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Petit-Hartlein I, Vermot A, Thepaut M, Humm AS, Dupeux F, Dupuy J, Chaptal V, Marquez JA, Smith SME, Fieschi F. X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX. eLife 2024; 13:RP93759. [PMID: 38640072 PMCID: PMC11031084 DOI: 10.7554/elife.93759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024] Open
Abstract
NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2's requirement for activation.
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Affiliation(s)
| | - Annelise Vermot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | - Michel Thepaut
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | | | - Florine Dupeux
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
- European Molecular Biology LaboratoryGrenobleFrance
| | - Jerome Dupuy
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | | | | | - Susan ME Smith
- Department of Molecular and Cellular Biology, Kennesaw State UniversityKennesawUnited States
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
- Institut Universitaire de FranceParisFrance
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2
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Morales BGDV, Evaristo JAM, Oliveira GARDE, Garay AFG, Diaz JJAR, Arruda A, Pereira SS, Zanchi FB. Expression and purification of active shikimate dehydrogenase from Plasmodium falciparum. AN ACAD BRAS CIENC 2024; 96:e20230382. [PMID: 38422345 DOI: 10.1590/0001-3765202420230382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 10/02/2023] [Indexed: 03/02/2024] Open
Abstract
Plasmodium falciparum is known to cause severe malaria, current treatment consists in artemisinin-based combination therapy, but resistance can lead to treatment failure. Knowledge concerning P. falciparum essential proteins can be used for searching new antimalarials, among these a potential candidate is shikimate dehydrogenase (SDH), an enzyme part of the shikimate pathway which is responsible for producing endogenous aromatic amino acids. SDH from P. falciparum (PfSDH) is unexplored by the scientific community, therefore, this study aims to establish the first protocol for active PfSDH expression. Putative PfSDH nucleotide sequence was used to construct an optimized expression vector pET28a+PfSDH inserted in E. coli BL21(DE3). As a result, optimal expression conditions were acquired by varying IPTG and temperature through time. Western Blot analysis was applied to verify appropriate PfSDH expression, solubilization and purification started with lysis followed by two-steps IMAC purification. Enzyme activity was measured spectrophotometrically by NADPH oxidation, optimal PfSDH expression occur at 0.1 mM IPTG for 48 hours growing at 37 °C and shaking at 200 rpm, recombinant PfSDH obtained after purification was soluble, pure and its physiological catalysis was confirmed. Thus, this study describes the first protocol for heterologous expression of PfSDH in soluble and active form.
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Affiliation(s)
- Bruno G Dalla Vecchia Morales
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Bioinformatics and Medicinal Chemistry, BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Federal University of Rondonia (UNIR), BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- São Lucas University Center (UniSL), Alexandre Guimarães Street, 1927, Areal, 76804-373 Porto Velho, RO, Brazil
| | - Joseph Albert M Evaristo
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Bioinformatics and Medicinal Chemistry, BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
| | - George A R DE Oliveira
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Bioinformatics and Medicinal Chemistry, BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Oswaldo Cruz Institute (IOC), Brasil Avenue 4365, Manguinhos, 21040-900 Rio de Janeiro, RJ, Brazil
| | - Ana Fidelina G Garay
- Centro para el Desarrollo de la Investigación Científica (CEDIC), P975+F58, Manduvira, Asuncion, Paraguay
| | - Jorge Javier A R Diaz
- Centro para el Desarrollo de la Investigación Científica (CEDIC), P975+F58, Manduvira, Asuncion, Paraguay
| | - Andrelisse Arruda
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Antibodies Engineering, Beira Street, 7671, Lagoa, 76812-245 Porto Velho, RO, Brazil
- Oswaldo Cruz Foundation Brasília (FIOCRUZ BRASÍLIA), L3 North Avenue, Gleba A, 70904-130 Brasília, DF, Brazil
| | - Soraya S Pereira
- Federal University of Rondonia (UNIR), BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Antibodies Engineering, Beira Street, 7671, Lagoa, 76812-245 Porto Velho, RO, Brazil
| | - Fernando B Zanchi
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Bioinformatics and Medicinal Chemistry, BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Federal University of Rondonia (UNIR), BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Oswaldo Cruz Institute (IOC), Brasil Avenue 4365, Manguinhos, 21040-900 Rio de Janeiro, RJ, Brazil
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3
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Degli Esposti M, Guerrero G, Rogel MA, Issotta F, Rojas-Villalobos C, Quatrini R, Martinez-Romero E. The phylogeny of Acetobacteraceae: photosynthetic traits and deranged respiratory enzymes. Microbiol Spectr 2023; 11:e0057523. [PMID: 37975678 PMCID: PMC10715153 DOI: 10.1128/spectrum.00575-23] [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: 02/06/2023] [Accepted: 09/21/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Acetobacteraceae are one of the best known and most extensively studied groups of bacteria, which nowadays encompasses a variety of taxa that are very different from the vinegar-producing species defining the family. Our paper presents the most detailed phylogeny of all current taxa classified as Acetobacteraceae, for which we propose a taxonomic revision. Several of such taxa inhabit some of the most extreme environments on the planet, from the deserts of Antarctica to the Sinai desert, as well as acidic niches in volcanic sites like the one we have been studying in Patagonia. Our work documents the progressive variation of the respiratory chain in early branching Acetobacteraceae into the different respiratory chains of acidophilic taxa such as Acidocella and acetous taxa such as Acetobacter. Remarkably, several genomes retain remnants of ancestral photosynthetic traits and functional bc 1 complexes. Thus, we propose that the common ancestor of Acetobacteraceae was photosynthetic.
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Affiliation(s)
- Mauro Degli Esposti
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Gabriela Guerrero
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Marco A. Rogel
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Francisco Issotta
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica, Santiago, Chile
| | - Camila Rojas-Villalobos
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Providencia, Santiago, Chile
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Meyer CT, Lynch GK, Stamo DF, Miller EJ, Chatterjee A, Kralj JM. A high-throughput and low-waste viability assay for microbes. Nat Microbiol 2023; 8:2304-2314. [PMID: 37919425 PMCID: PMC10686820 DOI: 10.1038/s41564-023-01513-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
Counting viable cells is a universal practice in microbiology. The colony-forming unit (CFU) assay has remained the gold standard to measure viability across disciplines, but it is time-intensive and resource-consuming. Here we describe the geometric viability assay (GVA) that replicates CFU measurements over 6 orders of magnitude while reducing over 10-fold the time and consumables required. GVA computes a sample's viable cell count on the basis of the distribution of embedded colonies growing inside a pipette tip. GVA is compatible with Gram-positive and Gram-negative planktonic bacteria (Escherichia coli, Pseudomonas aeruginosa and Bacillus subtilis), biofilms and fungi (Saccharomyces cerevisiae). Laborious CFU experiments such as checkerboard assays, treatment time-courses and drug screens against slow-growing cells are simplified by GVA. The ease and low cost of GVA evinces that it can replace existing viability assays and enable viability measurements at previously impractical scales.
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Affiliation(s)
- Christian T Meyer
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA.
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
- Antimicrobial Regeneration Consortium (ARC) Labs, Louisville, CO, USA.
- Duet Biosystems, Nashville, CO, USA.
| | - Grace K Lynch
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Dana F Stamo
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
- Antimicrobial Regeneration Consortium (ARC) Labs, Louisville, CO, USA
| | - Eugene J Miller
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
- Antimicrobial Regeneration Consortium (ARC) Labs, Louisville, CO, USA.
- Sachi Bio, Louisville, CO, USA.
| | - Joel M Kralj
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA.
- Think Bioscience, Boulder, CO, USA.
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5
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Zhou Y, Cheng Y, Ma T, Wang J, Li S, Wang J, Han L, Hou X, Ma X, Jiang S, Li P, Lv J, Han B, Da R. Transcriptomic and phenotype analysis revealed the role of rpoS in stress resistance and virulence of a novel ST3355 ESBL-producing hypervirulent Klebsiella pneumoniae isolate. Front Cell Infect Microbiol 2023; 13:1259472. [PMID: 37937207 PMCID: PMC10627032 DOI: 10.3389/fcimb.2023.1259472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction An extended-spectrum beta-lactamase (ESBL)-hypervirulent Klebsiella pneumoniae (HvKP) strain HKE9 was isolated from the blood in an outpatient. Methods The effect of the global regulatory factor RpoS on antimicrobial resistance, pathogenicity, and environmental adaptability was elucidated. Results HKE9 is a novel ST3355 (K20/O2a) hypervirulent strain with a positive string test and resistant to cephems except cefotetan. It has a genome size of 5.6M, including two plasmids. CTX-M-15 was found in plasmid 2, and only ompk37 was found in the chromosome. HKE9 could produce bacterial siderophores, and genes of enterobactin, yersiniabactin, aerobactin, and salmochelin have been retrieved in the genome. As a global regulatory factor, knockout of rpoS did not change antimicrobial resistance or hemolytic phenotype while increasing the virulence to Galleria mellonella larvae and showing higher viscosity. Moreover, rpoS knockout can increase bacterial competitiveness and cell adhesion ability. Interestingly, HKE9-M-rpoS decreased resistance to acidic pH, high osmotic pressure, heat shock, and ultraviolet and became sensitive to disinfectants (H2O2, alcohol, and sodium hypochlorite). Although there were 13 Type 6 secretion system (T6SS) core genes divided into two segments with tle1 between segments in the chromosome, transcriptomic analysis showed that rpoS negatively regulated T4SS located on plasmid 2, type 1, and type 3 fimbriae and positively regulate genes responsible for acidic response, hyperosmotic pressure, heat shock, oxidative stress, alcohol and hypochlorous acid metabolism, and quorum sensing. Discussion Here, this novel ST3355 ESBL-HvKP strain HKE9 may spread via various clonal types. The important regulation effect of rpoS is the enhanced tolerance and resistance to environmental stress and disinfectants, which may be at the cost of reducing virulence and regulated by T4SS.
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Affiliation(s)
- Yi Zhou
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Yue Cheng
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Tianyou Ma
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Jun Wang
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
- Department of Microbiology Laboratory, Tongchuan Center for Disease Control and Prevention, Tongchuan, Shaanxi, China
| | - Shaoru Li
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Jingdan Wang
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Lei Han
- School of Basic Medicine, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Xinyao Hou
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Xinxin Ma
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Sijin Jiang
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Pu Li
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Jia Lv
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Bei Han
- School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Rong Da
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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6
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Jiang Z, Kang X, Song Y, Zhou X, Yue M. Identification and Evaluation of Novel Antigen Candidates against Salmonella Pullorum Infection Using Reverse Vaccinology. Vaccines (Basel) 2023; 11:vaccines11040865. [PMID: 37112777 PMCID: PMC10143441 DOI: 10.3390/vaccines11040865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Pullorum disease, caused by the Salmonella enterica serovar Gallinarum biovar Pullorum, is a highly contagious disease in the poultry industry, leading to significant economic losses in many developing countries. Due to the emergence of multidrug-resistant (MDR) strains, immediate attention is required to prevent their endemics and global spreading. To mitigate the prevalence of MDR Salmonella Pullorum infections in poultry farms, it is urgent to develop effective vaccines. Reverse vaccinology (RV) is a promising approach using expressed genomic sequences to find new vaccine targets. The present study used the RV approach to identify new antigen candidates against Pullorum disease. Initial epidemiological investigation and virulent assays were conducted to select strain R51 for presentative and general importance. An additional complete genome sequence (4.7 Mb) for R51 was resolved using the Pacbio RS II platform. The proteome of Salmonella Pullorum was analyzed to predict outer membrane and extracellular proteins, and was further selected for evaluating transmembrane domains, protein prevalence, antigenicity, and solubility. Twenty-two high-scored proteins were identified among 4713 proteins, with 18 recombinant proteins successfully expressed and purified. The chick embryo model was used to assess protection efficacy, in which vaccine candidates were injected into 18-day-old chick embryos for in vivo immunogenicity and protective effects. The results showed that the PstS, SinH, LpfB, and SthB vaccine candidates were able to elicit a significant immune response. Particularly, PstS confers a significant protective effect, with a 75% survival rate compared to 31.25% for the PBS control group, confirming that identified antigens can be promising targets against Salmonella Pullorum infection. Thus, we offer RV to discover novel effective antigens in an important veterinary infectious agent with high priority.
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Affiliation(s)
- Zhijie Jiang
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiamei Kang
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Song
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao Zhou
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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7
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Vincent MS, Ezraty B. Methionine oxidation in bacteria: A reversible post-translational modification. Mol Microbiol 2023; 119:143-150. [PMID: 36350090 DOI: 10.1111/mmi.15000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Methionine is a sulfur-containing residue found in most proteins which are particularly susceptible to oxidation. Although methionine oxidation causes protein damage, it can in some cases activate protein function. Enzymatic systems reducing oxidized methionine have evolved in most bacterial species and methionine oxidation proves to be a reversible post-translational modification regulating protein activity. In this review, we inspect recent examples of methionine oxidation provoking protein loss and gain of function. We further speculate on the role of methionine oxidation as a multilayer endogenous antioxidant system and consider its potential consequences for bacterial virulence.
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Affiliation(s)
- Maxence S Vincent
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
| | - Benjamin Ezraty
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
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8
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Meyer CT, Lynch GK, Stamo DF, Miller EJ, Chatterjee A, Kralj JM. High Throughput Viability Assay for Microbiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522767. [PMID: 36712102 PMCID: PMC9881960 DOI: 10.1101/2023.01.04.522767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Counting viable cells is a universal practice in microbiology. The colony forming unit (CFU) assay has remained the gold standard to measure viability across disciplines; however, it is time-intensive and resource-consuming. Herein, we describe the Geometric Viability Assay (GVA) that replicates CFU measurements over 6-orders of magnitude while reducing over 10-fold the time and consumables. GVA computes a sample's viable cell count based on the distribution of embedded colonies growing inside a pipette tip. GVA is compatible with gram-positive and -negative planktonic bacteria, biofilms, and yeast. Laborious CFU experiments such as checkerboard assays, treatment time-courses, and drug screens against slow-growing cells are simplified by GVA. We therefore screened a drug library against exponential and stationary phase E. coli leading to the discovery of the ROS-mediated, bactericidal mechanism of diphenyliodonium. The ease and low cost of GVA evinces it can accelerate existing viability assays and enable measurements at previously impractical scales.
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Affiliation(s)
- Christian T. Meyer
- BioFrontiers and MCDB Department, University of Colorado Boulder, Boulder, CO, USA
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Grace K. Lynch
- BioFrontiers and MCDB Department, University of Colorado Boulder, Boulder, CO, USA
| | - Dana F. Stamo
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Eugene J. Miller
- BioFrontiers and MCDB Department, University of Colorado Boulder, Boulder, CO, USA
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
- Antimicrobial Regeneration Consortium (ARC) Labs, Louisville, CO, USA
- Sachi Bioworks, Louisville, CO, USA
| | - Joel M. Kralj
- BioFrontiers and MCDB Department, University of Colorado Boulder, Boulder, CO, USA
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9
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Neira G, Vergara E, Cortez D, Holmes DS. A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments. Antioxidants (Basel) 2021; 11:antiox11010059. [PMID: 35052563 PMCID: PMC8773360 DOI: 10.3390/antiox11010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/19/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (OH) and superoxide (O2−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.
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Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - Diego Cortez
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago 8420524, Chile
- Correspondence:
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10
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Caux C, Guigliarelli B, Vivès C, Biaso F, Horeau M, Hassoune H, Petit-Hartlein I, Juillan-Binard C, Torelli S, Fieschi F, Nivière V. Membrane-Bound Flavocytochrome MsrQ Is a Substrate of the Flavin Reductase Fre in Escherichia coli. ACS Chem Biol 2021; 16:2547-2559. [PMID: 34550690 DOI: 10.1021/acschembio.1c00613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
MsrPQ is a new type of methionine sulfoxide reductase (Msr) system found in bacteria. It is specifically involved in the repair of periplasmic methionine residues that are oxidized by hypochlorous acid. MsrP is a periplasmic molybdoenzyme that carries out the Msr activity, whereas MsrQ, an integral membrane-bound hemoprotein, acts as the physiological partner of MsrP to provide electrons for catalysis. Although MsrQ (YedZ) was associated since long with a protein superfamily named FRD (ferric reductase domain), including the eukaryotic NADPH oxidases and STEAP proteins, its biochemical properties are still sparsely documented. Here, we have investigated the cofactor content of the E. coli MsrQ and its mechanism of reduction by the flavin reductase Fre. We showed by electron paramagnetic resonance (EPR) spectroscopy that MsrQ contains a single highly anisotropic low-spin (HALS) b-type heme located on the periplasmic side of the membrane. We further demonstrated that MsrQ holds a flavin mononucleotide (FMN) cofactor that occupies the site where a second heme binds in other members of the FDR superfamily on the cytosolic side of the membrane. EPR spectroscopy indicates that the FMN cofactor can accommodate a radical semiquinone species. The cytosolic flavin reductase Fre was previously shown to reduce the MsrQ heme. Here, we demonstrated that Fre uses the FMN MsrQ cofactor as a substrate to catalyze the electron transfer from cytosolic NADH to the heme. Formation of a specific complex between MsrQ and Fre could favor this unprecedented mechanism, which most likely involves transfer of the reduced FMN cofactor from the Fre active site to MsrQ.
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Affiliation(s)
- Christelle Caux
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Bruno Guigliarelli
- CNRS, BIP-UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Univ., Marseille 13402, France
| | - Corinne Vivès
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Frédéric Biaso
- CNRS, BIP-UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Univ., Marseille 13402, France
| | - Marius Horeau
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Hawra Hassoune
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | | | - Céline Juillan-Binard
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Stephane Torelli
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Franck Fieschi
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Vincent Nivière
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
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11
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Draft Genome Sequences of Acidithrix sp. Strain C25 and Acidocella sp. Strain C78, Acidophiles Isolated from Iron-Rich Pelagic Aggregates (Iron Snow). Microbiol Resour Announc 2021; 10:e0010221. [PMID: 34165336 PMCID: PMC8223813 DOI: 10.1128/mra.00102-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We report the draft genome sequences of two acidophiles, the Fe-oxidizing bacterium Acidithrix sp. strain C25 and the putative Fe-reducing Acidocella sp. strain C78. Both strains were isolated from iron-rich pelagic aggregates (iron snow) collected below the redoxcline at a 5-m depth in an acidic pit lake located in Germany (51°31′8.2″N, 13°41′34.7″E).
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12
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Vermot A, Petit-Härtlein I, Smith SME, Fieschi F. NADPH Oxidases (NOX): An Overview from Discovery, Molecular Mechanisms to Physiology and Pathology. Antioxidants (Basel) 2021; 10:890. [PMID: 34205998 PMCID: PMC8228183 DOI: 10.3390/antiox10060890] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 01/17/2023] Open
Abstract
The reactive oxygen species (ROS)-producing enzyme NADPH oxidase (NOX) was first identified in the membrane of phagocytic cells. For many years, its only known role was in immune defense, where its ROS production leads to the destruction of pathogens by the immune cells. NOX from phagocytes catalyzes, via one-electron trans-membrane transfer to molecular oxygen, the production of the superoxide anion. Over the years, six human homologs of the catalytic subunit of the phagocyte NADPH oxidase were found: NOX1, NOX3, NOX4, NOX5, DUOX1, and DUOX2. Together with the NOX2/gp91phox component present in the phagocyte NADPH oxidase assembly itself, the homologs are now referred to as the NOX family of NADPH oxidases. NOX are complex multidomain proteins with varying requirements for assembly with combinations of other proteins for activity. The recent structural insights acquired on both prokaryotic and eukaryotic NOX open new perspectives for the understanding of the molecular mechanisms inherent to NOX regulation and ROS production (superoxide or hydrogen peroxide). This new structural information will certainly inform new investigations of human disease. As specialized ROS producers, NOX enzymes participate in numerous crucial physiological processes, including host defense, the post-translational processing of proteins, cellular signaling, regulation of gene expression, and cell differentiation. These diversities of physiological context will be discussed in this review. We also discuss NOX misregulation, which can contribute to a wide range of severe pathologies, such as atherosclerosis, hypertension, diabetic nephropathy, lung fibrosis, cancer, or neurodegenerative diseases, giving this family of membrane proteins a strong therapeutic interest.
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Affiliation(s)
- Annelise Vermot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000 Grenoble, France; (A.V.); (I.P.-H.)
| | - Isabelle Petit-Härtlein
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000 Grenoble, France; (A.V.); (I.P.-H.)
| | - Susan M. E. Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA;
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000 Grenoble, France; (A.V.); (I.P.-H.)
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13
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Méheust R, Huang S, Rivera-Lugo R, Banfield JF, Light SH. Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life. eLife 2021; 10:66878. [PMID: 34032212 PMCID: PMC8238504 DOI: 10.7554/elife.66878] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
Disparate redox activities that take place beyond the bounds of the prokaryotic cell cytosol must connect to membrane or cytosolic electron pools. Proteins post-translationally flavinylated by the enzyme ApbE mediate electron transfer in several characterized extracytosolic redox systems but the breadth of functions of this modification remains unknown. Here, we present a comprehensive bioinformatic analysis of 31,910 prokaryotic genomes that provides evidence of extracytosolic ApbEs within ~50% of bacteria and the involvement of flavinylation in numerous uncharacterized biochemical processes. By mining flavinylation-associated gene clusters, we identify five protein classes responsible for transmembrane electron transfer and two domains of unknown function (DUF2271 and DUF3570) that are flavinylated by ApbE. We observe flavinylation/iron transporter gene colocalization patterns that implicate functions in iron reduction and assimilation. We find associations with characterized and uncharacterized respiratory oxidoreductases that highlight roles of flavinylation in respiratory electron transport chains. Finally, we identify interspecies gene cluster variability consistent with flavinylation/cytochrome functional redundancies and discover a class of ‘multi-flavinylated proteins’ that may resemble multi-heme cytochromes in facilitating longer distance electron transfer. These findings provide mechanistic insight into an important facet of bacterial physiology and establish flavinylation as a functionally diverse mediator of extracytosolic electron transfer. In bacteria, certain chemical reactions required for life do not take place directly inside the cells. For instance, ‘redox’ reactions essential to gather minerals, repair proteins and obtain energy are localised in the membranes and space that surround a bacterium. These chemical reactions involve electrons being transferred from one molecule to another in a cascade that connects the exterior of a cell to its internal space. The enzyme ApbE allows proteins to perform electron transfer by equipping them with ring-like compounds called flavins, through a process known as flavinylation. Yet, the prevelance of flavinylation in bacteria and the scope of redox reactions it facilitates has remained unclear. To investigate this question, Méheust, Huang et al. analysed over 30,000 bacterial genomes, finding genes essential for ApbE flavinylation in about half of all bacterial species across the tree of life. The role of ApbE-flavinylated proteins was then deciphered using a ‘guilt by association’ approach. In bacteria, genes that perform similar roles are often close to each other in the genome, which helps to infer the function of a protein coded by a specific gene. This approach revealed that flavinylation is involved in processes that allow bacteria to acquire iron and to use various energy sources. A number of interesting proteins were also identified, including a group that carry multiple flavins, and could therefore, in theory, transfer electrons over long distances. This discovery could be relevant to bioelectronic applications, which are already considering another class of bacterial electron-carrying molecules as candidates to form minuscule electric wires.
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Affiliation(s)
- Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.,Innovative Genomics Institute, Berkeley, United States.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, Evry, France
| | - Shuo Huang
- Duchossois Family Institute, University of Chicago, Chicago, United States.,Department of Microbiology, University of Chicago, Chicago, United States
| | - Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.,Innovative Genomics Institute, Berkeley, United States
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, United States.,Department of Microbiology, University of Chicago, Chicago, United States
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14
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Andrieu C, Vergnes A, Loiseau L, Aussel L, Ezraty B. Characterisation of the periplasmic methionine sulfoxide reductase (MsrP) from Salmonella Typhimurium. Free Radic Biol Med 2020; 160:506-512. [PMID: 32750406 DOI: 10.1016/j.freeradbiomed.2020.06.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 11/23/2022]
Abstract
The oxidation of free methionine (Met) and Met residues inside proteins leads to the formation of methionine sulfoxide (Met-O). The reduction of Met-O to Met is catalysed by a ubiquitous enzyme family: the methionine sulfoxide reductases (Msr). The importance of Msr systems in bacterial physiology and virulence has been reported in many species. Salmonella Typhimurium, a facultative intracellular pathogen, contains four cytoplasmic Msr. Recently, a periplasmic Msr enzyme (MsrP) has been identified in Escherichia coli. In the present study, the STM14_4072 gene from Salmonella was shown to encode the MsrP protein (StMsrP). We describe the experimental procedure and precautions for the production of this molybdo-enzyme. StMsrP was also demonstrated to reduce free Met-O and to catalyse the complete repair of an oxidized protein. More importantly, this study provides for the first time access to the exhaustive list of the Msr systems of a pathogen, including four cytoplasmic enzymes (MsrA, MsrB, MsrC, BisC) and one periplasmic enzyme (MsrP).
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Affiliation(s)
- Camille Andrieu
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Alexandra Vergnes
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laurent Loiseau
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laurent Aussel
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Benjamin Ezraty
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France.
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15
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Shome A, Sarkhel R, Apoorva S, Nair SS, Chauhan TKS, Bhure SK, Mahawar M. Role of protein repair enzymes in oxidative stress survival and virulence of Salmonella. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01597-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Purpose
Proteins are the principal biomolecules in bacteria that are affected by the oxidants produced by the phagocytic cells. Most of the protein damage is irreparable though few unfolded proteins and covalently modified amino acids can be repaired by chaperones and repair enzymes respectively. This study reviews the three protein repair enzymes, protein l-isoaspartyl O-methyl transferase (PIMT), peptidyl proline cis-trans isomerase (PPIase), and methionine sulfoxide reductase (MSR).
Methods
Published articles regarding protein repair enzymes were collected from Google Scholar and PubMed. The information obtained from the research articles was analyzed and categorized into general information about the enzyme, mechanism of action, and role played by the enzymes in bacteria. Special emphasis was given to the importance of these enzymes in Salmonella Typhimurium.
Results
Protein repair is the direct and energetically preferred way of replenishing the cellular protein pool without translational synthesis. Under the oxidative stress mounted by the host during the infection, protein repair becomes very crucial for the survival of the bacterial pathogens. Only a few covalent modifications of amino acids are reversible by the protein repair enzymes, and they are highly specific in activity. Deletion mutants of these enzymes in different bacteria revealed their importance in the virulence and oxidative stress survival.
Conclusion
PIMT repairs isoaspartate residues, PPiase catalyzes the conversion of cis-trans forms of proline residues, while MSR repairs oxidized methionine (Met) residues in the proteins. These repair enzymes maintain the activities of the target protein(s), thus aid in bacterial survival and virulence. The interventions which can interfere with this mechanism could be used for the development of novel therapeutics.
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16
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Rodríguez-González V, Obregón S, Patrón-Soberano OA, Terashima C, Fujishima A. An approach to the photocatalytic mechanism in the TiO 2-nanomaterials microorganism interface for the control of infectious processes. APPLIED CATALYSIS. B, ENVIRONMENTAL 2020; 270:118853. [PMID: 32292243 DOI: 10.1016/j.apcatb.2020.118857] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 05/21/2023]
Abstract
The approach of this timely review considers the current literature that is focused on the interface nanostructure/cell-wall microorganism to understand the annihilation mechanism. Morphological studies use optical and electronic microscopes to determine the physical damage on the cell-wall and the possible cell lysis that confirms the viability and microorganism death. The key parameters of the tailoring the surface of the photoactive nanostructures such as the metal functionalization with bacteriostatic properties, hydrophilicity, textural porosity, morphology and the formation of heterojunction systems, can achieve the effective eradication of the microorganisms under natural conditions, ranging from practical to applications in environment, agriculture, and so on. However, to our knowledge, a comprehensive review of the microorganism/nanomaterial interface approach has rarely been conducted. The final remarks point the ideal photocatalytic way for the effective prevention/eradication of microorganisms, considering the resistance that the microorganism could develop without the appropriate regulatory aspects for human and ecosystem safety.
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Affiliation(s)
- Vicente Rodríguez-González
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), División de Materiales Avanzados, Camino a la Presa San José 2055, Lomas 4a, Sección, 78216, San Luis Potosí, Mexico
| | - Sergio Obregón
- Universidad Autónoma de Nuevo León, UANL, CICFIM-Facultad de Ciencias Físico Matemáticas, Av. Universidad S/N, San Nicolás de los Garza, 66455, Nuevo León, Mexico
| | - Olga A Patrón-Soberano
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), División de Biología Molecular, Camino a la Presa San José 2055, Lomas 4a, Sección, 78216, San Luis Potosí, Mexico
| | - Chiaki Terashima
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Akira Fujishima
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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17
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Rodríguez-González V, Obregón S, Patrón-Soberano OA, Terashima C, Fujishima A. An approach to the photocatalytic mechanism in the TiO 2-nanomaterials microorganism interface for the control of infectious processes. APPLIED CATALYSIS. B, ENVIRONMENTAL 2020; 270:118853. [PMID: 32292243 PMCID: PMC7111711 DOI: 10.1016/j.apcatb.2020.118853] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 05/08/2023]
Abstract
The approach of this timely review considers the current literature that is focused on the interface nanostructure/cell-wall microorganism to understand the annihilation mechanism. Morphological studies use optical and electronic microscopes to determine the physical damage on the cell-wall and the possible cell lysis that confirms the viability and microorganism death. The key parameters of the tailoring the surface of the photoactive nanostructures such as the metal functionalization with bacteriostatic properties, hydrophilicity, textural porosity, morphology and the formation of heterojunction systems, can achieve the effective eradication of the microorganisms under natural conditions, ranging from practical to applications in environment, agriculture, and so on. However, to our knowledge, a comprehensive review of the microorganism/nanomaterial interface approach has rarely been conducted. The final remarks point the ideal photocatalytic way for the effective prevention/eradication of microorganisms, considering the resistance that the microorganism could develop without the appropriate regulatory aspects for human and ecosystem safety.
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Affiliation(s)
- Vicente Rodríguez-González
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), División de Materiales Avanzados, Camino a la Presa San José 2055, Lomas 4a, Sección, 78216, San Luis Potosí, Mexico
| | - Sergio Obregón
- Universidad Autónoma de Nuevo León, UANL, CICFIM-Facultad de Ciencias Físico Matemáticas, Av. Universidad S/N, San Nicolás de los Garza, 66455, Nuevo León, Mexico
| | - Olga A. Patrón-Soberano
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), División de Biología Molecular, Camino a la Presa San José 2055, Lomas 4a, Sección, 78216, San Luis Potosí, Mexico
| | - Chiaki Terashima
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Akira Fujishima
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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18
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Vermot A, Petit-Härtlein I, Breyton C, Le Roy A, Thépaut M, Vivès C, Moulin M, Härtlein M, Grudinin S, Smith SME, Ebel C, Martel A, Fieschi F. Interdomain Flexibility within NADPH Oxidase Suggested by SANS Using LMNG Stealth Carrier. Biophys J 2020; 119:605-618. [PMID: 32668232 PMCID: PMC7399496 DOI: 10.1016/j.bpj.2020.06.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/26/2020] [Accepted: 06/23/2020] [Indexed: 11/12/2022] Open
Abstract
Small angle neutron scattering (SANS) provides a method to obtain important low-resolution information for integral membrane proteins (IMPs), challenging targets for structural determination. Specific deuteration furnishes a "stealth" carrier for the solubilized IMP. We used SANS to determine a structural envelope of SpNOX, the Streptococcus pneumoniae NADPH oxidase (NOX), a prokaryotic model system for exploring structure and function of eukaryotic NOXes. SpNOX was solubilized in the detergent lauryl maltose neopentyl glycol, which provides optimal SpNOX stability and activity. Using deuterated solvent and protein, the lauryl maltose neopentyl glycol was experimentally undetected in SANS. This affords a cost-effective SANS approach for obtaining novel structural information on IMPs. Combining SANS data with molecular modeling provided a first, to our knowledge, structural characterization of an entire NOX enzyme. It revealed a distinctly less compact structure than that predicted from the docking of homologous crystal structures of the separate transmembrane and dehydrogenase domains, consistent with a flexible linker connecting the two domains.
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Affiliation(s)
- Annelise Vermot
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | | | - Cécile Breyton
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Aline Le Roy
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Michel Thépaut
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Corinne Vivès
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | | | | | | | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia
| | - Christine Ebel
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | | | - Franck Fieschi
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France.
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19
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Li LY, Han ZZ, Zeng RC, Qi WC, Zhai XF, Yang Y, Lou YT, Gu T, Xu D, Duan JZ. Microbial ingress and in vitro degradation enhanced by glucose on bioabsorbable Mg-Li-Ca alloy. Bioact Mater 2020; 5:902-916. [PMID: 32637753 PMCID: PMC7329939 DOI: 10.1016/j.bioactmat.2020.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 01/10/2023] Open
Abstract
Biodegradable magnesium alloys are challenging to be implanted in patients with hyperglycemia and diabetes. A hypothesis is suggested that glucose accelerates microbial ingress and in vitro degradation of Mg-Li-Ca implants. Corrosion resistance and mechanical properties was demonstrated using electrochemical, hydrogen evolution and tensile tests. The bacteria from Hank's solution were isolated via 16S rRNA gene analysis. The results revealed that Mg-1Li-1Ca alloy exhibited different responses to Hank's solution with and without glucose. The solution acidity was ascribed to Microbacterium hominis and Enterobacter xiangfangensis, indicating that glucose promoted microbial activity and degradation and deterioration in mechanical property of Mg-1Li-1Ca alloy.
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Affiliation(s)
- Ling-Yu Li
- Corrosion Laboratory for Light Metals, College of Material Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Zhuang-Zhuang Han
- Corrosion Laboratory for Light Metals, College of Material Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Rong-Chang Zeng
- Corrosion Laboratory for Light Metals, College of Material Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, China.,School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450002, China
| | - Wei-Chen Qi
- Corrosion Laboratory for Light Metals, College of Material Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Xiao-Fan Zhai
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266590, China
| | - Yi Yang
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, 110819, China
| | - Yun-Tian Lou
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, 110819, China
| | - Tingyue Gu
- Department of Chemical & Biomolecular Engineering, Russ College of Engineering and Technology, Ohio University, Athens, OH, 45701-2979, USA
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, 110819, China
| | - Ji-Zhou Duan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266590, China
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20
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Zhang J, Liu GC, Dai XL, Wang J, Jin MH, Mi NN, Wang SQ. The N-terminus of MTRR plays a role in MTR reactivation cycle beyond electron transfer. Bioorg Chem 2020; 100:103836. [PMID: 32353563 DOI: 10.1016/j.bioorg.2020.103836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 03/20/2020] [Accepted: 04/06/2020] [Indexed: 11/26/2022]
Abstract
In eucaryotic cells, methionine synthase reductase (MSR/MTRR) is capable of dominating the folate-homocysteine metabolism as an irreplaceable partner in electron transfer for regeneration of methionine synthase. The N-terminus of MTRR containing a conserved domain of FMN_Red is closely concerned with the oxidation-reduction process. Maternal substitution of I22M in this domain can bring about pregnancy with high risk of spina bifida. A new variation of Arg2del was identified from a female conceiving a fetus with spina bifida cystica. Although the deletion is far from the N-terminal FMN_Red domain, the biochemical features of the variant had been seriously investigated. Curiously, the deletion of arginine(s) of MTRR could not affect the electron relay, if only the FMN_Red domain was intact, but by degrees reduced the ability to promote MTR catalysis in methionine formation. Confirmation of the interaction between the isolated MTRR N-terminal polypeptide and MTR suggested that the native MTRR N-terminus might play an extra role in MTR function. The tandem arginines at the end of MTRR N-terminus conferring high affinity to MTR were indispensable for stimulating methyltransferase activity perhaps via triggering allosteric effect that could be attenuated by removal of the arginine(s). It was concluded that MTRR could also propel MTR enzymatic reaction relying on the tandem arginines at N-terminus more than just only implicated in electron transfer in MTR reactivation cycle. Perturbance of the enzymatic cooperation due to the novel deletion could possibly invite spina bifida in clinics.
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Affiliation(s)
- Jun Zhang
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China; Institute of Molecular Medicine and Oncology, Chongqing Medical University, Chongqing 400016, China.
| | - Gui-Cen Liu
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Xiao-Lu Dai
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Juan Wang
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Mu-Hua Jin
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Nan-Nan Mi
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Shu-Qin Wang
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
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21
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Kirk ML, Kc K. Molybdenum and Tungsten Cofactors and the Reactions They Catalyze. Met Ions Life Sci 2020; 20:/books/9783110589757/9783110589757-015/9783110589757-015.xml. [PMID: 32851830 PMCID: PMC8176780 DOI: 10.1515/9783110589757-015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The last 20 years have seen a dramatic increase in our mechanistic understanding of the reactions catalyzed by pyranopterin Mo and W enzymes. These enzymes possess a unique cofactor (Moco) that contains a novel ligand in bioinorganic chemistry, the pyranopterin ene-1,2-dithiolate. A synopsis of Moco biosynthesis and structure is presented, along with our current understanding of the role Moco plays in enzymatic catalysis. Oxygen atom transfer (OAT) reactivity is discussed in terms of breaking strong metal-oxo bonds and the mechanism of OAT catalyzed by enzymes of the sulfite oxidase (SO) family that possess dioxo Mo(VI) active sites. OAT reactivity is also discussed in members of the dimethyl sulfoxide (DMSO) reductase family, which possess des-oxo Mo(IV) sites. Finally, we reveal what is known about hydride transfer reactivity in xanthine oxidase (XO) family enzymes and the formate dehydrogenases. The formal hydride transfer reactivity catalyzed by xanthine oxidase family enzymes is complex and cleaves substrate C-H bonds using a mechanism that is distinct from monooxygenases. The chapter primarily highlights developments in the field that have occurred since ~2000, which have contributed to our collective structural and mechanistic understanding of the three canonical pyranopterin Mo enzymes families: XO, SO, and DMSO reductase.
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Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates. Microorganisms 2020; 8:microorganisms8030314. [PMID: 32106516 PMCID: PMC7142476 DOI: 10.3390/microorganisms8030314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 12/04/2022] Open
Abstract
Iron-rich pelagic aggregates (iron snow) are hot spots for microbial interactions. Using iron snow isolates, we previously demonstrated that the iron-oxidizer Acidithrix sp. C25 triggers Acidiphilium sp. C61 aggregation by producing the infochemical 2-phenethylamine (PEA). Here, we showed slightly enhanced aggregate formation in the presence of PEA on different Acidiphilium spp. but not other iron-snow microorganisms, including Acidocella sp. C78 and Ferrovum sp. PN-J47. Next, we sequenced the Acidiphilium sp. C61 genome to reconstruct its metabolic potential. Pangenome analyses of Acidiphilium spp. genomes revealed the core genome contained 65 gene clusters associated with aggregation, including autoaggregation, motility, and biofilm formation. Screening the Acidiphilium sp. C61 genome revealed the presence of autotransporter, flagellar, and extracellular polymeric substances (EPS) production genes. RNA-seq analyses of Acidiphilium sp. C61 incubations (+/− 10 µM PEA) indicated genes involved in energy production, respiration, and genetic processing were the most upregulated differentially expressed genes in the presence of PEA. Additionally, genes involved in flagellar basal body synthesis were highly upregulated, whereas the expression pattern of biofilm formation-related genes was inconclusive. Our data shows aggregation is a common trait among Acidiphilium spp. and PEA stimulates the central cellular metabolism, potentially advantageous in aggregates rapidly falling through the water column.
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Ingersol LJ, Yang J, Kc K, Pokhrel A, Astashkin AV, Weiner JH, Johnston CA, Kirk ML. Addressing Ligand-Based Redox in Molybdenum-Dependent Methionine Sulfoxide Reductase. J Am Chem Soc 2020; 142:2721-2725. [PMID: 31989824 DOI: 10.1021/jacs.9b11762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A combination of pulsed EPR, CW EPR, and X-ray absorption spectroscopies has been employed to probe the geometric and electronic structure of the E. coli periplasmic molybdenum-dependent methionine sulfoxide reductase (MsrP). 17O and 1H pulsed EPR spectra show that the as-isolated Mo(V) enzyme form does not possess an exchangeable H2O/OH- ligand bound to Mo as found in the sulfite oxidizing enzymes of the same family. The nature of the unusual CW EPR spectrum has been re-evaluated in light of new data on the MsrP-N45R variant and related small-molecule analogues of the active site. These data point to a novel "thiol-blocked" [(PDT)MoVO(SCys)(thiolate)]- structure, which is supported by new EXAFS data. We discuss these new results in the context of ligand-based and metal-based redox chemistry in the enzymatic oxygen atom transfer reaction.
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Affiliation(s)
- Laura J Ingersol
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Jing Yang
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Khadanand Kc
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Amrit Pokhrel
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Andrei V Astashkin
- Department of Chemistry Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Joel H Weiner
- Department of Biochemistry , University of Alberta , 474 Medical Science Building , Edmonton , Alberta T6G 2H7 , Canada
| | - Christopher A Johnston
- Department of Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Martin L Kirk
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
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Kappler U, Nasreen M, McEwan A. New insights into the molecular physiology of sulfoxide reduction in bacteria. Adv Microb Physiol 2019; 75:1-51. [PMID: 31655735 DOI: 10.1016/bs.ampbs.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sulfoxides occur in biology as products of the S-oxygenation of small molecules as well as in peptides and proteins and their formation is often associated with oxidative stress and can affect biological function. In bacteria, sulfoxide damage can be reversed by different types of enzymes. Thioredoxin-dependent peptide methionine sulfoxide reductases (MSR proteins) repair oxidized methionine residues and are found in all Domains of life. In bacteria MSR proteins are often found in the cytoplasm but in some bacteria, including pathogenic Neisseria, Streptococci, and Haemophilus they are extracytoplasmic. Mutants lacking MSR proteins are often sensitive to oxidative stress and in pathogens exhibit decreased virulence as indicated by reduced survival in host cell or animal model systems. Molybdenum enzymes are also known to reduce S-oxides and traditionally their physiological role was considered to be in anaerobic respiration using dimethylsulfoxide (DMSO) as an electron acceptor. However, it now appears that some enzymes (MtsZ) of the DMSO reductase family of Mo enzymes use methionine sulfoxide as preferred physiological substrate and thus may be involved in scavenging/recycling of this amino acid. Similarly, an enzyme (MsrP/YedY) of the sulfite oxidase family of Mo enzymes has been shown to be involved in repair of methionine sulfoxides in periplasmic proteins. Again, some mutants deficient in Mo-dependent sulfoxide reductases exhibit reduced virulence, and there is evidence that these Mo enzymes and some MSR systems are induced by hypochlorite produced by the innate immune system. This review describes recent advances in the understanding of the molecular microbiology of MSR systems and the broadening of the role of Mo-dependent sulfoxide reductase to encompass functions beyond anaerobic respiration.
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Affiliation(s)
- Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Marufa Nasreen
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alastair McEwan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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Shimizu T, Lengalova A, Martínek V, Martínková M. Heme: emergent roles of heme in signal transduction, functional regulation and as catalytic centres. Chem Soc Rev 2019; 48:5624-5657. [DOI: 10.1039/c9cs00268e] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular mechanisms of unprecedented functions of exchangeable/labile heme and heme proteins including transcription, DNA binding, protein kinase activity, K+ channel functions, cis–trans isomerization, N–N bond formation, and other functions are described.
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Affiliation(s)
- Toru Shimizu
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Alzbeta Lengalova
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Václav Martínek
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Markéta Martínková
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
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Taylor AJ, Kelly DJ. The function, biogenesis and regulation of the electron transport chains in Campylobacter jejuni: New insights into the bioenergetics of a major food-borne pathogen. Adv Microb Physiol 2019; 74:239-329. [PMID: 31126532 DOI: 10.1016/bs.ampbs.2019.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Campylobacter jejuni is a zoonotic Epsilonproteobacterium that grows in the gastrointestinal tract of birds and mammals, and is the most frequent cause of food-borne bacterial gastroenteritis worldwide. As an oxygen-sensitive microaerophile, C. jejuni has to survive high environmental oxygen tensions, adapt to oxygen limitation in the host intestine and resist host oxidative attack. Despite its small genome size, C. jejuni is a versatile and metabolically active pathogen, with a complex and highly branched set of respiratory chains allowing the use of a wide range of electron donors and alternative electron acceptors in addition to oxygen, including fumarate, nitrate, nitrite, tetrathionate and N- or S-oxides. Several novel enzymes participate in these electron transport chains, including a tungsten containing formate dehydrogenase, a Complex I that uses flavodoxin and not NADH, a periplasmic facing fumarate reductase and a cytochrome c tetrathionate reductase. This review presents an updated description of the composition and bioenergetics of these various respiratory chains as they are currently understood, including recent work that gives new insights into energy conservation during electron transport to various alternative electron acceptors. The regulation of synthesis and assembly of the electron transport chains is also discussed. A deeper appreciation of the unique features of the respiratory systems of C. jejuni may be helpful in informing strategies to control this important pathogen.
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Affiliation(s)
- Aidan J Taylor
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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Rhodobacter sphaeroides methionine sulfoxide reductase P reduces R- and S-diastereomers of methionine sulfoxide from a broad-spectrum of protein substrates. Biochem J 2018; 475:3779-3795. [PMID: 30389844 DOI: 10.1042/bcj20180706] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/26/2018] [Accepted: 11/01/2018] [Indexed: 01/22/2023]
Abstract
Methionine (Met) is prone to oxidation and can be converted to Met sulfoxide (MetO), which exists as R- and S-diastereomers. MetO can be reduced back to Met by the ubiquitous methionine sulfoxide reductase (Msr) enzymes. Canonical MsrA and MsrB were shown to be absolutely stereospecific for the reduction of S-diastereomer and R-diastereomer, respectively. Recently, a new enzymatic system, MsrQ/MsrP which is conserved in all gram-negative bacteria, was identified as a key actor for the reduction of oxidized periplasmic proteins. The haem-binding membrane protein MsrQ transmits reducing power from the electron transport chains to the molybdoenzyme MsrP, which acts as a protein-MetO reductase. The MsrQ/MsrP function was well established genetically, but the identity and biochemical properties of MsrP substrates remain unknown. In this work, using the purified MsrP enzyme from the photosynthetic bacteria Rhodobacter sphaeroides as a model, we show that it can reduce a broad spectrum of protein substrates. The most efficiently reduced MetO is found in clusters, in amino acid sequences devoid of threonine and proline on the C-terminal side. Moreover, R. sphaeroides MsrP lacks stereospecificity as it can reduce both R- and S-diastereomers of MetO, similarly to its Escherichia coli homolog, and preferentially acts on unfolded oxidized proteins. Overall, these results provide important insights into the function of a bacterial envelop protecting system, which should help understand how bacteria cope in harmful environments.
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Methionine Sulfoxide Reductases of Archaea. Antioxidants (Basel) 2018; 7:antiox7100124. [PMID: 30241308 PMCID: PMC6211008 DOI: 10.3390/antiox7100124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 01/04/2023] Open
Abstract
Methionine sulfoxide reductases are found in all domains of life and are important in reversing the oxidative damage of the free and protein forms of methionine, a sulfur containing amino acid particularly sensitive to reactive oxygen species (ROS). Archaea are microbes of a domain of life distinct from bacteria and eukaryotes. Archaea are well known for their ability to withstand harsh environmental conditions that range from habitats of high ROS, such as hypersaline lakes of intense ultraviolet (UV) radiation and desiccation, to hydrothermal vents of low concentrations of dissolved oxygen at high temperature. Recent evidence reveals the methionine sulfoxide reductases of archaea function not only in the reduction of methionine sulfoxide but also in the ubiquitin-like modification of protein targets during oxidative stress, an association that appears evolutionarily conserved in eukaryotes. Here is reviewed methionine sulfoxide reductases and their distribution and function in archaea.
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Abstract
Transmembrane NADPH oxidase (NOX) enzymes have been so far only characterized in eukaryotes. In most of these organisms, they reduce molecular oxygen to superoxide and, depending on the presence of additional domains, are called NOX or dual oxidases (DUOX). Reactive oxygen species (ROS), including superoxide, have been traditionally considered accidental toxic by-products of aerobic metabolism. However, during the last decade it has become evident that both O2•− and H2O2 are key players in complex signaling networks and defense. A well-studied example is the production of O2•− during the bactericidal respiratory burst of phagocytes; this production is catalyzed by NOX2. Here, we devised and applied a novel algorithm to search for additional NOX genes in genomic databases. This procedure allowed us to discover approximately 23% new sequences from bacteria (in relation to the number of NOX-related sequences identified by the authors) that we have added to the existing eukaryotic NOX family and have used to build an expanded phylogenetic tree. We cloned and overexpressed the identified nox gene from Streptococcus pneumoniae and confirmed that it codes for an NADPH oxidase. The membrane of the S. pneumoniae NOX protein (SpNOX) shares many properties with its eukaryotic counterparts, such as affinity for NADPH and flavin adenine dinucleotide, superoxide dismutase and diphenylene iodonium inhibition, cyanide resistance, oxygen consumption, and superoxide production. Traditionally, NOX enzymes in eukaryotes are related to functions linked to multicellularity. Thus, the discovery of a large family of NOX-related enzymes in the bacterial world brings up fascinating questions regarding their role in this new biological context. NADPH oxidase (NOX) enzymes have not yet been reported in bacteria. Here, we carried out computational and experimental studies to provide the first characterization of a prokaryotic NOX. Out of 996 prokaryotic proteins showing NOX signatures, we initially selected, cloned, and overexpressed four of them. Subsequently, and based on preliminary testing, we concentrated our efforts on Streptococcus SpNOX, which shares many biochemical characteristics with NOX2, the referent model of NOX enzymes. Our work makes possible, for the first time, the study of pure forms of this important family of enzymes, allowing for biophysical and molecular characterization in an unprecedented way. Similar advances regarding other membrane protein families have led to new structures, further mechanistic studies, and the improvement of inhibitors. In addition, biological functions of these newly described bacterial enzymes will be certainly discovered in the near future.
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NADPH Oxidases: Insights into Selected Functions and Mechanisms of Action in Cancer and Stem Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017. [PMID: 28626501 PMCID: PMC5463201 DOI: 10.1155/2017/9420539] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
NADPH oxidases (NOX) are reactive oxygen species- (ROS-) generating enzymes regulating numerous redox-dependent signaling pathways. NOX are important regulators of cell differentiation, growth, and proliferation and of mechanisms, important for a wide range of processes from embryonic development, through tissue regeneration to the development and spread of cancer. In this review, we discuss the roles of NOX and NOX-derived ROS in the functioning of stem cells and cancer stem cells and in selected aspects of cancer cell physiology. Understanding the functions and complex activities of NOX is important for the application of stem cells in tissue engineering, regenerative medicine, and development of new therapies toward invasive forms of cancers.
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