOI: 10.1111/nph.18414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Plants, being sessile, are prone to genotoxin-induced macromolecule damage. Among the inevitable damaging agents are reactive carbonyls that induce glycation of DNA, RNA and proteins to result in the build-up of advanced glycated end-products. However, it is unclear how plants repair glycated macromolecules. DJ-1/PARK7 members are a highly conserved family of moonlighting proteins having double domains in higher plants and single domains in other phyla. Here we show that Arabidopsis DJ-1D offers robust tolerance to endogenous and exogenous stresses through its ability to repair glycated DNA, RNA and proteins. DJ-1D also reduced the formation of reactive carbonyls through its efficient methylglyoxalase activity. Strikingly, full-length double domain-containing DJ-1D suppressed the formation of advanced glycated end-products in yeast and plants. DJ-1D also efficiently repaired glycated nucleic acids and nucleotides in vitro and mitochondrial DNA in vivo under stress, indicating the existence of a new DNA repair pathway in plants. We propose that multi-stress responding plant DJ-1 members, often present in multiple copies among plants, probably contributed to the adaptation to a variety of endogenous and exogenous stresses.
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Affiliation(s)
- Melvin Prasad
- National Centre for Biological Sciences, GKVK Campus, Bangalore, 560 065, India
| | - Priyanka Kataria
- Department of Biochemistry, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560 012, India
| | - Sunayana Ningaraju
- Department of Biochemistry, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560 012, India
| | - Radhika Buddidathi
- National Centre for Biological Sciences, GKVK Campus, Bangalore, 560 065, India
| | - Kondalarao Bankapalli
- Department of Biochemistry, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560 012, India
| | - Chenna Swetha
- National Centre for Biological Sciences, GKVK Campus, Bangalore, 560 065, India
| | - Gautam Susarla
- Department of Biochemistry, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560 012, India
| | - Radhika Venkatesan
- National Centre for Biological Sciences, GKVK Campus, Bangalore, 560 065, India
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - Patrick D'Silva
- Department of Biochemistry, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560 012, India
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Schoppel K, Trachtmann N, Korzin EJ, Tzanavari A, Sprenger GA, Weuster-Botz D. Metabolic control analysis enables rational improvement of E. coli L-tryptophan producers but methylglyoxal formation limits glycerol-based production. Microb Cell Fact 2022; 21:201. [PMID: 36195869 PMCID: PMC9531422 DOI: 10.1186/s12934-022-01930-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/24/2022] [Indexed: 11/24/2022] Open
Abstract
Background Although efficient l-tryptophan production using engineered Escherichia coli is established from glucose, the use of alternative carbon sources is still very limited. Through the application of glycerol as an alternate, a more sustainable substrate (by-product of biodiesel preparation), the well-studied intracellular glycolytic pathways are rerouted, resulting in the activity of different intracellular control sites and regulations, which are not fully understood in detail. Metabolic analysis was applied to well-known engineered E. coli cells with 10 genetic modifications. Cells were withdrawn from a fed-batch production process with glycerol as a carbon source, followed by metabolic control analysis (MCA). This resulted in the identification of several additional enzymes controlling the carbon flux to l-tryptophan. Results These controlling enzyme activities were addressed stepwise by the targeted overexpression of 4 additional enzymes (trpC, trpB, serB, aroB). Their efficacy regarding l-tryptophan productivity was evaluated under consistent fed-batch cultivation conditions. Although process comparability was impeded by process variances related to a temporal, unpredictable break-off in l-tryptophan production, process improvements of up to 28% with respect to the l-tryptophan produced were observed using the new producer strains. The intracellular effects of these targeted genetic modifications were revealed by metabolic analysis in combination with MCA and expression analysis. Furthermore, it was discovered that the E. coli cells produced the highly toxic metabolite methylglyoxal (MGO) during the fed-batch process. A closer look at the MGO production and detoxification on the metabolome, fluxome, and transcriptome level of the engineered E. coli indicated that the highly toxic metabolite plays a critical role in the production of aromatic amino acids with glycerol as a carbon source. Conclusions A detailed process analysis of a new l-tryptophan producer strain revealed that several of the 4 targeted genetic modifications of the E. colil-tryptophan producer strain proved to be effective, and, for others, new engineering approaches could be derived from the results. As a starting point for further strain and process optimization, the up-regulation of MGO detoxifying enzymes and a lowering of the feeding rate during the last third of the cultivation seems reasonable. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01930-1.
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Affiliation(s)
- Kristin Schoppel
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Natalia Trachtmann
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Emil J Korzin
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Angelina Tzanavari
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Georg A Sprenger
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany.
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Abstract
Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal.
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Abstract
Availability of protein structural data is accelerating at an astounding rate, facilitating in silico biochemical and biophysical analyses that require visualization methods. In particular, increased accessibility of representatives within respective protein families is empowering investigators to perform structural model comparisons that provide both functional and evolutionary insights at much more refined levels than previously possible. Numerous software platforms, including several free and open source versions, are available for users to interrogate protein structural models. In this article, three structural alignment protocols are described using freely available software to investigate aspects of protein structure evolution at quaternary, tertiary, and domain levels, respectively. Mapping distinct subunit interfaces and active site positioning within the PfpI/DJ-1 protein superfamily reveals quaternary structure that can have a prominent role in determination of distinct enzyme activities. In contrast, cytochrome c proteins are under strong evolutionary constraints due to their critical role in energy generation, and as a result, structural conservation is observed. However, substitutions within these conserved folds occur in distinct species, presumably to influence interactions with protein complexes involved in electron transport. Lastly, evolution of distinct allosteric mechanisms within winged helix-turn-helix transcriptional regulators, as well as protein dynamics, are revealed through visualization of metal- and redox-responsive DNA-binding proteins. The software platforms used in these protocols are Swiss-PDBViewer and PyMOL. Swiss-PDBViewer is an easy to implement, end-user software that is excellent for entry into protein visualization methods. PyMOL is also easy to implement, but offers greater depth for advanced investigations and visualizations, as well as the ability to capture protein structure conformational changes. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Exploring quaternary structure evolution with Swiss-PDBViewer Alternate Protocol: Exploring tertiary structure evolution with Swiss-PDBViewer Basic Protocol 2: Visualizing allostery using PyMOL.
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Balotf S, Wilson R, Tegg RS, Nichols DS, Wilson CR. Quantitative proteomics provides an insight into germination-related proteins in the obligate biotrophic plant pathogen Spongospora subterranea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:521-532. [PMID: 33928759 DOI: 10.1111/1758-2229.12955] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
The soil-borne and obligate plant-associated nature of S. subterranea has hindered a detailed study of this pathogen and in particular, the regulatory pathways driving the germination of S. subterranea remain unknown. To better understand the mechanisms that control the transition from dormancy to germination, protein profiles between dormant and germination stimulant-treated resting spores were compared using label-free quantitative proteomics. Among the ~680 proteins identified 20 proteins were found to be differentially expressed during the germination of S. subterranea resting spores. Elongation factor Tu, histones (H2A and H15), proteasome and DJ-1_PfpI, involved in transcription and translation, were upregulated during the germination of resting spores. Downregulation of both actin and beta-tubulin proteins occurred in the germinating spores, indicating that the changes in the cell wall cytoskeleton may be necessary for the morphological changes during the germination of the resting spore in S. subterranea. Our findings provide new approaches for the study of these and similar recalcitrant micro-organisms provide the first insights into the basic protein components of S. subterranea spores. A better understanding of S. subterranea biology may lead to the development of novel approaches for the management of persistent soil inoculum.
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Affiliation(s)
- Sadegh Balotf
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tas., 7008, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tas., 7001, Australia
| | - Robert S Tegg
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tas., 7008, Australia
| | - David S Nichols
- Central Science Laboratory, University of Tasmania, Hobart, Tas., 7001, Australia
| | - Calum R Wilson
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tas., 7008, Australia
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Impact of DJ-1 and Helix 8 on the Proteome and Degradome of Neuron-Like Cells. Cells 2021; 10:cells10020404. [PMID: 33669258 PMCID: PMC7920061 DOI: 10.3390/cells10020404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/04/2022] Open
Abstract
DJ-1 is an abundant and ubiquitous component of cellular proteomes. DJ-1 supposedly exerts a wide variety of molecular functions, ranging from enzymatic activities as a deglycase, protease, and esterase to chaperone functions. However, a consensus perspective on its molecular function in the cellular context has not yet been reached. Structurally, the C-terminal helix 8 of DJ-1 has been proposed to constitute a propeptide whose proteolytic removal transforms a DJ-1 zymogen to an active hydrolase with potential proteolytic activity. To better understand the cell-contextual functionality of DJ-1 and the role of helix 8, we employed post-mitotically differentiated, neuron-like SH-SY5Y neuroblastoma cells with stable over-expression of full length DJ-1 or DJ-1 lacking helix 8 (ΔH8), either with a native catalytically active site (C106) or an inactive site (C106A active site mutation). Global proteome comparison of cells over-expressing DJ-1 ΔH8 with native or mutated active site cysteine indicated a strong impact on mitochondrial biology. N-terminomic profiling however did not highlight direct protease substrate candidates for DJ-1 ΔH8, but linked DJ-1 to elevated levels of activated lysosomal proteases, albeit presumably in an indirect manner. Finally, we show that DJ-1 ΔH8 loses the deglycation activity of full length DJ-1. Our study further establishes DJ-1 as deglycation enzyme. Helix 8 is essential for the deglycation activity but dispensable for the impact on lysosomal and mitochondrial biology; further illustrating the pleiotropic nature of DJ-1.
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12
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Arginine glycosylation enhances methylglyoxal detoxification. Sci Rep 2021; 11:3834. [PMID: 33589708 PMCID: PMC7884692 DOI: 10.1038/s41598-021-83437-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Type III secretion system effector proteins have primarily been characterized for their interactions with host cell proteins and their ability to disrupt host signaling pathways. We are testing the hypothesis that some effectors are active within the bacterium, where they modulate bacterial signal transduction and physiology. We previously determined that the Citrobacter rodentium effector NleB possesses an intra-bacterial glycosyltransferase activity that increases glutathione synthetase activity to protect the bacterium from oxidative stress. Here we investigated the potential intra-bacterial activities of NleB orthologs in Salmonella enterica and found that SseK1 and SseK3 mediate resistance to methylglyoxal. SseK1 glycosylates specific arginine residues on four proteins involved in methylglyoxal detoxification, namely GloA (R9), GloB (R190), GloC (R160), and YajL (R149). SseK1-mediated Arg-glycosylation of these four proteins significantly enhances their catalytic activity, thus providing another important example of the intra-bacterial activities of type three secretion system effector proteins. These data are also the first demonstration that a Salmonella T3SS effector is active within the bacterium.
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De Lazzari F, Prag HA, Gruszczyk AV, Whitworth AJ, Bisaglia M. DJ-1: A promising therapeutic candidate for ischemia-reperfusion injury. Redox Biol 2021; 41:101884. [PMID: 33561740 PMCID: PMC7872972 DOI: 10.1016/j.redox.2021.101884] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 12/31/2022] Open
Abstract
DJ-1 is a multifaceted protein with pleiotropic functions that has been implicated in multiple diseases, ranging from neurodegeneration to cancer and ischemia-reperfusion injury. Ischemia is a complex pathological state arising when tissues and organs do not receive adequate levels of oxygen and nutrients. When the blood flow is restored, significant damage occurs over and above that of ischemia alone and is termed ischemia-reperfusion injury. Despite great efforts in the scientific community to ameliorate this pathology, its complex nature has rendered it challenging to obtain satisfactory treatments that translate to the clinic. In this review, we will describe the recent findings on the participation of the protein DJ-1 in the pathophysiology of ischemia-reperfusion injury, firstly introducing the features and functions of DJ-1 and, successively highlighting the therapeutic potential of the protein. DJ-1 has been shown to confer protection in ischemia-reperfusion injury models. DJ-1 protection relies on the activation of antioxidant signaling pathways. DJ-1 regulates mitochondrial homeostasis during ischemia and reperfusion. DJ-1 seems to modulate ion homeostasis during ischemia and reperfusion. DJ-1 may represent a promising therapeutic target for ischemia-reperfusion injury.
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Affiliation(s)
- Federica De Lazzari
- Physiology, Genetics and Behaviour Unit, Department of Biology, University of Padova, 35131, Padova, Italy
| | - Hiran A Prag
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Anja V Gruszczyk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Alexander J Whitworth
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Marco Bisaglia
- Physiology, Genetics and Behaviour Unit, Department of Biology, University of Padova, 35131, Padova, Italy.
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Lassak J, Koller F, Krafczyk R, Volkwein W. Exceptionally versatile – arginine in bacterial post-translational protein modifications. Biol Chem 2019; 400:1397-1427. [DOI: 10.1515/hsz-2019-0182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/01/2019] [Indexed: 12/24/2022]
Abstract
Abstract
Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.
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Affiliation(s)
- Jürgen Lassak
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Franziska Koller
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Wolfram Volkwein
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
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15
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Boteva E, Mironova R. Maillard reaction and aging: can bacteria shed light on the link? BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1590160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Elitsa Boteva
- Department of Gene Regulation, Institute of Molecular Biology ‘Roumen Tsanev’, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Roumyana Mironova
- Department of Gene Regulation, Institute of Molecular Biology ‘Roumen Tsanev’, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Jin SE, Jin JE, Hwang W, Hong SW. Photocatalytic antibacterial application of zinc oxide nanoparticles and self-assembled networks under dual UV irradiation for enhanced disinfection. Int J Nanomedicine 2019; 14:1737-1751. [PMID: 30880977 PMCID: PMC6413819 DOI: 10.2147/ijn.s192277] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background Zinc oxide (ZnO) nanoparticles and their networks have been developed for use in various applications such as gas sensors and semiconductors. Aim In this study, their antibacterial activity against Escherichia coli under dual ultraviolet (UV) irradiation for disinfection was investigated. Materials and methods ZnO nanoparticles were synthesized and immobilized onto silicon (Si) wafers by self-assembly. The physicochemical properties and antibacterial activity of ZnO nanoparticles and their networks were evaluated. Gene ontology was analyzed and toxicity levels were also monitored. Results Synthesized ZnO nanoparticles were spherical nanocrystals (<100 nm; Zn, 47%; O, 53%) that formed macro–mesoporous three-dimensional nanostructures on Si wafers in a concentration-dependent manner. ZnO nanoparticles and their networks on Si wafers had an excellent antibacterial activity against E. coli under dual UV irradiation (>3log CFU/mL). Specifically, arrayed ZnO nanoparticle networks showed superior activity compared with free synthesized ZnO nanoparticles. Oxidative stress-responsive proteins in E. coli were identified and categorized, which indicated antibacterial activity. Synthesized ZnO nanoparticles were less cytotoxic in HaCaT with an IC50 of 6.632 mg/mL, but phototoxic in Balb/c 3T3. Conclusion The results suggested that ZnO nanoparticles and their networks can be promising photocatalytic antibiotics for use in next-generation disinfection systems. Their application could also be extended to industrial and clinical use as effective and safe photocatalytic antibiotics.
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Affiliation(s)
- Su-Eon Jin
- Research Institute for Medical Sciences, College of Medicine, Inha University, Incheon 22212, Korea,
| | - Jun Eon Jin
- College of Electrical Engineering, Korea University, Seoul 02841, Korea
| | | | - Seok Won Hong
- Korea Institute of Science and Technology, Seoul 02792, Korea
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Bifunctional Chloroplastic DJ-1B from Arabidopsis thaliana is an Oxidation-Robust Holdase and a Glyoxalase Sensitive to H₂O₂. Antioxidants (Basel) 2019; 8:antiox8010008. [PMID: 30609642 PMCID: PMC6356872 DOI: 10.3390/antiox8010008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 12/15/2018] [Accepted: 12/22/2018] [Indexed: 01/04/2023] Open
Abstract
Members of the DJ-1 protein family are multifunctional enzymes whose loss increases the susceptibility of the cell to oxidative stress. However, little is known about the function of the plant DJ-1 homologs. Therefore, we analyzed the effect of oxidation on the structure and function of chloroplastic AtDJ-1B and studied the phenotype of T-DNA lines lacking the protein. In vitro oxidation of AtDJ-1B with H₂O₂ lowers its glyoxalase activity, but has no effect on its holdase chaperone function. Remarkably, upon oxidation, the thermostability of AtDJ-1B increases with no significant alteration of the overall secondary structure. Moreover, we found that AtDJ-1B transcript levels are invariable, and loss of AtDJ-1B does not affect plant viability, growth and stress response. All in all, two discrete functions of AtDJ-1B respond differently to H₂O₂, and AtDJ-1B is not essential for plant development under stress.
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18
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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Golubev A, Hanson AD, Gladyshev VN. A Tale of Two Concepts: Harmonizing the Free Radical and Antagonistic Pleiotropy Theories of Aging. Antioxid Redox Signal 2018; 29:1003-1017. [PMID: 28874059 PMCID: PMC6104246 DOI: 10.1089/ars.2017.7105] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/09/2017] [Accepted: 08/31/2017] [Indexed: 12/18/2022]
Abstract
SIGNIFICANCE The two foremost concepts of aging are the mechanistic free radical theory (FRT) of how we age and the evolutionary antagonistic pleiotropy theory (APT) of why we age. Both date from the late 1950s. The FRT holds that reactive oxygen species (ROS) are the principal contributors to the lifelong cumulative damage suffered by cells, whereas the APT is generally understood as positing that genes that are good for young organisms can take over a population even if they are bad for the old organisms. Recent Advances: Here, we provide a common ground for the two theories by showing how aging can result from the inherent chemical reactivity of many biomolecules, not just ROS, which imposes a fundamental constraint on biological evolution. Chemically reactive metabolites spontaneously modify slowly renewable macromolecules in a continuous way over time; the resulting buildup of damage wrought by the genes coding for enzymes that generate such small molecules eventually masquerades as late-acting pleiotropic effects. In aerobic organisms, ROS are major agents of this damage but they are far from alone. CRITICAL ISSUES Being related to two sides of the same phenomenon, these theories should be compatible. However, the interface between them is obscured by the FRT mistaking a subset of damaging processes for the whole, and the APT mistaking a cumulative quantitative process for a qualitative switch. FUTURE DIRECTIONS The manifestations of ROS-mediated cumulative chemical damage at the population level may include the often-observed negative correlation between fitness and the rate of its decline with increasing age, further linking FRT and APT. Antioxid. Redox Signal. 29, 1003-1017.
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Affiliation(s)
- Alexey Golubev
- Department of Carcinogenesis and Oncogerontology, Petrov Research Institute of Oncology, Saint Petersburg, Russia
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow Russia
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Richarme G, Abdallah J, Mathas N, Gautier V, Dairou J. Further characterization of the Maillard deglycase DJ-1 and its prokaryotic homologs, deglycase 1/Hsp31, deglycase 2/YhbO, and deglycase 3/YajL. Biochem Biophys Res Commun 2018; 503:703-709. [PMID: 29932913 DOI: 10.1016/j.bbrc.2018.06.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/13/2018] [Indexed: 12/26/2022]
Abstract
We reported recently that the Parkinsonism-associated protein DJ-1 and its bacterial homologs Hsp31, YhbO and YajL function as deglycases that repair proteins and nucleotides from endogeneous glycation by glyoxal and methylglyoxal, two reactive by-products of glucose metabolism responsible for up to 60% of glycation damage. Here, we show that DJ-1, deglycase 1 and deglycase 2 repair glyoxal- and methylglyoxal-glycated substrates, whereas deglycase 3 principally repairs glyoxal-glycated substrates. Moreover, deglycase 1 and 2 are overexpressed in stationary phase, whereas deglycase 3 is steadily expressed throughout bacterial growth. Finally, deglycase mutants overexpress glyoxalases, aldoketoreductases, glutathione-S-transferase and efflux pumps to alleviate carbonyl stress. In the discussion, we present an overview of the multiple functions of DJ-1 proteins. Our thourough work on deglycases provides compelling evidence that their previously reported glyoxalase III activity merely reflects their deglycase activity. Moreover, for their deglycase activity the Maillard deglycases likely recruit: i) their chaperone activity to interact with glycated proteins, ii) glyoxalase 1 activity to catalyze the rearrangement of Maillard products (aminocarbinols and hemithioacetals) into amides and thioesters, respectively, iii) their protease activity to cleave amide bonds of glycated arginine, lysine and guanine, and iv) glyoxalase 2 activity to cleave thioester bonds of glycated cysteine. Finally, because glycation affects many cellular processes, the discovery of the Maillard deglycases, awaited since 1912, likely constitutes a major advance for medical research, including ageing, cancer, atherosclerosis, neurodegenerative, post-diabetic, renal and autoimmune diseases.
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Affiliation(s)
- Gilbert Richarme
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes-Sorbonne Paris Cité, 75270, Paris, France.
| | - Jad Abdallah
- School of Pharmacy, Lebanese American University, Byblos, 2038 1401, Lebanon
| | - Nicolas Mathas
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes-Sorbonne Paris Cité, 75270, Paris, France
| | - Valérie Gautier
- Stress Molecules, Institut Jacques Monod, Université Paris Diderot-UMR7592, 15 Rue Hélène Brion, 75013, Paris, France
| | - Julien Dairou
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes-Sorbonne Paris Cité, 75270, Paris, France
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Structural Biology of the DJ-1 Superfamily. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1037:5-24. [PMID: 29147900 DOI: 10.1007/978-981-10-6583-5_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The DJ-1 (also called the DJ-1/PfpI, ThiJ/PfpI, or DJ-1/ThiJ/PfpI) superfamily is a structural and functional diverse group of proteins that are present in most organisms. Many of these proteins remain poorly characterized at the biochemical level, but include some known chaperones, proteases, and various stress response proteins that remain mechanistically mysterious. This chapter outlines what is known from a structural perspective about the cellular and biochemical functions of many of these proteins from distinct clades of the superfamily in several organisms. In humans, DJ-1 appears to function primarily as a redox-responsive protein that may act as a sensor for imbalances in cellular redox state. Because mutations in human DJ-1 cause certain types of heritable Parkinson's disease, the role of oxidative posttranslational modifications and pathogenic mutations in human DJ-1 is emphasized in the latter sections of this chapter.
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22
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Borriss R, Danchin A, Harwood CR, Médigue C, Rocha EP, Sekowska A, Vallenet D. Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement. Microb Biotechnol 2018; 11:3-17. [PMID: 29280348 PMCID: PMC5743806 DOI: 10.1111/1751-7915.13043] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genome annotation is, nowadays, performed via automatic pipelines that cannot discriminate between right and wrong annotations. Given their importance in increasing the accuracy of the genome annotations of other organisms, it is critical that the annotations of model organisms reflect the current annotation gold standard. The genome of Bacillus subtilis strain 168 was sequenced twenty years ago. Using a combination of inductive, deductive and abductive reasoning, we present a unique, manually curated annotation, essentially based on experimental data. This reveals how this bacterium lives in a plant niche, while carrying a paleome operating system common to Firmicutes and Tenericutes. Dozens of new genomic objects and an extensive literature survey have been included for the sequence available at the INSDC (AccNum AL009126.3). We also propose an extension to Demerec's nomenclature rules that will help investigators connect to this type of curated annotation via the use of common gene names.
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Affiliation(s)
- Rainer Borriss
- Department of PhytomedicineHumboldt‐Universität zu BerlinLentzeallee 55‐5714195BerlinGermany
| | - Antoine Danchin
- Hôpital de la Pitié‐SalpêtrièreInstitute of Cardiometabolism and Nutrition47 Boulevard de l'Hôpital75013ParisFrance
- School of Biomedical SciencesLi Kashing Faculty of MedicineUniversity of Hong Kong21 Sassoon RoadPok Fu LamSAR Hong KongChina
| | - Colin R. Harwood
- The Centre for Bacterial Cell BiologyNewcastle UniversityBaddiley‐Clark BuildingRichardson RoadNewcastle upon TyneNE2 4AXUK
| | - Claudine Médigue
- CEA DRF Genoscope LABGeMCNRS, UMR8030 Génomique MétaboliqueUniversité d'Evry Val d'EssonneUniversité Paris‐SaclayF‐91057EvryFrance
| | - Eduardo P.C. Rocha
- Microbial Evolutionary Genomics UnitInstitut Pasteur28 rue du Docteur Roux75724Paris Cedex 15France
| | - Agnieszka Sekowska
- Hôpital de la Pitié‐SalpêtrièreInstitute of Cardiometabolism and Nutrition47 Boulevard de l'Hôpital75013ParisFrance
| | - David Vallenet
- CEA DRF Genoscope LABGeMCNRS, UMR8030 Génomique MétaboliqueUniversité d'Evry Val d'EssonneUniversité Paris‐SaclayF‐91057EvryFrance
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Structural and functional studies of SAV0551 from Staphylococcus aureus as a chaperone and glyoxalase III. Biosci Rep 2017; 37:BSR20171106. [PMID: 29046369 PMCID: PMC5691139 DOI: 10.1042/bsr20171106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/10/2017] [Accepted: 12/10/2017] [Indexed: 11/17/2022] Open
Abstract
The DJ-1/ThiJ/PfpI superfamily of proteins is highly conserved across all biological kingdoms showing divergent multifunctions, such as chaperone, catalase, protease, and kinase. The common theme of these functions is responding to and managing various cellular stresses. DJ-1/ThiJ/PfpI superfamily members are classified into three subfamilies according to their quaternary structure (DJ-1-, YhbO-, and Hsp-types). The Hsp-type subfamily includes Hsp31, a chaperone and glyoxalase III. SAV0551, an Hsp-type subfamily member from Staphylococcus aureus, is a hypothetical protein that is predicted as Hsp31. Thus, to reveal the function and reaction mechanism of SAV0551, the crystal structure of SAV0551 was determined. The overall folds in SAV0551 are similar to other members of the Hsp-type subfamily. We have shown that SAV0551 functions as a chaperone and that the surface structure is crucial for holding unfolded substrates. As many DJ-1/ThiJ/PfpI superfamily proteins have been characterized as glyoxalase III, our study also demonstrates SAV0551 as a glyoxalase III that is independent of any cofactors. The reaction mechanism was evaluated via a glyoxylate-bound structure that mimics the hemithioacetal reaction intermediate. We have confirmed that the components required for reaction are present in the structure, including a catalytic triad for a catalytic action, His78 as a base, and a water molecule for hydrolysis. Our functional studies based on the crystal structures of native and glyoxylate-bound SAV0551 will provide a better understanding of the reaction mechanism of a chaperone and glyoxalase III.
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Biosa A, Sandrelli F, Beltramini M, Greggio E, Bubacco L, Bisaglia M. Recent findings on the physiological function of DJ-1: Beyond Parkinson's disease. Neurobiol Dis 2017; 108:65-72. [PMID: 28823929 DOI: 10.1016/j.nbd.2017.08.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/26/2017] [Accepted: 08/16/2017] [Indexed: 01/16/2023] Open
Abstract
Several mutations in the gene coding for DJ-1 have been associated with early onset forms of parkinsonism. In spite of the massive effort spent by the scientific community in understanding the physiological role of DJ-1, a consensus on what DJ-1 actually does within the cells has not been reached, with several diverse functions proposed. At present, the most accepted function for DJ-1 is a neuronal protective role against oxidative stress. However, how exactly this function is exerted by DJ-1 is not clear. In recent years, novel molecular mechanisms have been suggested that may account for the antioxidant properties of DJ-1. In this review, we critically analyse the experimental evidence, including some very recent findings, supporting the purported neuroprotective role of DJ-1 through different mechanisms linked to oxidative stress handling, as well as the relevance of these processes in the context of Parkinson's disease.
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Affiliation(s)
- Alice Biosa
- Molecular Physiology and Biophysics Unit, Department of Biology, University of Padova, 35131 Padova, Italy
| | - Federica Sandrelli
- Neurogenetics and Chronobiology Unit, Department of Biology, University of Padova, 35131 Padova, Italy
| | - Mariano Beltramini
- Molecular Physiology and Biophysics Unit, Department of Biology, University of Padova, 35131 Padova, Italy
| | - Elisa Greggio
- Molecular Physiology and Biophysics Unit, Department of Biology, University of Padova, 35131 Padova, Italy
| | - Luigi Bubacco
- Molecular Physiology and Biophysics Unit, Department of Biology, University of Padova, 35131 Padova, Italy
| | - Marco Bisaglia
- Molecular Physiology and Biophysics Unit, Department of Biology, University of Padova, 35131 Padova, Italy.
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Melvin P, Bankapalli K, D'Silva P, Shivaprasad PV. Methylglyoxal detoxification by a DJ-1 family protein provides dual abiotic and biotic stress tolerance in transgenic plants. PLANT MOLECULAR BIOLOGY 2017; 94:381-397. [PMID: 28444544 DOI: 10.1007/s11103-017-0613-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/18/2017] [Indexed: 05/15/2023]
Abstract
Methylglyoxal (MG) is a key signaling molecule resulting from glycolysis and other metabolic pathways. During abiotic stress, MG levels accumulate to toxic levels in affected cells. However, MG is routinely detoxified through the action of DJ1/PARK7/Hsp31 proteins that are highly conserved across kingdoms and mutations in such genes are associated with neurodegenerative diseases. Here, we report for the first time that, similar to abiotic stresses, MG levels increase during biotic stresses in plants, likely contributing to enhanced susceptibility to a wide range of stresses. We show that overexpression of yeast Heat shock protein 31 (Hsp31), a DJ-1 homolog with robust MG detoxifying capabilities, confers dual biotic and abiotic stress tolerance in model plant Nicotiana tabacum. Strikingly, overexpression of Hsp31 in tobacco imparts robust stress tolerance against diverse biotic stress inducers such as viruses, bacteria and fungi, in addition to tolerance against a range of abiotic stress inducers. During stress, Hsp31 was targeted to mitochondria and induced expression of key stress-related genes. These results indicate that Hsp31 is a novel attractive tool to engineer plants against both biotic and abiotic stresses.
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Affiliation(s)
- Prasad Melvin
- National Centre for Biological Sciences, GKVK Campus, Bangalore, 560 065, India
| | - Kondalarao Bankapalli
- Department of Biochemistry, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560 012, India
| | - Patrick D'Silva
- Department of Biochemistry, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560 012, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, GKVK Campus, Bangalore, 560 065, India.
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Richarme G, Liu C, Mihoub M, Abdallah J, Leger T, Joly N, Liebart JC, Jurkunas UV, Nadal M, Bouloc P, Dairou J, Lamouri A. Guanine glycation repair by DJ-1/Park7 and its bacterial homologs. Science 2017; 357:208-211. [DOI: 10.1126/science.aag1095] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 05/17/2017] [Indexed: 01/05/2023]
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27
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Bunik V, Aleshin V. Analysis of the Protein Binding Sites for Thiamin and Its Derivatives to Elucidate the Molecular Mechanisms of the Noncoenzyme Action of Thiamin (Vitamin B1). STUDIES IN NATURAL PRODUCTS CHEMISTRY 2017. [DOI: 10.1016/b978-0-444-63930-1.00011-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Mihoub M, Abdallah J, Richarme G. Protein Repair from Glycation by Glyoxals by the DJ-1 Family Maillard Deglycases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1037:133-147. [PMID: 29147907 DOI: 10.1007/978-981-10-6583-5_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
DJ-1 and its prokaryotic homologs, Hsp31, YhbO and YajL from Escherichia coli and PfpI from Pyrococcus furiosus, repair proteins from glycation by glyoxals (R-CO-CHO), which constitute their major glycating agents. Glycation is a non-enzymatic covalent reaction discovered by Louis Camille Maillard in 1912, between reactive carbonyls (reducing sugars and glyoxals) and amino acids (cysteine, arginine and lysine), which inactivates proteins. By degrading Maillard adducts formed between carbonyls and thiols or amino groups, the DJ-1 family Maillard deglycases prevent the formation of the so-called advanced glycation end products (AGEs) that arise from Maillard adducts after dehydrations, oxidations and rearrangements. Since glycation is involved in ageing, cancer, atherosclerosis and cataracts, as well as post-diabetic, neurovegetatives and renal and autoimmune diseases, the DJ-1 deglycases are likely to play an important role in preventing these diseases. These deglycases, especially those from thermophilic organisms, may also be used to prevent the formation of dietary AGEs during food processing, sterilization and storage. They also prevent acrylamide formation in food, likely by degrading the asparagine/glyoxal Maillard adducts responsible for its formation. Since Maillard adducts are the substrates of the DJ-1 family deglycases, we propose renaming them Maillard deglycases.
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Affiliation(s)
- Mouadh Mihoub
- Stress Molecules, Institut Jacques Monod, Université Paris 7, UMR 7592, 15 rue Hélène Brion, 75013, Paris, France
| | - Jad Abdallah
- Stress Molecules, Institut Jacques Monod, Université Paris 7, UMR 7592, 15 rue Hélène Brion, 75013, Paris, France.,School of Pharmacy, Lebanese American University, Byblos, Lebanon
| | - Gilbert Richarme
- Stress Molecules, Institut Jacques Monod, Université Paris 7, UMR 7592, 15 rue Hélène Brion, 75013, Paris, France.
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Abstract
Genomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being 'predicted', while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.
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Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'HôpitalParis75013France
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De Lazzari F, Bisaglia M. DJ-1 as a deglycating enzyme: A unique function to explain a multifaceted protein? Neural Regen Res 2017; 12:1797-1798. [PMID: 29239319 PMCID: PMC5745827 DOI: 10.4103/1673-5374.219035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Federica De Lazzari
- Molecular Physiology and Biophysics Unit, Department of Biology, University of Padova, Padova, Italy
| | - Marco Bisaglia
- Molecular Physiology and Biophysics Unit, Department of Biology, University of Padova, Padova, Italy
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Richarme G, Dairou J. Parkinsonism-associated protein DJ-1 is a bona fide deglycase. Biochem Biophys Res Commun 2016; 483:387-391. [PMID: 28013050 DOI: 10.1016/j.bbrc.2016.12.134] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 12/20/2016] [Indexed: 12/21/2022]
Abstract
We discovered recently that Parkinsonism-associated DJ-1 and its bacterial homologs function as protein deglycases that repair glyoxal- and methylglyoxal-glycated proteins. Protein glycation levels are 2- to 10-fold increased in deglycase-depleted cells, and deglycase mutants display up to 500-fold loss of viability in methylglyoxal or glucose-containing media, suggesting that these deglycases play important roles in protecting cells against electrophile and carbonyl stress. Although the deglycase activity of DJ-1 is well supported by extensive biochemical work, Pfaff et al. (J. Biol. Chem. in presshttp://dx.doi.org/10.1074/jbc.M116.743823) claimed in a recent study that deglycation of the hemithioacetal formed upon cysteine glycation by methylglyoxal results from a Tris buffer artefact. Here, we show that this is not the case, and that DJ-1 and its homologs are the bona fide deglycases awaited since the Maillard discovery.
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Affiliation(s)
- Gilbert Richarme
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 Rue Hélène Brion, 75013, Paris, France.
| | - Julien Dairou
- UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes-Sorbonne Paris Cité, 75270, Paris, France
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Richarme G, Marguet E, Forterre P, Ishino S, Ishino Y. DJ-1 family Maillard deglycases prevent acrylamide formation. Biochem Biophys Res Commun 2016; 478:1111-6. [PMID: 27530919 DOI: 10.1016/j.bbrc.2016.08.077] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 08/12/2016] [Indexed: 11/30/2022]
Abstract
The presence of acrylamide in food is a worldwide concern because it is carcinogenic, reprotoxic and neurotoxic. Acrylamide is generated in the Maillard reaction via condensation of reducing sugars and glyoxals arising from their decomposition, with asparagine, the amino acid forming the backbone of the acrylamide molecule. We reported recently the discovery of the Maillard deglycases (DJ-1/Park7 and its prokaryotic homologs) which degrade Maillard adducts formed between glyoxals and lysine or arginine amino groups, and prevent glycation damage in proteins. Here, we show that these deglycases prevent acrylamide formation, likely by degrading asparagine/glyoxal Maillard adducts. We also report the discovery of a deglycase from the hyperthermophilic archaea Pyrococcus furiosus, which prevents acrylamide formation at 100 °C. Thus, Maillard deglycases constitute a unique enzymatic method to prevent acrylamide formation in food without depleting the components (asparagine and sugars) responsible for its formation.
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Affiliation(s)
- Gilbert Richarme
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 rue Hélène Brion, 75013 Paris, France.
| | - Evelyne Marguet
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F-75015, Paris, France
| | - Patrick Forterre
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F-75015, Paris, France
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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The Parkinsonism-associated protein DJ-1/Park7 prevents glycation damage in human keratinocyte. Biochem Biophys Res Commun 2016; 473:87-91. [PMID: 26995087 DOI: 10.1016/j.bbrc.2016.03.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 03/14/2016] [Indexed: 11/24/2022]
Abstract
Reducing sugars and dicarbonyls form covalent adducts with proteins through a nonenzymatic process known as glycation, which inactivates proteins, is increased in diabetic patients and is associated with diabetic complications, including retinopathy, cataracts, nephropathy, neuropathy, cardiomyopathy and skin defects. We recently characterized DJ-1/Park7 as a protein deglycase that repairs proteins from glycation by glyoxal and methylglyoxal, two major glycating agents which are responsible for up to 65% of glycation events. In this study, we investigated the ability of DJ-1 to prevent protein glycation in keratinocytes. Glycation of collagen and keratinocyte proteins was tested by measuring ultraviolet absorption and fluorescence emission. Protein glycation in HaCaT keratinocytes was investigated by immunodetection with anti-advanced glycation endproduct antibodies, after DJ-1 depletion or overexpression. In vitro, DJ-1 prevented glycation of collagen and keratinocyte protein extracts. In cell culture, DJ-1 depletion by small interfering RNAs resulted in a 3-fold increase in protein glycation levels. Moreover, protein glycation levels were decreased several-fold in cells overexpressing DJ-1 after addition of the Nrf2 inducer sulforaphane or after transfection with a DJ-1 plasmid. Thus, the DJ-1 deglycase plays a major role in preventing protein glycation in eukaryotic cells and might be important for preventing skin glycation.
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