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Dolan SK, Duong AT, Whiteley M. Convergent evolution in toxin detection and resistance provides evidence for conserved bacterial-fungal interactions. Proc Natl Acad Sci U S A 2024; 121:e2304382121. [PMID: 39088389 PMCID: PMC11317636 DOI: 10.1073/pnas.2304382121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/12/2024] [Indexed: 08/03/2024] Open
Abstract
Microbes rarely exist in isolation and instead form complex polymicrobial communities. As a result, microbes have developed intricate offensive and defensive strategies that enhance their fitness in these complex communities. Thus, identifying and understanding the molecular mechanisms controlling polymicrobial interactions is critical for understanding the function of microbial communities. In this study, we show that the gram-negative opportunistic human pathogen Pseudomonas aeruginosa, which frequently causes infection alongside a plethora of other microbes including fungi, encodes a genetic network which can detect and defend against gliotoxin, a potent, disulfide-containing antimicrobial produced by the ubiquitous filamentous fungus Aspergillus fumigatus. We show that gliotoxin exposure disrupts P. aeruginosa zinc homeostasis, leading to transcriptional activation of a gene encoding a previously uncharacterized dithiol oxidase (herein named as DnoP), which detoxifies gliotoxin and structurally related toxins. Despite sharing little homology to the A. fumigatus gliotoxin resistance protein (GliT), the enzymatic mechanism of DnoP from P. aeruginosa appears to be identical that used by A. fumigatus. Thus, DnoP and its transcriptional induction by low zinc represent a rare example of both convergent evolution of toxin defense and environmental cue sensing across kingdoms. Collectively, these data provide compelling evidence that P. aeruginosa has evolved to survive exposure to an A. fumigatus disulfide-containing toxin in the natural environment.
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Affiliation(s)
- Stephen K. Dolan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30310
- Department of Genetics and Biochemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC29634
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30310
| | - Ashley T. Duong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30310
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30310
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30310
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2
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Bhat A, Sharma R, Desigan K, Lucas MM, Mishra A, Bowers RM, Woyke T, Epstein B, Tiffin P, Pueyo JJ, Paape T. Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria. BMC Microbiol 2024; 24:247. [PMID: 38971740 PMCID: PMC11227200 DOI: 10.1186/s12866-024-03391-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 07/08/2024] Open
Abstract
BACKGROUND Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg. RESULTS Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg. CONCLUSIONS Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.
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Affiliation(s)
- Aditi Bhat
- Brookhaven National Laboratory, Upton, USA
| | | | | | | | - Ankita Mishra
- Institute for Advancing Health Through Agriculture, Texas A&M, College Station, TX, USA
| | - Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brendan Epstein
- Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - José J Pueyo
- Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Tim Paape
- Institute for Advancing Health Through Agriculture, Texas A&M, College Station, TX, USA.
- USDA-ARS Children's Nutrition Research Center, Houston, TX, USA.
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3
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Bonanata J. The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase. Comput Biol Chem 2024; 110:108075. [PMID: 38678729 DOI: 10.1016/j.compbiolchem.2024.108075] [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: 11/22/2023] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reaction mechanism of FAD reduction by NADPH was studied using QM/MM molecular modeling. The two possible protonation states of Lys-66 were considered: neutral and protonated. Molecular dynamics results suggest that the active site is more structured for neutral Lys-66 than for protonated Lys-66. QM/MM modeling results suggest that Lys-66 should be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH. Since the reaction is unfavorable with protonated Lys-66, the reverse reaction (the reduction of NADP+ by FADH-) is expected to take place. A phylogenetic analysis of various tDBDFs was performed, finding that an active site lysine is present in different the tDBDFs enzymes, suggesting that it has a conserved biological role. Overall, these results suggest that the protonation state of the active site lysine determines the energetics of the reaction, controlling its reversibility.
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Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay.
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4
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Smith MM, Moran GR. Building on a theme: The redox hierarchy of pyridine nucleotide-disulfide oxidoreductases. Arch Biochem Biophys 2024; 755:109966. [PMID: 38537870 DOI: 10.1016/j.abb.2024.109966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/24/2024]
Abstract
Flavin disulfide reductases (FDRs) are FAD-dependent enzymes that transmit electrons from NAD(P)H to reduce specific oxidant substrate disulfides. These enzymes have been studied extensively, most particularly the paradigm examples: glutathione reductase and thioredoxin reductase. The common, though not universal, traits of the family include a tyrosine- or phenylalanine-gated binding pocket for NAD(P) nicotinamides adjacent to the FAD isoalloxazine re-face, and a disulfide stacked against the si-face of the isoalloxazine whose dithiol form is activated for subsequent exchange reactions by a nearby histidine acting as a base. This arrangement promotes transduction of the reducing equivalents for disulfide exchange relay reactions. From an observational standpoint the proximal parallel stacking of three redox moieties induces up to three opportunities for unique charge transfer interactions (NAD(P)H FAD, NAD(P)+•FADH2, and FAD•thiolate). In transient state, the charge transfer transitions provide discrete signals to assign reaction sequences. This review summarizes the lineage of observations for the FDR enzymes that have been extensively studied. Where applicable and in order to chart a consistent interpretation of the record, only data derived from studies that used anaerobic methods are cited. These data reveal a recurring theme for catalysis that is elaborated with specific additional functionalities for each oxidant substrate.
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Affiliation(s)
- Madison M Smith
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, United States.
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5
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Pan X, Heacock ML, Abdulaziz EN, Violante S, Zuckerman AL, Shrestha N, Yao C, Goodman RP, Cross JR, Cracan V. A genetically encoded tool to increase cellular NADH/NAD + ratio in living cells. Nat Chem Biol 2024; 20:594-604. [PMID: 37884806 PMCID: PMC11045668 DOI: 10.1038/s41589-023-01460-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Impaired redox metabolism is a key contributor to the etiology of many diseases, including primary mitochondrial disorders, cancer, neurodegeneration and aging. However, mechanistic studies of redox imbalance remain challenging due to limited strategies that can perturb redox metabolism in various cellular or organismal backgrounds. Most studies involving impaired redox metabolism have focused on oxidative stress; consequently, less is known about the settings where there is an overabundance of NADH reducing equivalents, termed reductive stress. Here we introduce a soluble transhydrogenase from Escherichia coli (EcSTH) as a novel genetically encoded tool to promote reductive stress in living cells. When expressed in mammalian cells, EcSTH, and a mitochondrially targeted version (mitoEcSTH), robustly elevated the NADH/NAD+ ratio in a compartment-specific manner. Using this tool, we determined that metabolic and transcriptomic signatures of the NADH reductive stress are cellular background specific. Collectively, our novel genetically encoded tool represents an orthogonal strategy to promote reductive stress.
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Affiliation(s)
- Xingxiu Pan
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
| | - Mina L Heacock
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
- Calibr, The Scripps Research Institute, La Jolla, CA, USA
| | - Evana N Abdulaziz
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
- Process Development Associate, Amgen, Thousand Oaks, CA, USA
| | - Sara Violante
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Austin L Zuckerman
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
- Program in Mathematics and Science Education, University of California San Diego, San Diego, CA, USA
- Program in Mathematics and Science Education, San Diego State University, San Diego, USA
| | - Nirajan Shrestha
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Canglin Yao
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
| | - Russell P Goodman
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valentin Cracan
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA.
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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6
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Shearer HL, Currie MJ, Agnew HN, Trappetti C, Stull F, Pace PE, Paton JC, Dobson RCJ, Dickerhof N. Hypothiocyanous acid reductase is critical for host colonization and infection by Streptococcus pneumoniae. J Biol Chem 2024; 300:107282. [PMID: 38604564 PMCID: PMC11107202 DOI: 10.1016/j.jbc.2024.107282] [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: 02/27/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024] Open
Abstract
The major human pathogen Streptococcus pneumoniae encounters the immune-derived oxidant hypothiocyanous acid (HOSCN) at sites of colonization and infection. We recently identified the pneumococcal hypothiocyanous acid reductase (Har), a member of the flavoprotein disulfide reductase enzyme family, and showed that it contributes to the HOSCN tolerance of S. pneumoniae in vitro. Here, we demonstrate in mouse models of pneumococcal infection that Har is critical for colonization and invasion. In a colonization model, bacterial load was attenuated dramatically in the nasopharynx when har was deleted in S. pneumoniae. The Δhar strain was also less virulent compared to wild type in an invasion model as reflected by a significant reduction in bacteria in the lungs and no dissemination to the blood and brain. Kinetic measurements with recombinant Har demonstrated that this enzyme reduced HOSCN with near diffusion-limited catalytic efficiency, using either NADH (kcat/KM = 1.2 × 108 M-1s-1) or NADPH (kcat/KM = 2.5 × 107 M-1s-1) as electron donors. We determined the X-ray crystal structure of Har in complex with the FAD cofactor to 1.50 Å resolution, highlighting the active site architecture characteristic for this class of enzymes. Collectively, our results demonstrate that pneumococcal Har is a highly efficient HOSCN reductase, enabling survival against oxidative host immune defenses. In addition, we provide structural insights that may aid the design of Har inhibitors.
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Affiliation(s)
- Heather L Shearer
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago Christchurch, Christchurch, New Zealand; Biomolecular Interaction Centre, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
| | - Hannah N Agnew
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Claudia Trappetti
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan, USA
| | - Paul E Pace
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago Christchurch, Christchurch, New Zealand
| | - James C Paton
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Nina Dickerhof
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago Christchurch, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand.
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7
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Gutiérrez-Fernández J, Hersleth HP, Hammerstad M. The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria. Acta Crystallogr D Struct Biol 2024; 80:181-193. [PMID: 38372589 PMCID: PMC10910545 DOI: 10.1107/s205979832400113x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
Low-molecular-weight (LMW) thiols are involved in many processes in all organisms, playing a protective role against reactive species, heavy metals, toxins and antibiotics. Actinobacteria, such as Mycobacterium tuberculosis, use the LMW thiol mycothiol (MSH) to buffer the intracellular redox environment. The NADPH-dependent FAD-containing oxidoreductase mycothiol disulfide reductase (Mtr) is known to reduce oxidized mycothiol disulfide (MSSM) to MSH, which is crucial to maintain the cellular redox balance. In this work, the first crystal structures of Mtr are presented, expanding the structural knowledge and understanding of LMW thiol reductases. The structural analyses and docking calculations provide insight into the nature of Mtrs, with regard to the binding and reduction of the MSSM substrate, in the context of related oxidoreductases. The putative binding site for MSSM suggests a similar binding to that described for the homologous glutathione reductase and its respective substrate glutathione disulfide, but with distinct structural differences shaped to fit the bulkier MSSM substrate, assigning Mtrs as uniquely functioning reductases. As MSH has been acknowledged as an attractive antitubercular target, the structural findings presented in this work may contribute towards future antituberculosis drug development.
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Affiliation(s)
- Javier Gutiérrez-Fernández
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Hans-Petter Hersleth
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Marta Hammerstad
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
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8
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Pardhe BD, Lee MJ, Lee JH, Do H, Oh TJ. Biochemical and structural basis of mercuric reductase, GbsMerA, from Gelidibacter salicanalis PAMC21136. Sci Rep 2023; 13:17854. [PMID: 37857791 PMCID: PMC10587081 DOI: 10.1038/s41598-023-44968-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023] Open
Abstract
Heavy metals, including mercury, are non-biodegradable and highly toxic to microorganisms even at low concentrations. Understanding the mechanisms underlying the environmental adaptability of microorganisms with Hg resistance holds promise for their use in Hg bioremediation. We characterized GbsMerA, a mercury reductase belonging to the mercury-resistant operon of Gelidibacter salicanalis PAMC21136, and found its maximum activity of 474.7 µmol/min/mg in reducing Hg+2. In the presence of Ag and Mn, the enzyme exhibited moderate activity as 236.5 µmol/min/mg and 69 µmol/min/mg, respectively. GbsMerA exhibited optimal activity at pH 7.0 and a temperature of 60 °C. Moreover, the crystal structure of GbsMerA and structural comparison with homologues indicated that GbsMerA contains residues, Tyr437´ and Asp47, which may be responsible for metal transfer at the si-face by providing a hydroxyl group (-OH) to abstract a proton from the thiol group of cysteine. The complex structure with NADPH indicated that Y174 in the re-face can change its side chain direction upon NADPH binding, indicating that Y174 may have a role as a gate for NADPH binding. Moreover, the heterologous host expressing GbsMerA (pGbsMerA) is more resistant to Hg toxicity when compared to the host lacking GbsMerA. Overall, this study provides a background for understanding the catalytic mechanism and Hg detoxification by GbsMerA and suggests the application of genetically engineered E. coli strains for environmental Hg removal.
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Affiliation(s)
- Bashu Dev Pardhe
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea
| | - Min Ju Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea.
- Genome-Based BioIT Convergence Institute, Asan, 31460, Republic of Korea.
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, 31460, Republic of Korea.
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9
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Li L, Zhou L, Jiang C, Liu Z, Meng D, Luo F, He Q, Yin H. AI-driven pan-proteome analyses reveal insights into the biohydrometallurgical properties of Acidithiobacillia. Front Microbiol 2023; 14:1243987. [PMID: 37744906 PMCID: PMC10512742 DOI: 10.3389/fmicb.2023.1243987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Microorganism-mediated biohydrometallurgy, a sustainable approach for metal recovery from ores, relies on the metabolic activity of acidophilic bacteria. Acidithiobacillia with sulfur/iron-oxidizing capacities are extensively studied and applied in biohydrometallurgy-related processes. However, only 14 distinct proteins from Acidithiobacillia have experimentally determined structures currently available. This significantly hampers in-depth investigations of Acidithiobacillia's structure-based biological mechanisms pertaining to its relevant biohydrometallurgical processes. To address this issue, we employed a state-of-the-art artificial intelligence (AI)-driven approach, with a median model confidence of 0.80, to perform high-quality full-chain structure predictions on the pan-proteome (10,458 proteins) of the type strain Acidithiobacillia. Additionally, we conducted various case studies on de novo protein structural prediction, including sulfate transporter and iron oxidase, to demonstrate how accurate structure predictions and gene co-occurrence networks can contribute to the development of mechanistic insights and hypotheses regarding sulfur and iron utilization proteins. Furthermore, for the unannotated proteins that constitute 35.8% of the Acidithiobacillia proteome, we employed the deep-learning algorithm DeepFRI to make structure-based functional predictions. As a result, we successfully obtained gene ontology (GO) terms for 93.6% of these previously unknown proteins. This study has a significant impact on improving protein structure and function predictions, as well as developing state-of-the-art techniques for high-throughput analysis of large proteomic data.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, United States
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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10
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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11
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Shearer HL, Loi VV, Weiland P, Bange G, Altegoer F, Hampton MB, Antelmann H, Dickerhof N. MerA functions as a hypothiocyanous acid reductase and defense mechanism in Staphylococcus aureus. Mol Microbiol 2023; 119:456-470. [PMID: 36779383 DOI: 10.1111/mmi.15035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/14/2023]
Abstract
The major pathogen Staphylococcus aureus has to cope with host-derived oxidative stress to cause infections in humans. Here, we report that S. aureus tolerates high concentrations of hypothiocyanous acid (HOSCN), a key antimicrobial oxidant produced in the respiratory tract. We discovered that the flavoprotein disulfide reductase (FDR) MerA protects S. aureus from this oxidant by functioning as a HOSCN reductase, with its deletion sensitizing bacteria to HOSCN. Crystal structures of homodimeric MerA (2.4 Å) with a Cys43 -Cys48 intramolecular disulfide, and reduced MerACys43 S (1.6 Å) showed the FAD cofactor close to the active site, supporting that MerA functions as a group I FDR. MerA is controlled by the redox-sensitive repressor HypR, which we show to be oxidized to intermolecular disulfides under HOSCN stress, resulting in its inactivation and derepression of merA transcription to promote HOSCN tolerance. Our study highlights the HOSCN tolerance of S. aureus and characterizes the structure and function of MerA as a major HOSCN defense mechanism. Crippling the capacity to respond to HOSCN may be a novel strategy for treating S. aureus infections.
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Affiliation(s)
- Heather L Shearer
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Vu V Loi
- Freie Universität Berlin, Institute of Biology-Microbiology, Berlin, Germany
| | - Paul Weiland
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Center for Tumor Biology and Immunology, Department of Medicine, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Institute of Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Haike Antelmann
- Freie Universität Berlin, Institute of Biology-Microbiology, Berlin, Germany
| | - Nina Dickerhof
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
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12
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M S, N RP, Rajendrasozhan S. Bacterial redox response factors in the management of environmental oxidative stress. World J Microbiol Biotechnol 2022; 39:11. [PMID: 36369499 DOI: 10.1007/s11274-022-03456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Bacteria evolved to survive in the available environmental chemosphere via several cellular mechanisms. A rich pool of antioxidants and stress regulators plays a significant role in the survival of bacteria in unfavorable environmental conditions. Most of the microbes exhibit resistant phenomena in toxic environment niches. Naturally, bacteria possess efficient thioredoxin reductase, glutaredoxin, and peroxiredoxin redox systems to handle environmental oxidative stress. Further, an array of transcriptional regulators senses the oxidative stress conditions. Transcription regulators, such as OxyR, SoxRS, PerR, UspA, SsrB, MarA, OhrR, SarZ, etc., sense and transduce bacterial oxidative stress responses. The redox-sensitive transcription regulators continuously recycle the utilized antioxidant enzymes during oxidative stress. These regulators promote the expression of antioxidant enzymes such as superoxide dismutase, catalase, and peroxides that overcome oxidative insults. Therefore, the transcriptional regulations maintain steady-state activities of antioxidant enzymes representing the resistance against host cell/environmental oxidative insults. Further, the redox system provides reducing equivalents to synthesize biomolecules, thereby contributing to cellular repair mechanisms. The inactive transcriptional regulators in the undisturbed cells are activated by oxidative stress. The oxidized transcriptional regulators modulate the expression of antioxidant and cellular repair enzymes to survive in extreme environmental conditions. Therefore, targeting these antioxidant systems and response regulators could alter cellular redox homeostasis. This review presents the mechanisms of different redox systems that favor bacterial survival in extreme environmental oxidative stress conditions.
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Affiliation(s)
- Sudharsan M
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, Chidambaram, Tamil Nadu, 608 002, India
| | - Rajendra Prasad N
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, Chidambaram, Tamil Nadu, 608 002, India.
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13
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Partipilo M, Yang G, Mascotti ML, Wijma HJ, Slotboom DJ, Fraaije MW. A conserved sequence motif in the Escherichia coli soluble FAD-containing pyridine nucleotide transhydrogenase is important for reaction efficiency. J Biol Chem 2022; 298:102304. [PMID: 35933012 PMCID: PMC9460512 DOI: 10.1016/j.jbc.2022.102304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/06/2022] Open
Abstract
Soluble pyridine nucleotide transhydrogenases (STHs) are flavoenzymes involved in the redox homeostasis of the essential cofactors NAD(H) and NADP(H). They catalyze the reversible transfer of reducing equivalents between the two nicotinamide cofactors. The soluble transhydrogenase from Escherichia coli (SthA) has found wide use in both in vivo and in vitro applications to steer reducing equivalents toward NADPH-requiring reactions. However, mechanistic insight into SthA function is still lacking. In this work, we present a biochemical characterization of SthA, focusing for the first time on the reactivity of the flavoenzyme with molecular oxygen. We report on oxidase activity of SthA that takes place both during transhydrogenation and in the absence of an oxidized nicotinamide cofactor as an electron acceptor. We find that this reaction produces the reactive oxygen species hydrogen peroxide and superoxide anion. Furthermore, we explore the evolutionary significance of the well-conserved CXXXXT motif that distinguishes STHs from the related family of flavoprotein disulfide reductases in which a CXXXXC motif is conserved. Our mutational analysis revealed the cysteine and threonine combination in SthA leads to better coupling efficiency of transhydrogenation and reduced reactive oxygen species release compared to enzyme variants with mutated motifs. These results expand our mechanistic understanding of SthA by highlighting reactivity with molecular oxygen and the importance of the evolutionarily conserved sequence motif.
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Affiliation(s)
- Michele Partipilo
- Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Guang Yang
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Maria Laura Mascotti
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Hein J Wijma
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands.
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands.
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14
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Gerber JL, Köhler S, Peschek J. Eukaryotic tRNA splicing - one goal, two strategies, many players. Biol Chem 2022; 403:765-778. [PMID: 35621519 DOI: 10.1515/hsz-2021-0402] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/10/2022] [Indexed: 12/28/2022]
Abstract
Transfer RNAs (tRNAs) are transcribed as precursor molecules that undergo several maturation steps before becoming functional for protein synthesis. One such processing mechanism is the enzyme-catalysed splicing of intron-containing pre-tRNAs. Eukaryotic tRNA splicing is an essential process since intron-containing tRNAs cannot fulfil their canonical function at the ribosome. Splicing of pre-tRNAs occurs in two steps: The introns are first excised by a tRNA-splicing endonuclease and the exons are subsequently sealed by an RNA ligase. An intriguing complexity has emerged from newly identified tRNA splicing factors and their interplay with other RNA processing pathways during the past few years. This review summarises our current understanding of eukaryotic tRNA splicing and the underlying enzyme machinery. We highlight recent structural advances and how they have shaped our mechanistic understanding of tRNA splicing in eukaryotic cells. A special focus lies on biochemically distinct strategies for exon-exon ligation in fungi versus metazoans.
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Affiliation(s)
- Janina L Gerber
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
| | - Sandra Köhler
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
| | - Jirka Peschek
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany
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15
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Fata F, Gencheva R, Cheng Q, Lullo R, Ardini M, Silvestri I, Gabriele F, Ippoliti R, Bulman CA, Sakanari JA, Williams DL, Arnér ESJ, Angelucci F. Biochemical and structural characterizations of thioredoxin reductase selenoproteins of the parasitic filarial nematodes Brugia malayi and Onchocerca volvulus. Redox Biol 2022; 51:102278. [PMID: 35276442 PMCID: PMC8914392 DOI: 10.1016/j.redox.2022.102278] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 01/21/2023] Open
Abstract
Enzymes in the thiol redox systems of microbial pathogens are promising targets for drug development. In this study we characterized the thioredoxin reductase (TrxR) selenoproteins from Brugia malayi and Onchocerca volvulus, filarial nematode parasites and causative agents of lymphatic filariasis and onchocerciasis, respectively. The two filarial enzymes showed similar turnover numbers and affinities for different thioredoxin (Trx) proteins, but with a clear preference for the autologous Trx. Human TrxR1 (hTrxR1) had a high and similar specific activity versus the human and filarial Trxs, suggesting that, in vivo, hTrxR1 could possibly be the reducing agent of parasite Trxs once they are released into the host. Both filarial TrxRs were efficiently inhibited by auranofin and by a recently described inhibitor of human TrxR1 (TRi-1), but not as efficiently by the alternative compound TRi-2. The enzyme from B. malayi was structurally characterized also in complex with NADPH and auranofin, producing the first crystallographic structure of a nematode TrxR. The protein represents an unusual fusion of a mammalian-type TrxR protein architecture with an N-terminal glutaredoxin-like (Grx) domain lacking typical Grx motifs. Unlike thioredoxin glutathione reductases (TGRs) found in platyhelminths and mammals, which are also Grx-TrxR domain fusion proteins, the TrxRs from the filarial nematodes lacked glutathione disulfide reductase and Grx activities. The structural determinations revealed that the Grx domain of TrxR from B. malayi contains a cysteine (C22), conserved in TrxRs from clade IIIc nematodes, that directly interacts with the C-terminal cysteine-selenocysteine motif of the homo-dimeric subunit. Interestingly, despite this finding we found that altering C22 by mutation to serine did not affect enzyme catalysis. Thus, although the function of the Grx domain in these filarial TrxRs remains to be determined, the results obtained provide insights on key properties of this important family of selenoprotein flavoenzymes that are potential drug targets for treatment of filariasis.
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Affiliation(s)
- Francesca Fata
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Radosveta Gencheva
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Rachel Lullo
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Matteo Ardini
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Ilaria Silvestri
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Federica Gabriele
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Rodolfo Ippoliti
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy
| | - Christina A Bulman
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Judy A Sakanari
- Dept. of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - David L Williams
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden; Department of Selenoprotein Research, National Institute of Oncology, 1122, Budapest, Hungary
| | - Francesco Angelucci
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy.
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16
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Ran M, Li Q, Xin Y, Ma S, Zhao R, Wang M, Xun L, Xia Y. Rhodaneses minimize the accumulation of cellular sulfane sulfur to avoid disulfide stress during sulfide oxidation in bacteria. Redox Biol 2022; 53:102345. [PMID: 35653932 PMCID: PMC9163753 DOI: 10.1016/j.redox.2022.102345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 10/27/2022] Open
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17
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Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance. Antioxidants (Basel) 2022; 11:antiox11030561. [PMID: 35326211 PMCID: PMC8945050 DOI: 10.3390/antiox11030561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 12/10/2022] Open
Abstract
Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.
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18
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Pourzand C, Albieri-Borges A, Raczek NN. Shedding a New Light on Skin Aging, Iron- and Redox-Homeostasis and Emerging Natural Antioxidants. Antioxidants (Basel) 2022; 11:471. [PMID: 35326121 PMCID: PMC8944509 DOI: 10.3390/antiox11030471] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 12/10/2022] Open
Abstract
Reactive oxygen species (ROS) are necessary for normal cell signaling and the antimicrobial defense of the skin. However excess production of ROS can disrupt the cellular redox balance and overwhelm the cellular antioxidant (AO) capacity, leading to oxidative stress. In the skin, oxidative stress plays a key role in driving both extrinsic and intrinsic aging. Sunlight exposure has also been a major contributor to extrinsic photoaging of the skin as its oxidising components disrupt both redox- and iron-homeostasis, promoting oxidative damage to skin cells and tissue constituents. Upon oxidative insults, the interplay between excess accumulation of ROS and redox-active labile iron (LI) and its detrimental consequences to the skin are often overlooked. In this review we have revisited the oxidative mechanisms underlying skin damage and aging by focussing on the concerted action of ROS and redox-active LI in the initiation and progression of intrinsic and extrinsic skin aging processes. Based on these, we propose to redefine the selection criteria for skin antiaging and photoprotective ingredients to include natural antioxidants (AOs) exhibiting robust redox-balancing and/or iron-chelating properties. This would promote the concept of natural-based or bio-inspired bifunctional anti-aging and photoprotective ingredients for skincare and sunscreen formulations with both AO and iron-chelating properties.
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Affiliation(s)
- Charareh Pourzand
- Medicines Design, Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, UK
- Medicines Development, Centre for Therapeutic Innovation, University of Bath, Bath BA2 7AY, UK
| | - Andrea Albieri-Borges
- Research and Development, ASEA LLC., Pleasant Grove, UT 84062, USA; (A.A.-B.); (N.N.R.)
| | - Nico N. Raczek
- Research and Development, ASEA LLC., Pleasant Grove, UT 84062, USA; (A.A.-B.); (N.N.R.)
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19
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Identification and Characterization of a Novel Soluble Pyridine Nucleotide Transhydrogenase from Streptomyces avermitilis. Curr Microbiol 2021; 79:32. [PMID: 34931264 DOI: 10.1007/s00284-021-02727-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/25/2021] [Indexed: 10/19/2022]
Abstract
Soluble pyridine nucleotide transhydrogenase (STH) transfers hydride between NADH and NADPH to maintain redox balance. In the present study, the sth gene from Gram-positive bacterium Streptomyces avermitilis (SaSTH) was expressed in Escherichia coli, and the recombinant STH protein was purified to homogeneity. Activity assays indicated that SaSTH was able to catalyze transhydrogenase reactions by using NADH or NADPH as reductants and thio-NAD+ as an oxidant. The apparent Km value for NADPH (74.5 μM) was lower than that for NADH (104.0 μM) and the apparent kcat/Km for NADPH (2704.7 mM-1 s-1) was higher than that for NADH (1129.8 mM-1 s-1). SaSTH showed optimal activity at 25 °C and at a pH of 6.2. Heat-inactivation studies revealed that SaSTH remained stable below 55 °C and that approximately 50% activity was preserved at 57 °C for 20 min. Analyses also showed that SaSTH activity was inhibited by divalent ions, particularly Co2+, Ni2+, and Zn2+. In addition, the transhydrogenase activity of SaSTH was inhibited by ATP and strongly stimulated by ADP and AMP. In summary, we characterized a recombinant enzyme exhibiting STH activity from Gram-positive bacteria for the first time. Our findings provide new options for cofactor engineering and industrial biocatalytic processes.
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20
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Savio LEB, Leite-Aguiar R, Alves VS, Coutinho-Silva R, Wyse ATS. Purinergic signaling in the modulation of redox biology. Redox Biol 2021; 47:102137. [PMID: 34563872 PMCID: PMC8479832 DOI: 10.1016/j.redox.2021.102137] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 01/07/2023] Open
Abstract
Purinergic signaling is a cell communication pathway mediated by extracellular nucleotides and nucleosides. Tri- and diphosphonucleotides are released in physiological and pathological circumstances activating purinergic type 2 receptors (P2 receptors): P2X ion channels and P2Y G protein-coupled receptors. The activation of these receptors triggers the production of reactive oxygen and nitrogen species and alters antioxidant defenses, modulating the redox biology of cells. The activation of P2 receptors is controlled by ecto-enzymes named ectonucleotidases, E-NTPDase1/CD39 and ecto-5'-nucleotidase/CD73) being the most relevant. The first enzyme hydrolyzes adenosine triphosphate (ATP) and adenosine diphosphate (ADP) into adenosine monophosphate (AMP), and the second catalyzes the hydrolysis of AMP to adenosine. The activity of these enzymes is diminished by oxidative stress. Adenosine actives P1 G-coupled receptors that, in general, promote the maintenance of redox hemostasis by decreasing reactive oxygen species (ROS) production and increase antioxidant enzymes. Intracellular purine metabolism can also contribute to ROS generation via xanthine oxidase activity, which converts hypoxanthine into xanthine, and finally, uric acid. In this review, we describe the mechanisms of redox biology modulated by purinergic signaling and how this signaling may be affected by disturbances in the redox homeostasis of cells.
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Affiliation(s)
- Luiz Eduardo Baggio Savio
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Raíssa Leite-Aguiar
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vinícius Santos Alves
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robson Coutinho-Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Angela T S Wyse
- Laboratório de Neuroproteção e Doenças Metabólicas, Departamento de Bioquímica, ICBS, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
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21
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Betts HD, Neville SL, McDevitt CA, Sumby CJ, Harris HH. The biochemical fate of Ag + ions in Staphylococcus aureus, Escherichia coli, and biological media. J Inorg Biochem 2021; 225:111598. [PMID: 34517168 DOI: 10.1016/j.jinorgbio.2021.111598] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/03/2021] [Accepted: 08/28/2021] [Indexed: 01/16/2023]
Abstract
Silver is commonly included in a range of household and medical items to provide bactericidal action. Despite this, the chemical fate of the metal in both mammalian and bacterial systems remains poorly understood. Here, we applied a metallomics approach using X-ray absorption spectroscopy (XAS) and size-exclusion chromatography hyphenated with inductively coupled plasma mass spectrometry (SEC-ICP-MS) to advance our understanding of the biochemical fate of silver ions in bacterial culture and cells, and the chemistry associated with these interactions. When silver ions were added to lysogeny broth, silver was exclusively associated with moderately-sized species (~30 kDa) and bound by thiolate ligands. In two representative bacterial pathogens cultured in lysogeny broth including sub-lethal concentrations of ionic silver, silver was found in cells to be predominantly coordinated by thiolate species. The silver biomacromolecule-binding profile in Staphylococcus aureus and Escherichia coli was complex, with silver bound by a range of species spanning from 20 kDa to >1220 kDa. In bacterial cells, silver was nonuniformly colocalised with copper-bound proteins, suggesting that cellular copper processing may, in part, confuse silver for nutrient copper. Notably, in the treated cells, silver was not detected bound to low molecular weight compounds such as glutathione or bacillithiol.
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Affiliation(s)
- Harley D Betts
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia
| | - Stephanie L Neville
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria 3000, Australia
| | - Christopher A McDevitt
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria 3000, Australia
| | - Christopher J Sumby
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia
| | - Hugh H Harris
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia,.
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22
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Čėnas N, Nemeikaitė-Čėnienė A, Kosychova L. Single- and Two-Electron Reduction of Nitroaromatic Compounds by Flavoenzymes: Mechanisms and Implications for Cytotoxicity. Int J Mol Sci 2021; 22:ijms22168534. [PMID: 34445240 PMCID: PMC8395237 DOI: 10.3390/ijms22168534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Nitroaromatic compounds (ArNO2) maintain their importance in relation to industrial processes, environmental pollution, and pharmaceutical application. The manifestation of toxicity/therapeutic action of nitroaromatics may involve their single- or two-electron reduction performed by various flavoenzymes and/or their physiological redox partners, metalloproteins. The pivotal and still incompletely resolved questions in this area are the identification and characterization of the specific enzymes that are involved in the bioreduction of ArNO2 and the establishment of their contribution to cytotoxic/therapeutic action of nitroaromatics. This review addresses the following topics: (i) the intrinsic redox properties of ArNO2, in particular, the energetics of their single- and two-electron reduction in aqueous medium; (ii) the mechanisms and structure-activity relationships of reduction in ArNO2 by flavoenzymes of different groups, dehydrogenases-electrontransferases (NADPH:cytochrome P-450 reductase, ferredoxin:NADP(H) oxidoreductase and their analogs), mammalian NAD(P)H:quinone oxidoreductase, bacterial nitroreductases, and disulfide reductases of different origin (glutathione, trypanothione, and thioredoxin reductases, lipoamide dehydrogenase), and (iii) the relationships between the enzymatic reactivity of compounds and their activity in mammalian cells, bacteria, and parasites.
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Affiliation(s)
- Narimantas Čėnas
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
- Correspondence: ; Tel.: +370-5-223-4392
| | - Aušra Nemeikaitė-Čėnienė
- State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08406 Vilnius, Lithuania;
| | - Lidija Kosychova
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
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23
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Prussia GA, Shisler KA, Zadvornyy OA, Streit BR, DuBois JL, Peters JW. The unique Phe-His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S-C bond cleavage. J Biol Chem 2021; 297:100961. [PMID: 34265301 PMCID: PMC8358701 DOI: 10.1016/j.jbc.2021.100961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 12/02/2022] Open
Abstract
The 2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) enzyme is the only member of the disulfide oxidoreductase (DSOR) family of enzymes, which are important for reductively cleaving S-S bonds, to have carboxylation activity. 2-KPCC catalyzes the conversion of 2-ketopropyl-coenzyme M to acetoacetate, which is used as a carbon source, in a controlled reaction to exclude protons. A conserved His-Glu motif present in DSORs is key in the protonation step; however, in 2-KPCC, the dyad is substituted by Phe-His. Here, we propose that this difference is important for coupling carboxylation with C-S bond cleavage. We substituted the Phe-His dyad in 2-KPCC to be more DSOR like, replacing the phenylalanine with histidine (F501H) and the histidine with glutamate (H506E), and solved crystal structures of F501H and the double variant F501H_H506E. We found that F501 protects the enolacetone intermediate from protons and that the F501H variant strongly promotes protonation. We also provided evidence for the involvement of the H506 residue in stabilizing the developing charge during the formation of acetoacetate, which acts as a product inhibitor in the WT but not the H506E variant enzymes. Finally, we determined that the F501H substitution promotes a DSOR-like charge transfer interaction with flavin adenine dinucleotide, eliminating the need for cysteine as an internal base. Taken together, these results indicate that the 2-KPCC dyad is responsible for selectively promoting carboxylation and inhibiting protonation in the formation of acetoacetate.
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Affiliation(s)
- Gregory A Prussia
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Krista A Shisler
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Bennett R Streit
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.
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Structural perspectives on H 2S homeostasis. Curr Opin Struct Biol 2021; 71:27-35. [PMID: 34214926 DOI: 10.1016/j.sbi.2021.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/05/2021] [Accepted: 05/23/2021] [Indexed: 11/21/2022]
Abstract
The enzymes involved in H2S homeostasis regulate its production from sulfur-containing amino acids and its oxidation to thiosulfate and sulfate. Two gatekeepers in this homeostatic circuit are cystathionine beta-synthase, which commits homocysteine to cysteine, and sulfide quinone oxidoreductase, which commits H2S to oxidation via a mitochondrial pathway. Inborn errors at either locus affect sulfur metabolism, increasing homocysteine-derived H2S synthesis in the case of CBS deficiency and reducing complex IV activity in the case of SQOR deficiency. In this review, we focus on structural perspectives on the reaction mechanisms and regulation of these two enzymes, which are key to understanding H2S homeostasis in health and its dysregulation and potential targeting in disease.
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Molecular Basis for the Interactions of Human Thioredoxins with Their Respective Reductases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6621292. [PMID: 34122725 PMCID: PMC8189816 DOI: 10.1155/2021/6621292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/20/2021] [Accepted: 05/20/2021] [Indexed: 12/03/2022]
Abstract
The mammalian cytosolic thioredoxin (Trx) system consists of Trx1 and its reductase, the NADPH-dependent seleno-enzyme TrxR1. These proteins function as electron donor for metabolic enzymes, for instance in DNA synthesis, and the redox regulation of numerous processes. In this work, we analysed the interactions between these two proteins. We proposed electrostatic complementarity as major force controlling the formation of encounter complexes between the proteins and thus the efficiency of the subsequent electron transfer reaction. If our hypothesis is valid, formation of the encounter complex should be independent of the redox reaction. In fact, we were able to confirm that also a redox inactive mutant of Trx1 lacking both active site cysteinyl residues (C32,35S) binds to TrxR1 in a similar manner and with similar kinetics as the wild-type protein. We have generated a number of mutants with alterations in electrostatic properties and characterised their interaction with TrxR1 in kinetic assays. For human Trx1 and TrxR1, complementary electrostatic surfaces within the area covered in the encounter complex appear to control the affinity of the reductase for its substrate Trx. Electrostatic compatibility was even observed in areas that do not form direct molecular interactions in the encounter complex, and our results suggest that the electrostatic complementarity in these areas influences the catalytic efficiency of the reduction. The human genome encodes ten cytosolic Trx-like or Trx domain-containing proteins. In agreement with our hypothesis, the proteins that have been characterised as TrxR1 substrates also show the highest similarity in their electrostatic properties.
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Zhang J, Duan D, Osama A, Fang J. Natural Molecules Targeting Thioredoxin System and Their Therapeutic Potential. Antioxid Redox Signal 2021; 34:1083-1107. [PMID: 33115246 DOI: 10.1089/ars.2020.8213] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Significance: Thioredoxin (Trx) and thioredoxin reductase are two core members of the Trx system. The system bridges the gap between the universal reducing equivalent NADPH and various biological molecules and plays an essential role in maintaining cellular redox homeostasis and regulating multiple cellular redox signaling pathways. Recent Advance: In recent years, the Trx system has been well documented as an important regulator of many diseases, especially tumorigenesis. Thus, the development of potential therapeutic molecules targeting the system is of great significance for disease treatment. Critical Issues: We herein first discuss the physiological functions of the Trx system and the role that the Trx system plays in various diseases. Then, we focus on the introduction of natural small molecules with potential therapeutic applications, especially the anticancer activity, and review their mechanisms of pharmacological actions via interfering with the Trx system. Finally, we further discuss several natural molecules that harbor therapeutic potential and have entered different clinical trials. Future Directions: Further studies on the functions of the Trx system in multiple diseases will not only improve our understanding of the pathogenesis of many human disorders but also help develop novel therapeutic strategies against these diseases. Antioxid. Redox Signal. 34, 1083-1107.
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Affiliation(s)
- Junmin Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, and School of Pharmacy, Lanzhou University, Lanzhou, China
- Shaanxi Key Laboratory of Phytochemistry, Baoji University of Arts and Sciences, Baoji, China
| | - Dongzhu Duan
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, and School of Pharmacy, Lanzhou University, Lanzhou, China
- Shaanxi Key Laboratory of Phytochemistry, Baoji University of Arts and Sciences, Baoji, China
| | - Alsiddig Osama
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, and School of Pharmacy, Lanzhou University, Lanzhou, China
- Shaanxi Key Laboratory of Phytochemistry, Baoji University of Arts and Sciences, Baoji, China
| | - Jianguo Fang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, and School of Pharmacy, Lanzhou University, Lanzhou, China
- Shaanxi Key Laboratory of Phytochemistry, Baoji University of Arts and Sciences, Baoji, China
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Asanović I, Strandback E, Kroupova A, Pasajlic D, Meinhart A, Tsung-Pin P, Djokovic N, Anrather D, Schuetz T, Suskiewicz MJ, Sillamaa S, Köcher T, Beveridge R, Nikolic K, Schleiffer A, Jinek M, Hartl M, Clausen T, Penninger J, Macheroux P, Weitzer S, Martinez J. The oxidoreductase PYROXD1 uses NAD(P) + as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response. Mol Cell 2021; 81:2520-2532.e16. [PMID: 33930333 DOI: 10.1016/j.molcel.2021.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/09/2021] [Accepted: 04/09/2021] [Indexed: 12/19/2022]
Abstract
The tRNA ligase complex (tRNA-LC) splices precursor tRNAs (pre-tRNA), and Xbp1-mRNA during the unfolded protein response (UPR). In aerobic conditions, a cysteine residue bound to two metal ions in its ancient, catalytic subunit RTCB could make the tRNA-LC susceptible to oxidative inactivation. Here, we confirm this hypothesis and reveal a co-evolutionary association between the tRNA-LC and PYROXD1, a conserved and essential oxidoreductase. We reveal that PYROXD1 preserves the activity of the mammalian tRNA-LC in pre-tRNA splicing and UPR. PYROXD1 binds the tRNA-LC in the presence of NAD(P)H and converts RTCB-bound NAD(P)H into NAD(P)+, a typical oxidative co-enzyme. However, NAD(P)+ here acts as an antioxidant and protects the tRNA-LC from oxidative inactivation, which is dependent on copper ions. Genetic variants of PYROXD1 that cause human myopathies only partially support tRNA-LC activity. Thus, we establish the tRNA-LC as an oxidation-sensitive metalloenzyme, safeguarded by the flavoprotein PYROXD1 through an unexpected redox mechanism.
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Affiliation(s)
- Igor Asanović
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Emilia Strandback
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Alena Kroupova
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Djurdja Pasajlic
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Pai Tsung-Pin
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; AnnJi Pharmaceutical, Taipei, Taiwan
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Dorothea Anrather
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Thomas Schuetz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Internal Medicine III (Cardiology and Angiology), Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Marcin Józef Suskiewicz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria; Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Sirelin Sillamaa
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Thomas Köcher
- Vienna BioCenter Core Facilities, Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Rebecca Beveridge
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria; Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, G1 1XL Glasgow, UK
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Markus Hartl
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Josef Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Medical Genetics, Life Science Institute, University of British Columbia, C201 - 4500 Oak Street, V6H 3N1 Vancouver, BC, Canada
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria.
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria.
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28
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Landry AP, Ballou DP, Banerjee R. Hydrogen Sulfide Oxidation by Sulfide Quinone Oxidoreductase. Chembiochem 2021; 22:949-960. [PMID: 33080111 PMCID: PMC7969369 DOI: 10.1002/cbic.202000661] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/19/2020] [Indexed: 02/05/2023]
Abstract
Hydrogen sulfide (H2 S) is an environmental toxin and a heritage of ancient microbial metabolism that has stimulated new interest following its discovery as a neuromodulator. While many physiological responses have been attributed to low H2 S levels, higher levels inhibit complex IV in the electron transport chain. To prevent respiratory poisoning, a dedicated set of enzymes that make up the mitochondrial sulfide oxidation pathway exists to clear H2 S. The committed step in this pathway is catalyzed by sulfide quinone oxidoreductase (SQOR), which couples sulfide oxidation to coenzyme Q10 reduction in the electron transport chain. The SQOR reaction prevents H2 S accumulation and generates highly reactive persulfide species as products; these can be further oxidized or can modify cysteine residues in proteins by persulfidation. Here, we review the kinetic and structural characteristics of human SQOR, and how its unconventional redox cofactor configuration and substrate promiscuity lead to sulfide clearance and potentially expand the signaling potential of H2 S. This dual role of SQOR makes it a promising target for H2 S-based therapeutics.
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Affiliation(s)
- Aaron P. Landry
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - David P. Ballou
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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29
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Liu Y, Wang H, Li S, Zhang Y, Cheng X, Xiang W, Wang X. Engineering of primary metabolic pathways for titer improvement of milbemycins in Streptomyces bingchenggensis. Appl Microbiol Biotechnol 2021; 105:1875-1887. [PMID: 33564920 DOI: 10.1007/s00253-021-11164-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022]
Abstract
Milbemycins are used commercially as insect repellents and acaricides; however, their high cost remains a significant challenge to commercial production. Hence, improving the titer of milbemycins for commercial application is an urgent priority. The present study aimed to effectively increase the titer of milbemycins using a combination of genome re-sequencing and metabolic engineering. First, 133 mutation sites were identified by genome re-sequencing in the mutagenized high-yielding strain BC04. Among them, three modifiable candidate genes (sbi_04868 encoding citrate synthase, sbi_06921 and sbi_06922 encoding alpha and beta subunits of acetyl-CoA carboxylase, and sbi_04683 encoding carbon uptake system gluconate transporter) related to primary metabolism were screened and identified. Next, the DNase-deactivated Cpf1-based integrative CRISPRi system was used in S. bingchenggensis to downregulate the transcription level of gene sbi_04868. Then, overexpression of the potential targets sbi_06921-06922 and sbi_04683 further facilitated milbemycin biosynthesis. Finally, those candidate genes were engineered to produce strains with combinatorial downregulation and overexpression, which resulted in the titer of milbemycin A3/A4 increased by 27.6% to 3164.5 mg/L. Our research not only identified three genes in S. bingchenggensis that are closely related to the production of milbemycins, but also offered an efficient engineering strategy to improve the titer of milbemycins using genome re-sequencing. KEY POINTS: • We compared the genomes of two strains with different titers of milbemycins. • We found three genes belonging to primary metabolism influence milbemycin production. • We improved titer of milbemycins by a combinatorial engineering of three targets.
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Affiliation(s)
- Yuqing Liu
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Haiyan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yanyan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xu Cheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Wensheng Xiang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Xiangjing Wang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.
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30
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Castillo-Villanueva A, Reyes-Vivas H, Oria-Hernández J. Kinetic stability of the water-forming NADH oxidase from Giardia lamblia: implications for biotechnological processes. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1987325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
| | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Ciudad de México, México
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Ciudad de México, México
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31
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Cao Z, Meng R, Wang P, Zhu G. Heterologous expression and enzymatic identification of two novel soluble pyridine nucleotide transhydrogenases from Acidobacteria bacterium KBS 146 and Nocardia jiangxiensis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1988708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Zhengyu Cao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Rui Meng
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
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32
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Tsunematsu Y, Maeda N, Sato M, Hara K, Hashimoto H, Watanabe K, Hertweck C. Specialized Flavoprotein Promotes Sulfur Migration and Spiroaminal Formation in Aspirochlorine Biosynthesis. J Am Chem Soc 2020; 143:206-213. [PMID: 33351612 DOI: 10.1021/jacs.0c08879] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epidithiodiketopiperazines (ETPs) are a class of ecologically and medicinally important cyclodipeptides bearing a reactive transannular disulfide bridge. Aspirochlorine, an antifungal and toxic ETP isolated from Aspergillus oryzae used in sake brewing, deviates from the common ETP scaffold owing to its unusual ring-enlarged disulfide bridge linked to a spiroaminal ring system. Although this disulfide ring system is implicated in the biological activity of ETPs the biochemical basis for this derailment has remained a mystery. Here we report the discovery of a novel oxidoreductase (AclR) that represents the first-in-class enzyme catalyzing both a carbon-sulfur bond migration and spiro-ring formation, and that the acl pathway involves a cryptic acetylation as a prerequisite for the rearrangement. Genetic screening in A. oryzae identified aclR as the candidate for the complex biotransformation, and the aclR-deficient mutant provided the biosynthetic intermediate, unexpectedly harboring an acetyl group. In vitro assays showed that AclR alone promotes 1,2-sulfamyl migration, elimination of the acetoxy group, and spiroaminal formation. AclR features a thioredoxin oxidoreductase fold with a noncanonical CXXH motif that is distinct from the CXXC in the disulfide forming oxidase for the ETP biosynthesis. Crystallographic and mutational analyses of AclR revealed that the CXXH motif is crucial for catalysis, whereas the flavin-adenine dinucleotide is required as a support of the protein fold, and not as a redox cofactor. AclR proved to be a suitable bioinformatics handle to discover a number of related fungal gene clusters that potentially code for the biosynthesis of derailed ETP compounds. Our results highlight a specialized role of the thioredoxin oxidoreductase family enzyme in the ETP pathway and expand the chemical diversity of small molecules bearing an aberrant disulfide pharmacophore.
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Affiliation(s)
- Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.,Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Naoya Maeda
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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33
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Harasgama JC, Kasthuriarachchi TDW, Kwon H, Wan Q, Lee J. Molecular and functional characterization of a mitochondrial glutathione reductase homolog from redlip mullet (Liza haematocheila): Disclosing its antioxidant properties in the fish immune response mechanism. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 113:103785. [PMID: 32735957 DOI: 10.1016/j.dci.2020.103785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/28/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Glutathione reductase (GSHR) is a biologically important enzyme involved in the conversion of oxidized glutathione (GSSG) into its reduced form, reduced glutathione (GSH), with the catalytic activity of NADPH. Most animals and aquatic organisms, including fish, possess high levels of this enzyme system to neutralize oxidative stress in cells. The current study was conducted to broaden our knowledge of GSHR in fish by identifying a mitochondrial isoform of this enzyme (LhGSHRm) in redlip mullet, Liza haematocheila, and clarifying its structure and function. The complete open reading frame of LhGSHRm consists of 1527 base pairs, encoding 508 amino acids, with a predicted molecular weight of 55.43 kDa. Multiple sequence alignment revealed the conservation of important amino acids in this fish. Phylogenetic analysis demonstrated the closest evolutionary relationship between LhGSHRm and other fish GSHRm counterparts. In tissue distribution analysis, the highest mRNA expression of LhGSHRm was observed in the gill tissue under normal physiological conditions. Following pathogenic challenges, the LhGSHRm transcription level was upregulated in a time-dependent manner in the gill and liver tissues, which may modulate the immune reaction against pathogens. rLhGSHRm showed considerable glutathione reductase activity in an enzyme assay. Further, the biological activity of rLhGSHRm in balancing cellular oxidative stress was observed in both disk diffusion and DPPH assays. Collectively, these results support that LhGSHRm has profound effects on modulating the immune reaction in fish to sustain precise redox homeostasis.
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Affiliation(s)
- J C Harasgama
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, Self-Governing Province, 63333, Republic of Korea
| | - T D W Kasthuriarachchi
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, Self-Governing Province, 63333, Republic of Korea
| | - Hyukjae Kwon
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, Self-Governing Province, 63333, Republic of Korea
| | - Qiang Wan
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, Self-Governing Province, 63333, Republic of Korea.
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, Self-Governing Province, 63333, Republic of Korea.
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34
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Linzner N, Loi VV, Fritsch VN, Antelmann H. Thiol-based redox switches in the major pathogen Staphylococcus aureus. Biol Chem 2020; 402:333-361. [PMID: 33544504 DOI: 10.1515/hsz-2020-0272] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/05/2020] [Indexed: 12/15/2022]
Abstract
Staphylococcus aureus is a major human pathogen, which encounters reactive oxygen, nitrogen, chlorine, electrophile and sulfur species (ROS, RNS, RCS, RES and RSS) by the host immune system, during cellular metabolism or antibiotics treatments. To defend against redox active species and antibiotics, S. aureus is equipped with redox sensing regulators that often use thiol switches to control the expression of specific detoxification pathways. In addition, the maintenance of the redox balance is crucial for survival of S. aureus under redox stress during infections, which is accomplished by the low molecular weight (LMW) thiol bacillithiol (BSH) and the associated bacilliredoxin (Brx)/BSH/bacillithiol disulfide reductase (YpdA)/NADPH pathway. Here, we present an overview of thiol-based redox sensors, its associated enzymatic detoxification systems and BSH-related regulatory mechanisms in S. aureus, which are important for the defense under redox stress conditions. Application of the novel Brx-roGFP2 biosensor provides new insights on the impact of these systems on the BSH redox potential. These thiol switches of S. aureus function in protection against redox active desinfectants and antimicrobials, including HOCl, the AGXX® antimicrobial surface coating, allicin from garlic and the naphthoquinone lapachol. Thus, thiol switches could be novel drug targets for the development of alternative redox-based therapies to combat multi-drug resistant S. aureus isolates.
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Affiliation(s)
- Nico Linzner
- Freie Universität Berlin, Institute of Biology-Microbiology, Königin-Luise-Straße 12-16, D-14195Berlin, Germany
| | - Vu Van Loi
- Freie Universität Berlin, Institute of Biology-Microbiology, Königin-Luise-Straße 12-16, D-14195Berlin, Germany
| | - Verena Nadin Fritsch
- Freie Universität Berlin, Institute of Biology-Microbiology, Königin-Luise-Straße 12-16, D-14195Berlin, Germany
| | - Haike Antelmann
- Freie Universität Berlin, Institute of Biology-Microbiology, Königin-Luise-Straße 12-16, D-14195Berlin, Germany
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35
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Duzs Á, Miklovics N, Paragi G, Rákhely G, Tóth A. Insights into the catalytic mechanism of type VI sulfide:quinone oxidoreductases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148337. [PMID: 33202220 DOI: 10.1016/j.bbabio.2020.148337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/09/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Sulfide oxidation is catalyzed by ancient membrane-bound sulfide:quinone oxidoreductases (SQR) which are classified into six different types. For catalysis of sulfide oxidation, all SQRs require FAD cofactor and a redox-active centre in the active site, usually formed between conserved essential cysteines. SQRs of different types have variation in the number and position of cysteines, highlighting the potential for diverse catalytic mechanisms. The photosynthetic purple sulfur bacterium, Thiocapsa roseopersicina contains a type VI SQR enzyme (TrSqrF) having unusual catalytic parameters and four cysteines likely involved in the catalysis. Site-directed mutagenesis was applied to identify the role of cysteines in the catalytic process of TrSqrF. Based on biochemical and kinetic characterization of these TrSqrF variants, Cys121 is identified as crucial for enzyme activity. The cofactor is covalently bound via a heterodisulfide bridge between Cys121 and the C8M group of FAD. Mutation of another cysteine present in all SQRs (Cys332) causes remarkably decreased enzyme activity (14.6% of wild type enzyme) proving important, but non-essential role of this residue in enzyme catalysis. The sulfhydril-blocking agent, iodoacetamide can irreversibly inactivate TrSqrF but only if substrates are present and the enzyme is actively catalyzing its reaction. When the enzyme is inhibited by iodoacetamide, the FAD cofactor is released. The inhibition studies support a mechanism that entails opening and reforming of the heterodisulfide bridge during the catalytic cycle of TrSqrF. Our study thus reports the first detailed structure-function analysis of a type VI SQR enzyme which enables the proposal of a distinct mechanism of sulfide oxidation for this class.
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Affiliation(s)
- Ágnes Duzs
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
| | - Nikolett Miklovics
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary; Doctoral School in Biology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
| | - Gábor Paragi
- Institute of Physics, University of Pécs, Ifjúság útja 6., H-7624 Pécs, Hungary; MTA-SZTE Biomimetic Systems Research Group, Department of Medical Chemistry, University of Szeged, Dóm square 8, H-6720 Szeged, Hungary
| | - Gábor Rákhely
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary.
| | - András Tóth
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
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36
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Rubredoxin from the green sulfur bacterium Chlorobaculum tepidum donates a redox equivalent to the flavodiiron protein in an NAD(P)H dependent manner via ferredoxin-NAD(P) + oxidoreductase. Arch Microbiol 2020; 203:799-808. [PMID: 33051772 DOI: 10.1007/s00203-020-02079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 10/23/2022]
Abstract
The green sulfur bacterium, Chlorobaculum tepidum, is an anaerobic photoautotroph that performs anoxygenic photosynthesis. Although genes encoding rubredoxin (Rd) and a putative flavodiiron protein (FDP) were reported in the genome, a gene encoding putative NADH-Rd oxidoreductase is not identified. In this work, we expressed and purified the recombinant Rd and FDP and confirmed dioxygen reductase activity in the presence of ferredoxin-NAD(P)+ oxidoreductase (FNR). FNR from C. tepidum and Bacillus subtilis catalyzed the reduction of Rd at rates comparable to those reported for NADH-Rd oxidoreductases. Also, we observed substrate inhibition at high concentrations of NADPH similar to that observed with ferredoxins. In the presence of NADPH, B. subtilis FNR and Rd, FDP promoted dioxygen reduction at rates comparable to those reported for other bacterial FDPs. Taken together, our results suggest that Rd and FDP participate in the reduction of dioxygen in C. tepidum and that FNR can promote the reduction of Rd in this bacterium.
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Landry AP, Moon S, Bonanata J, Cho US, Coitiño EL, Banerjee R. Dismantling and Rebuilding the Trisulfide Cofactor Demonstrates Its Essential Role in Human Sulfide Quinone Oxidoreductase. J Am Chem Soc 2020; 142:14295-14306. [PMID: 32787249 DOI: 10.1021/jacs.0c06066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sulfide quinone oxidoreductase (SQOR) catalyzes the first step in sulfide clearance, coupling H2S oxidation to coenzyme Q reduction. Recent structures of human SQOR revealed a sulfur atom bridging the SQOR active site cysteines in a trisulfide configuration. Here, we assessed the importance of this cofactor using kinetic, crystallographic, and computational modeling approaches. Cyanolysis of SQOR proceeds via formation of an intense charge transfer complex that subsequently decays to eliminate thiocyanate. We captured a disulfanyl-methanimido thioate intermediate in the SQOR crystal structure, revealing how cyanolysis leads to reversible loss of SQOR activity that is restored in the presence of sulfide. Computational modeling and MD simulations revealed an ∼105-fold rate enhancement for nucleophilic addition of sulfide into the trisulfide versus a disulfide cofactor. The cysteine trisulfide in SQOR is thus critical for activity and provides a significant catalytic advantage over a cysteine disulfide.
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Affiliation(s)
- Aaron P Landry
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Sojin Moon
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Jenner Bonanata
- Laboratorio de Química Teórica y Computacional (LQTC), Instituto de Química Biológica, Facultad de Ciencias and Centro de Investigaciones Biomédicas (CeInBio), Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Uhn Soo Cho
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - E Laura Coitiño
- Laboratorio de Química Teórica y Computacional (LQTC), Instituto de Química Biológica, Facultad de Ciencias and Centro de Investigaciones Biomédicas (CeInBio), Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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38
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Heyes DJ, Lakavath B, Hardman SJO, Sakuma M, Hedison TM, Scrutton NS. Photochemical Mechanism of Light-Driven Fatty Acid Photodecarboxylase. ACS Catal 2020; 10:6691-6696. [PMID: 32905273 PMCID: PMC7469136 DOI: 10.1021/acscatal.0c01684] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/18/2020] [Indexed: 01/06/2023]
Abstract
![]()
Fatty
acid photodecarboxylase (FAP) is a promising target for the
production of biofuels and fine chemicals. It contains a flavin adenine
dinucleotide cofactor and catalyzes the blue-light-dependent decarboxylation
of fatty acids to generate the corresponding alkane. However, little
is known about the catalytic mechanism of FAP, or how light is used
to drive enzymatic decarboxylation. Here, we have used a combination
of time-resolved and cryogenic trapping UV–visible absorption
spectroscopy to characterize a red-shifted flavin intermediate observed
in the catalytic cycle of FAP. We show that this intermediate can
form below the “glass transition” temperature of proteins,
whereas the subsequent decay of the species proceeds only at higher
temperatures, implying a role for protein motions in the decay of
the intermediate. Solvent isotope effect measurements, combined with
analyses of selected site-directed variants of FAP, suggest that the
formation of the red-shifted flavin species is directly coupled with
hydrogen atom transfer from a nearby active site cysteine residue,
yielding the final alkane product. Our study suggests that this cysteine
residue forms a thiolate-flavin charge-transfer species, which is
assigned as the red-shifted flavin intermediate. Taken together, our
data provide insights into light-dependent decarboxylase mechanisms
catalyzed by FAP and highlight important considerations in the (re)design
of flavin-based photoenzymes.
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Affiliation(s)
- Derren J. Heyes
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Balaji Lakavath
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Samantha J. O. Hardman
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Tobias M. Hedison
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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Feng X, Guo K, Gao H. Plasticity of the peroxidase AhpC links multiple substrates to diverse disulfide-reducing pathways in Shewanella oneidensis. J Biol Chem 2020; 295:11118-11130. [PMID: 32532818 DOI: 10.1074/jbc.ra120.014010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/29/2020] [Indexed: 12/25/2022] Open
Abstract
AhpC is a bacterial representative of 2-Cys peroxiredoxins (Prxs) with broad substrate specificity and functional plasticity. However, details underpinning these two important attributes of AhpC remain unclear. Here, we studied the functions and mechanisms of regulation of AhpC in the facultative Gram-negative anaerobic bacterium Shewanella oneidensis, in which AhpC's physiological roles can be conveniently assessed through its suppression of a plating defect due to the genetic loss of a major catalase. We show that successful suppression can be achieved only when AhpC is produced in a dose- and time-dependent manner through a complex mechanism involving activation of the transcriptional regulator OxyR, transcription attenuation, and translation reduction. By analyzing AhpC truncation variants, we demonstrate that reactivity with organic peroxides (OPs) rather than H2O2 is resilient to mutagenesis, implying that OP reduction is the core catalytic function of AhpC. Intact AhpC could be recycled only by its cognate reductase AhpF, and AhpC variants lacking the Prx domain or the extreme C-terminal five residues became promiscuous electron acceptors from the thioredoxin reductase TrxR and the GSH reductase Gor in addition to AhpF, implicating an additional dimension to functional plasticity of AhpC. Finally, we show that the activity of S. oneidensis AhpC is less affected by mutations than that of its Escherichia coli counterpart. These findings suggest that the physiological roles of bacterial AhpCs are adapted to different oxidative challenges, depending on the organism, and that its functional plasticity is even more extensive than previously reported.
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Affiliation(s)
- Xue Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kailun Guo
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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40
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Baek Y, Kim J, Ahn J, Jo I, Hong S, Ryu S, Ha NC. Structure and function of the hypochlorous acid-induced flavoprotein RclA from Escherichia coli. J Biol Chem 2020; 295:3202-3212. [PMID: 31988242 DOI: 10.1074/jbc.ra119.011530] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/22/2020] [Indexed: 12/24/2022] Open
Abstract
In response to microbial invasion, the animal immune system generates hypochlorous acid (HOCl) that kills microorganisms in the oxidative burst. HOCl toxicity is amplified in the phagosome through import of the copper cation (Cu2+). In Escherichia coli and Salmonella, the transcriptional regulator RclR senses HOCl stress and induces expression of the RclA, -B, and -C proteins involved in bacterial defenses against oxidative stress. However, the structures and biochemical roles of the Rcl proteins remain to be elucidated. In this study, we first examined the role of the flavoprotein disulfide reductase (FDR) RclA in the survival of Salmonella in macrophage phagosomes, finding that RclA promotes Salmonella survival in macrophage vacuoles containing sublethal HOCl levels. To clarify the molecular mechanism, we determined the crystal structure of RclA from E. coli at 2.9 Å resolution. This analysis revealed that the structure of homodimeric RclA is similar to those of typical FDRs, exhibiting two conserved cysteine residues near the flavin ring of the cofactor flavin adenine dinucleotide (FAD). Of note, we observed that Cu2+ accelerated RclA-mediated oxidation of NADH, leading to a lowering of oxygen levels in vitro Compared with the RclA WT enzyme, substitution of the conserved cysteine residues lowered the specificity to Cu2+ or substantially increased the production of superoxide anion in the absence of Cu2+ We conclude that RclA-mediated lowering of oxygen levels could contribute to the inhibition of oxidative bursts in phagosomes. Our study sheds light on the molecular basis for how bacteria can survive HOCl stress in macrophages.
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Affiliation(s)
- Yeongjin Baek
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinwoo Kim
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsook Ahn
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Seokho Hong
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Sangryeol Ryu
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea.
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41
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Landry AP, Moon S, Kim H, Yadav PK, Guha A, Cho US, Banerjee R. A Catalytic Trisulfide in Human Sulfide Quinone Oxidoreductase Catalyzes Coenzyme A Persulfide Synthesis and Inhibits Butyrate Oxidation. Cell Chem Biol 2019; 26:1515-1525.e4. [PMID: 31591036 DOI: 10.1016/j.chembiol.2019.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/29/2019] [Accepted: 09/17/2019] [Indexed: 01/09/2023]
Abstract
Mitochondrial sulfide quinone oxidoreductase (SQR) catalyzes the oxidation of H2S to glutathione persulfide with concomitant reduction of CoQ10. We report herein that the promiscuous activity of human SQR supported the conversion of CoA to CoA-SSH (CoA-persulfide), a potent inhibitor of butyryl-CoA dehydrogenase, and revealed a molecular link between sulfide and butyrate metabolism, which are known to interact. Three different CoQ1-bound crystal structures furnished insights into how diverse substrates access human SQR, and provided snapshots of the reaction coordinate. Unexpectedly, the active site cysteines in SQR are configured in a bridging trisulfide at the start and end of the catalytic cycle, and the presence of sulfane sulfur was confirmed biochemically. Importantly, our study leads to a mechanistic proposal for human SQR in which sulfide addition to the trisulfide cofactor eliminates 201Cys-SSH, forming an intense charge-transfer complex with flavin adenine dinucleotide, and 379Cys-SSH, which transfers sulfur to an external acceptor.
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Affiliation(s)
- Aaron P Landry
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sojin Moon
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hanseong Kim
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pramod K Yadav
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Arkajit Guha
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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42
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Lencina AM, Koepke J, Preu J, Muenke C, Gennis RB, Michel H, Schurig-Briccio LA. Characterization and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148080. [PMID: 31520616 DOI: 10.1016/j.bbabio.2019.148080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/28/2019] [Accepted: 09/08/2019] [Indexed: 11/25/2022]
Abstract
The crystal structure of the enzyme previously characterized as a type-2 NADH:menaquinone oxidoreductase (NDH-2) from Thermus thermophilus has been solved at a resolution of 2.9 Å and revealed that this protein is, in fact, a coenzyme A-disulfide reductase (CoADR). Coenzyme A (CoASH) replaces glutathione as the major low molecular weight thiol in Thermus thermophilus and is maintained in the reduced state by this enzyme (CoADR). Although the enzyme does exhibit NADH:menadione oxidoreductase activity expected for NDH-2 enzymes, the specific activity with CoAD as an electron acceptor is about 5-fold higher than with menadione. Furthermore, the crystal structure contains coenzyme A covalently linked Cys44, a catalytic intermediate (Cys44-S-S-CoA) reduced by NADH via the FAD cofactor. Soaking the crystals with menadione shows that menadione can bind to a site near the redox active FAD, consistent with the observed NADH:menadione oxidoreductase activity. CoADRs from other species were also examined and shown to have measurable NADH:menadione oxidoreductase activity. Although a common feature of this family of enzymes, no biological relevance is proposed. The CoADR from T. thermophilus is a soluble homodimeric enzyme. Expression of the recombinant TtCoADR at high levels in E. coli results in a small fraction that co-purifies with the membrane fraction, which was used previously to isolate the enzyme wrongly identified as a membrane-bound NDH-2. It is concluded that T. thermophilus does not contain an authentic NDH-2 component in its aerobic respiratory chain.
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Affiliation(s)
- Andrea M Lencina
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Juergen Koepke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Julia Preu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Cornelia Muenke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany.
| | - Lici A Schurig-Briccio
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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43
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Shabani S, Mahjoubi F, Moosavi MA. A siRNA‐based method for efficient silencing of
PYROXD1
gene expression in the colon cancer cell line HCT116. J Cell Biochem 2019; 120:19310-19317. [DOI: 10.1002/jcb.26858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 03/13/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Samira Shabani
- Department of Clinical Genetic National Institute of Genetic Engineering and Biotechnology (NIGEB) Tehran Iran
- Colorectal Research Centre (CRRC), Hazrate‐Rasoule‐Akram Hospital Iran University of Medical Sciences Tehran Iran
| | - Frouzandeh Mahjoubi
- Department of Clinical Genetic National Institute of Genetic Engineering and Biotechnology (NIGEB) Tehran Iran
| | - Mohammad A. Moosavi
- Department of Clinical Genetic National Institute of Genetic Engineering and Biotechnology (NIGEB) Tehran Iran
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44
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Aguilar-Galvez A, Pedreschi R, Carpentier S, Chirinos R, García-Ríos D, Campos D. Proteomic analysis of mashua (Tropaeolum tuberosum) tubers subjected to postharvest treatments. Food Chem 2019; 305:125485. [PMID: 31522126 DOI: 10.1016/j.foodchem.2019.125485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/03/2019] [Accepted: 09/04/2019] [Indexed: 12/31/2022]
Abstract
Mashua (Tropaeolum tuberosum) is an important food in certain areas of the Andean region, where it is popularly believed to possess medicinal properties. Several studies have previously shown the potential of this tuber as a source of bioactive compounds. Traditionally, the tuber is exposed to the sun before consumption, in order to reduce its bitterness. The present work aims to study, at the proteome level, the differential abundance of proteins in tubers subjected to different postharvest treatments: sun-exposure (SUN), shade (SHA), refrigeration (COLD) and shade combined with sun-exposure (SHA-SUN) compared to recently harvested tubers (INIT). Results showed that sun exposure for prolonged times (9 days) resulted in increased abundance of proteins classified as heat shock proteins, intracellular traffic, disease/defense and protein degradation. Our results reflect that the sun treatment activates defense systems and osmoprotection adjustment against water loss and reactive oxygen species.
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Affiliation(s)
- Ana Aguilar-Galvez
- Universidad Nacional Agraria - La Molina, Instituto de Biotecnología, Av. La Molina s/n, Lima, Peru
| | - Romina Pedreschi
- Pontificia Universidad Católica de Valparaíso, Escuela de Agronomía, Calle San Francisco s/n, La Palma, Chile
| | - Sebastien Carpentier
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Belgium; SYBIOMA: Facility for Systems Biology Mass Spectrometry, Leuven, Belgium
| | - Rosana Chirinos
- Universidad Nacional Agraria - La Molina, Instituto de Biotecnología, Av. La Molina s/n, Lima, Peru
| | - Diego García-Ríos
- Universidad Nacional Agraria - La Molina, Instituto de Biotecnología, Av. La Molina s/n, Lima, Peru
| | - David Campos
- Universidad Nacional Agraria - La Molina, Instituto de Biotecnología, Av. La Molina s/n, Lima, Peru.
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45
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Linzner N, Loi VV, Fritsch VN, Tung QN, Stenzel S, Wirtz M, Hell R, Hamilton CJ, Tedin K, Fulde M, Antelmann H. Staphylococcus aureus Uses the Bacilliredoxin (BrxAB)/Bacillithiol Disulfide Reductase (YpdA) Redox Pathway to Defend Against Oxidative Stress Under Infections. Front Microbiol 2019; 10:1355. [PMID: 31275277 PMCID: PMC6591457 DOI: 10.3389/fmicb.2019.01355] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/31/2019] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen and has to cope with reactive oxygen and chlorine species (ROS, RCS) during infections. The low molecular weight thiol bacillithiol (BSH) is an important defense mechanism of S. aureus for detoxification of ROS and HOCl stress to maintain the reduced state of the cytoplasm. Under HOCl stress, BSH forms mixed disulfides with proteins, termed as S-bacillithiolations, which are reduced by bacilliredoxins (BrxA and BrxB). The NADPH-dependent flavin disulfide reductase YpdA is phylogenetically associated with the BSH synthesis and BrxA/B enzymes and was recently suggested to function as BSSB reductase (Mikheyeva et al., 2019). Here, we investigated the role of the complete bacilliredoxin BrxAB/BSH/YpdA pathway in S. aureus COL under oxidative stress and macrophage infection conditions in vivo and in biochemical assays in vitro. Using HPLC thiol metabolomics, a strongly enhanced BSSB level and a decreased BSH/BSSB ratio were measured in the S. aureus COL ΔypdA deletion mutant under control and NaOCl stress. Monitoring the oxidation degree (OxD) of the Brx-roGFP2 biosensor revealed that YpdA is required for regeneration of the reduced BSH redox potential (EBSH) upon recovery from oxidative stress. In addition, the ΔypdA mutant was impaired in H2O2 detoxification as measured with the novel H2O2-specific Tpx-roGFP2 biosensor. Phenotype analyses further showed that BrxA and YpdA are required for survival under NaOCl and H2O2 stress in vitro and inside murine J-774A.1 macrophages in infection assays in vivo. Finally, NADPH-coupled electron transfer assays provide evidence for the function of YpdA in BSSB reduction, which depends on the conserved Cys14 residue. YpdA acts together with BrxA and BSH in de-bacillithiolation of S-bacillithiolated GapDH. In conclusion, our results point to a major role of the BrxA/BSH/YpdA pathway in BSH redox homeostasis in S. aureus during recovery from oxidative stress and under infections.
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Affiliation(s)
- Nico Linzner
- Institute for Biology - Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Vu Van Loi
- Institute for Biology - Microbiology, Freie Universität Berlin, Berlin, Germany
| | | | - Quach Ngoc Tung
- Institute for Biology - Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Saskia Stenzel
- Institute for Biology - Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Markus Wirtz
- Plant Molecular Biology, Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Rüdiger Hell
- Plant Molecular Biology, Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Chris J Hamilton
- School of Pharmacy, University of East Anglia, Norwich, United Kingdom
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Haike Antelmann
- Institute for Biology - Microbiology, Freie Universität Berlin, Berlin, Germany
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Sedláček V, Kučera I. Functional and mechanistic characterization of an atypical flavin reductase encoded by the pden_5119 gene in Paracoccus denitrificans. Mol Microbiol 2019; 112:166-183. [PMID: 30977245 DOI: 10.1111/mmi.14260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2019] [Indexed: 01/25/2023]
Abstract
Pden_5119, annotated as an NADPH-dependent FMN reductase, shows homology to proteins assisting in utilization of alkanesulfonates in other bacteria. Here, we report that inactivation of the pden_5119 gene increased susceptibility to oxidative stress, decreased growth rate and increased growth yield; growth on lower alkanesulfonates as sulfur sources was not specifically influenced. Pden_5119 transcript rose in response to oxidative stressors, respiratory chain inhibitors and terminal oxidase downregulation. Kinetic analysis of a fusion protein suggested a sequential mechanism in which FMN binds first, followed by NADH. The affinity of flavin toward the protein decreased only slightly upon reduction. The observed strong viscosity dependence of kcat demonstrated that reduced FMN formed tends to remain bound to the enzyme where it can be re-oxidized by oxygen or, less efficiently, by various artificial electron acceptors. Stopped flow data were consistent with the enzyme-FMN complex being a functional oxidase that conducts the reduction of oxygen by NADH. Hydrogen peroxide was identified as the main product. As shown by isotope effects, hydride transfer occurs from the pro-S C4 position of the nicotinamide ring and partially limits the overall turnover rate. Collectively, our results point to a role for the Pden_5119 protein in maintaining the cellular redox state.
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Affiliation(s)
- Vojtěch Sedláček
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Igor Kučera
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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Koch K, Strandback E, Jha S, Richter G, Bourgeois B, Madl T, Macheroux P. Oxidative stress-induced structural changes in the microtubule-associated flavoenzyme Irc15p from Saccharomyces cerevisiae. Protein Sci 2019; 28:176-190. [PMID: 30267443 PMCID: PMC6296175 DOI: 10.1002/pro.3517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 11/07/2022]
Abstract
The genome of the yeast Saccharomyces cerevisiae encodes a canonical lipoamide dehydrogenase (Lpd1p) as part of the pyruvate dehydrogenase complex and a highly similar protein termed Irc15p (increased recombination centers 15). In contrast to Lpd1p, Irc15p lacks a pair of redox active cysteine residues required for the reduction of lipoamide and thus it is very unlikely that Irc15p performs a similar dithiol-disulfide exchange reaction as reported for lipoamide dehydrogenases. We expressed IRC15 in Escherichia coli and purified the produced protein to conduct a detailed biochemical characterization. Here, we show that Irc15p is a dimeric protein with one FAD per protomer. Photoreduction of the protein generates the fully reduced hydroquinone without the occurrence of a flavin semiquinone radical. Similarly, reduction with NADH or NADPH yields the flavin hydroquinone without the occurrence of intermediates as observed for lipoamide dehydrogenase. The redox potential of Irc15p was -313 ± 1 mV and is thus similar to lipoamide dehydrogenase. Reduced Irc15p is oxidized by several artificial electron acceptors such as potassium ferricyanide, 2,6-dichlorophenol-indophenol, 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide, and menadione. However, disulfides such as cystine, glutathione, and lipoamide were unable to react with reduced Irc15p. Limited proteolysis and SAXS-measurements revealed that the NADH-dependent formation of hydrogen peroxide caused a substantial structural change in the dimeric protein. Therefore, we hypothesize that Irc15p undergoes a conformational change in the presence of elevated levels of hydrogen peroxide, which is a putative biomarker of oxidative stress. This conformational change may in turn modulate the interaction of Irc15p with other key players involved in regulating microtubule dynamics.
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Affiliation(s)
- Karin Koch
- Institute of BiochemistryGraz University of TechnologyGrazAustria
| | | | - Shalinee Jha
- Institute of BiochemistryGraz University of TechnologyGrazAustria
| | - Gesa Richter
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and BiochemistryMedical University of GrazGrazAustria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and BiochemistryMedical University of GrazGrazAustria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and BiochemistryMedical University of GrazGrazAustria
- BioTechMed‐GrazGrazAustria
| | - Peter Macheroux
- Institute of BiochemistryGraz University of TechnologyGrazAustria
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Zhang B, Liu Y, Li X, Xu J, Fang J. Small Molecules to Target the Selenoprotein Thioredoxin Reductase. Chem Asian J 2018; 13:3593-3600. [DOI: 10.1002/asia.201801136] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/11/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Baoxin Zhang
- State Key Laboratory of Applied Organic Chemistry & College of Chemistry and Chemical Engineering; Lanzhou University; Lanzhou 730000 China
| | - Yuxin Liu
- State Key Laboratory of Applied Organic Chemistry & College of Chemistry and Chemical Engineering; Lanzhou University; Lanzhou 730000 China
| | - Xinming Li
- State Key Laboratory of Applied Organic Chemistry & College of Chemistry and Chemical Engineering; Lanzhou University; Lanzhou 730000 China
| | - Jianqiang Xu
- School of Life Science and Medicine & Panjin Industrial Technology Institute; Dalian University of Technology; Panjin 124221 China
| | - Jianguo Fang
- State Key Laboratory of Applied Organic Chemistry & College of Chemistry and Chemical Engineering; Lanzhou University; Lanzhou 730000 China
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Loi VV, Busche T, Tedin K, Bernhardt J, Wollenhaupt J, Huyen NTT, Weise C, Kalinowski J, Wahl MC, Fulde M, Antelmann H. Redox-Sensing Under Hypochlorite Stress and Infection Conditions by the Rrf2-Family Repressor HypR in Staphylococcus aureus. Antioxid Redox Signal 2018; 29:615-636. [PMID: 29237286 PMCID: PMC6067689 DOI: 10.1089/ars.2017.7354] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AIMS Staphylococcus aureus is a major human pathogen and has to cope with reactive oxygen and chlorine species (ROS, RCS) during infections, which requires efficient protection mechanisms to avoid destruction. Here, we have investigated the changes in the RNA-seq transcriptome by the strong oxidant sodium hypochlorite (NaOCl) in S. aureus USA300 to identify novel redox-sensing mechanisms that provide protection under infection conditions. RESULTS NaOCl stress caused an oxidative stress response in S. aureus as indicated by the induction of the PerR, QsrR, HrcA, and SigmaB regulons in the RNA-seq transcriptome. The hypR-merA (USA300HOU_0588-87) operon was most strongly upregulated under NaOCl stress, which encodes for the Rrf2-family regulator HypR and the pyridine nucleotide disulfide reductase MerA. We have characterized HypR as a novel redox-sensitive repressor that controls MerA expression and directly senses and responds to NaOCl and diamide stress via a thiol-based mechanism in S. aureus. Mutational analysis identified Cys33 and the conserved Cys99 as essential for NaOCl sensing, while Cys99 is also important for repressor activity of HypR in vivo. The redox-sensing mechanism of HypR involves Cys33-Cys99 intersubunit disulfide formation by NaOCl stress both in vitro and in vivo. Moreover, the HypR-controlled flavin disulfide reductase MerA was shown to protect S. aureus against NaOCl stress and increased survival in J774A.1 macrophage infection assays. Conclusion and Innovation: Here, we identified a new member of the widespread Rrf2 family as redox sensor of NaOCl stress in S. aureus that uses a thiol/disulfide switch to regulate defense mechanisms against the oxidative burst under infections in S. aureus. Antioxid. Redox Signal. 29, 615-636.
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Affiliation(s)
- Vu Van Loi
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Tobias Busche
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany .,2 Center for Biotechnology, Bielefeld University , Bielefeld, Germany
| | - Karsten Tedin
- 3 Centre for Infection Medicine, Institute of Microbiology and Epizootics , Freie Universität Berlin, Berlin, Germany
| | - Jörg Bernhardt
- 4 Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald , Greifswald, Germany
| | - Jan Wollenhaupt
- 5 Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nguyen Thi Thu Huyen
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Christoph Weise
- 6 Institute of Chemistry and Biochemistry , Freie Universität Berlin, Berlin, Germany
| | - Jörn Kalinowski
- 2 Center for Biotechnology, Bielefeld University , Bielefeld, Germany
| | - Markus C Wahl
- 5 Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marcus Fulde
- 3 Centre for Infection Medicine, Institute of Microbiology and Epizootics , Freie Universität Berlin, Berlin, Germany
| | - Haike Antelmann
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
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Shen J, Walsh BJC, Flores-Mireles AL, Peng H, Zhang Y, Zhang Y, Trinidad JC, Hultgren SJ, Giedroc DP. Hydrogen Sulfide Sensing through Reactive Sulfur Species (RSS) and Nitroxyl (HNO) in Enterococcus faecalis. ACS Chem Biol 2018; 13:1610-1620. [PMID: 29712426 PMCID: PMC6088750 DOI: 10.1021/acschembio.8b00230] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent studies of hydrogen sulfide (H2S) signaling implicate low molecular weight (LMW) thiol persulfides and other reactive sulfur species (RSS) as signaling effectors. Here, we show that a CstR protein from the human pathogen Enterococcus faecalis ( E. faecalis), previously identified in Staphylococcus aureus ( S. aureus), is an RSS-sensing repressor that transcriptionally regulates a cst-like operon in response to both exogenous sulfide stress and Angeli's salt, a precursor of nitroxyl (HNO). E. faecalis CstR reacts with coenzyme A persulfide (CoASSH) to form interprotomer disulfide and trisulfide bridges between C32 and C61', which negatively regulate DNA binding to a consensus CstR DNA operator. A Δ cstR strain exhibits deficiency in catheter colonization in a catheter-associated urinary tract infection (CAUTI) mouse model, suggesting sulfide regulation and homeostasis is critical for pathogenicity. Cellular polysulfide metabolite profiling of sodium sulfide-stressed E. faecalis confirms an increase in both inorganic polysulfides and LMW thiols and persulfides sensed by CstR. The cst-like operon encodes two authentic thiosulfate sulfurtransferases and an enzyme we characterize here as an NADH and FAD-dependent coenzyme A (CoA) persulfide reductase (CoAPR) that harbors an N-terminal CoA disulfide reductase (CDR) domain and a C-terminal rhodanese homology domain (RHD). Both cysteines in the CDR (C42) and RHD (C508) domains are required for CoAPR activity and complementation of a sulfide-induced growth phenotype of a S. aureus strain lacking cstB, encoding a nonheme FeII persulfide dioxygenase. We propose that S. aureus CstB and E. faecalis CoAPR employ orthogonal chemistries to lower CoASSH that accumulates under conditions of cellular sulfide toxicity and signaling.
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Affiliation(s)
- Jiangchuan Shen
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Biochemistry Graduate Program, Indiana University, Bloomington, Indiana 47405, United States
| | - Brenna J. C. Walsh
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Ana Lidia Flores-Mireles
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63011, United States
| | - Hui Peng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Biochemistry Graduate Program, Indiana University, Bloomington, Indiana 47405, United States
| | - Yifan Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Biochemistry Graduate Program, Indiana University, Bloomington, Indiana 47405, United States
| | - Yixiang Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Jonathan C. Trinidad
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Scott J. Hultgren
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63011, United States
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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