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Davignon G, Pietrosemoli N, Benaroudj N, Soupé-Gilbert ME, Cagliero J, Turc É, Picardeau M, Guentas L, Goarant C, Thibeaux R. Leptospira interrogans biofilm transcriptome highlights adaption to starvation and general stress while maintaining virulence. NPJ Biofilms Microbiomes 2024; 10:95. [PMID: 39349472 PMCID: PMC11442865 DOI: 10.1038/s41522-024-00570-0] [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: 05/03/2024] [Accepted: 09/15/2024] [Indexed: 10/02/2024] Open
Abstract
Life-threatening Leptospira interrogans navigate a dual existence: surviving in the environment and infecting mammalian hosts. Biofilm formation is presumably an important survival strategy to achieve this process. Understanding the relation between biofilm and virulence might improve our comprehension of leptospirosis epidemiology. Our study focused on elucidating Leptospira's adaptations and regulations involved in such complex microenvironments. To determine the transcriptional profile of Leptospira in biofilm, we compared the transcriptomes in late biofilms and in exponential planktonic cultures. While genes for motility, energy production, and metabolism were downregulated, those governing general stress response, defense against metal stress, and redox homeostasis showed a significant upsurge, hinting at a tailored defensive strategy against stress. Further, despite a reduced metabolic state, biofilm disruption swiftly restored metabolic activity. Crucially, bacteria in late biofilms or resulting from biofilm disruption retained virulence in an animal model. In summary, our study highlights Leptospira's adaptive equilibrium in biofilms: minimizing energy expenditure, potentially aiding in withstanding stresses while maintaining pathogenicity. These insights are important for explaining the survival strategies of Leptospira, revealing that a biofilm lifestyle may confer an advantage in maintaining virulence, an understanding essential for managing leptospirosis across both environmental and mammalian reservoirs.
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Affiliation(s)
- Grégoire Davignon
- Leptospirosis Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Nouméa, New Caledonia
- Exact and Applied Sciences Institute (ISEA), University of New Caledonia, BP R4, 98851, Nouméa, New Caledonia
| | - Natalia Pietrosemoli
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France
| | - Nadia Benaroudj
- Biology of Spirochetes, Institut Pasteur, Université Paris Cité, CNRS UMR 6047, F-75015, Paris, France
| | - Marie-Estelle Soupé-Gilbert
- Leptospirosis Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Nouméa, New Caledonia
| | - Julie Cagliero
- Leptospirosis Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Nouméa, New Caledonia
| | - Élodie Turc
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015, Paris, France
| | - Mathieu Picardeau
- Biology of Spirochetes, Institut Pasteur, Université Paris Cité, CNRS UMR 6047, F-75015, Paris, France
| | - Linda Guentas
- Exact and Applied Sciences Institute (ISEA), University of New Caledonia, BP R4, 98851, Nouméa, New Caledonia
| | - Cyrille Goarant
- Pacific Community SPC - Public Health Division - B.P. D5, Nouméa, New Caledonia
| | - Roman Thibeaux
- Leptospirosis Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Nouméa, New Caledonia.
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2
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Martínez LE, Gómez G, Ramírez N, Franco B, Robleto EA, Pedraza-Reyes M. 8-OxoG-Dependent Regulation of Global Protein Responses Leads to Mutagenesis and Stress Survival in Bacillus subtilis. Antioxidants (Basel) 2024; 13:332. [PMID: 38539865 PMCID: PMC10968225 DOI: 10.3390/antiox13030332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
The guanine oxidized (GO) system of Bacillus subtilis, composed of the YtkD (MutT), MutM and MutY proteins, counteracts the cytotoxic and genotoxic effects of the oxidized nucleobase 8-OxoG. Here, we report that in growing B. subtilis cells, the genetic inactivation of GO system potentiated mutagenesis (HPM), and subsequent hyperresistance, contributes to the damaging effects of hydrogen peroxide (H2O2) (HPHR). The mechanism(s) that connect the accumulation of the mutagenic lesion 8-OxoG with the ability of B. subtilis to evolve and survive the noxious effects of oxidative stress were dissected. Genetic and biochemical evidence indicated that the synthesis of KatA was exacerbated, in a PerR-independent manner, and the transcriptional coupling repair factor, Mfd, contributed to HPHR and HPM of the ΔGO strain. Moreover, these phenotypes are associated with wider pleiotropic effects, as revealed by a global proteome analysis. The inactivation of the GO system results in the upregulated production of KatA, and it reprograms the synthesis of the proteins involved in distinct types of cellular stress; this has a direct impact on (i) cysteine catabolism, (ii) the synthesis of iron-sulfur clusters, (iii) the reorganization of cell wall architecture, (iv) the activation of AhpC/AhpF-independent organic peroxide resistance, and (v) increased resistance to transcription-acting antibiotics. Therefore, to contend with the cytotoxic and genotoxic effects derived from the accumulation of 8-OxoG, B. subtilis activates the synthesis of proteins belonging to transcriptional regulons that respond to a wide, diverse range of cell stressors.
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Affiliation(s)
- Lissett E. Martínez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Gerardo Gómez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Norma Ramírez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Bernardo Franco
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Eduardo A. Robleto
- School of Life Sciences, University of Nevada, Las Vegas, NV 89557, USA;
| | - Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
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3
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Igbaria-Jaber Y, Hofmann L, Gevorkyan-Airapetov L, Shenberger Y, Ruthstein S. Revealing the DNA Binding Modes of CsoR by EPR Spectroscopy. ACS OMEGA 2023; 8:39886-39895. [PMID: 37901548 PMCID: PMC10601412 DOI: 10.1021/acsomega.3c06336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/31/2023]
Abstract
In pathogens, a unique class of metalloregulator proteins, called gene regulatory proteins, sense specific metal ions that initiate gene transcription of proteins that export metal ions from the cell, thereby preventing toxicity and cell death. CsoR is a metalloregulator protein found in various bacterial systems that "sense" Cu(I) ions with high affinity. Upon copper binding, CsoR dissociates from the DNA promoter region, resulting in initiation of gene transcription. Crystal structures of CsoR in the presence and absence of Cu(I) from various bacterial systems have been reported, suggesting either a dimeric or tetrameric structure of these helical proteins. However, structural information about the CsoR-DNA complex is missing. Here, we applied electron paramagnetic resonance (EPR) spectroscopy to follow the conformational and dynamical changes that Mycobacterium tuberculosis CsoR undergoes upon DNA binding in solution. We showed that the quaternary structure is predominantly dimeric in solution, and only minor conformational and dynamical changes occur in the DNA bound state. Also, labeling of the unresolved C- terminus revealed no significant change in dynamics upon DNA binding. These observations are unique, since for other bacterial copper metalloregulators, such as the MerR and CopY families, major conformational changes were observed upon DNA binding, indicating a different mode of action for this protein family.
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Affiliation(s)
- Yasmin Igbaria-Jaber
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Lukas Hofmann
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yulia Shenberger
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Sharon Ruthstein
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
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4
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Gautam P, Erill I, Cusick KD. Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria. Microorganisms 2023; 11:microorganisms11041012. [PMID: 37110435 PMCID: PMC10141476 DOI: 10.3390/microorganisms11041012] [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: 03/13/2023] [Revised: 04/07/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Copper is an essential trace element for living cells. However, copper can be potentially toxic for bacterial cells when it is present in excess amounts due to its redox potential. Due to its biocidal properties, copper is prevalent in marine systems due to its use in antifouling paints and as an algaecide. Thus, marine bacteria must possess means of sensing and responding to both high copper levels and those in which it is present at only typical trace metal levels. Bacteria harbor diverse regulatory mechanisms that respond to intracellular and extracellular copper and maintain copper homeostasis in cells. This review presents an overview of the copper-associated signal transduction systems in marine bacteria, including the copper efflux systems, detoxification, and chaperone mechanisms. We performed a comparative genomics study of the copper-regulatory signal transduction system on marine bacteria to examine the influence of the environment on the presence, abundance, and diversity of copper-associated signal transduction systems across representative phyla. Comparative analyses were performed among species isolated from sources, including seawater, sediment, biofilm, and marine pathogens. Overall, we observed many putative homologs of copper-associated signal transduction systems from various copper systems across marine bacteria. While the distribution of the regulatory components is mainly influenced by phylogeny, our analyses identified several intriguing trends: (1) Bacteria isolated from sediment and biofilm displayed an increased number of homolog hits to copper-associated signal transduction systems than those from seawater. (2) A large variability exists for hits to the putative alternate σ factor CorE hits across marine bacteria. (3) Species isolated from seawater and marine pathogens harbored fewer CorE homologs than those isolated from the sediment and biofilm.
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Affiliation(s)
- Pratima Gautam
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Kathleen D Cusick
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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5
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Guzmán-Moreno J, García-Ortega LF, Torres-Saucedo L, Rivas-Noriega P, Ramírez-Santoyo RM, Sánchez-Calderón L, Quiroz-Serrano IN, Vidales-Rodríguez LE. Bacillus megaterium HgT21: a Promising Metal Multiresistant Plant Growth-Promoting Bacteria for Soil Biorestoration. Microbiol Spectr 2022; 10:e0065622. [PMID: 35980185 PMCID: PMC9604106 DOI: 10.1128/spectrum.00656-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022] Open
Abstract
The environmental deterioration produced by heavy metals derived from anthropogenic activities has gradually increased. The worldwide dissemination of toxic metals in crop soils represents a threat for sustainability and biosafety in agriculture and requires strategies for the recovery of metal-polluted crop soils. The biorestoration of metal-polluted soils using technologies that combine plants and microorganisms has gained attention in recent decades due to the beneficial and synergistic effects produced by its biotic interactions. In this context, native and heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in the development of strategies for sustainable biorestoration of metal-contaminated soils. In this study, we present a genomic analysis and characterization of the rhizospheric bacterium Bacillus megaterium HgT21 isolated from metal-polluted soil from Zacatecas, Mexico. The results reveal that this autochthonous bacterium contains an important set of genes related to a variety of operons associated with mercury, arsenic, copper, cobalt, cadmium, zinc and aluminum resistance. Additionally, halotolerance-, beta-lactam resistance-, phosphate solubilization-, and plant growth-promotion-related genes were identified. The analysis of resistance to metal ions revealed resistance to mercury (HgII+), arsenate [AsO4]³-, cobalt (Co2+), zinc (Zn2+), and copper (Cu2+). Moreover, the ability of the HgT21 strain to produce indole acetic acid (a phytohormone) and promote the growth of Arabidopsis thaliana seedlings in vitro was also demonstrated. The genotype and phenotype of Bacillus megaterium HgT21 reveal its potential to be used as a model of both plant growth-promoting and metal multiresistant bacteria. IMPORTANCE Metal-polluted environments are natural sources of a wide variety of PGPB adapted to cope with toxic metal concentrations. In this work, the bacterial strain Bacillus megaterium HgT21 was isolated from metal-contaminated soil and is proposed as a model for the study of metal multiresistance in spore-forming Gram-positive bacteria due to the presence of a variety of metal resistance-associated genes similar to those encountered in the metal multiresistant Gram-negative Cupriavidus metallidurans CH34. The ability of B. megaterium HgT21 to promote the growth of plants also makes it suitable for the study of plant-bacteria interactions in metal-polluted environments, which is key for the development of techniques for the biorestoration of metal-contaminated soils used for agriculture.
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Affiliation(s)
- Jesús Guzmán-Moreno
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Luis Fernando García-Ortega
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - Lilia Torres-Saucedo
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Paulina Rivas-Noriega
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Rosa María Ramírez-Santoyo
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Lenin Sánchez-Calderón
- Laboratorio de Genómica Evolutiva, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Iliana Noemi Quiroz-Serrano
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Luz Elena Vidales-Rodríguez
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
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6
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Lee J, Dalton RA, Dennison C. Copper delivery to an endospore coat protein of Bacillus subtilis. Front Cell Dev Biol 2022; 10:916114. [PMID: 36133923 PMCID: PMC9484137 DOI: 10.3389/fcell.2022.916114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
A family of cytosolic copper (Cu) storage proteins (the Csps) bind large quantities of Cu(I) via their Cys-lined four-helix bundles, and the majority are cytosolic (Csp3s). The presence of Csp3s in many bacteria appears inconsistent with the current dogma that bacteria, unlike eukaryotes, have evolved not to maintain intracellular pools of Cu due to its potential toxicity. Sporulation in Bacillus subtilis has been used to investigate if a Csp3 binds Cu(I) in the cytosol for a target enzyme. The activity of the Cu-requiring endospore multi-Cu oxidase BsCotA (a laccase) increases under Cu-replete conditions in wild type B. subtilis. In the strain lacking BsCsp3 lower BsCotA activity is observed and is unaffected by Cu levels. BsCsp3 loaded with Cu(I) readily activates apo-BsCotA in vitro. Experiments with a high affinity Cu(I) chelator demonstrate that Cu(I) transfer from Cu(I)-BsCsp3 must occur via an associative mechanism. BsCsp3 and BsCotA are both upregulated during late sporulation. We hypothesise that BsCsp3 acquires cuprous ions in the cytosol of B. subtilis for BsCotA.
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7
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Novoa-Aponte L, Argüello JM. Unique underlying principles shaping copper homeostasis networks. J Biol Inorg Chem 2022; 27:509-528. [PMID: 35802193 PMCID: PMC9470648 DOI: 10.1007/s00775-022-01947-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/27/2022] [Indexed: 12/27/2022]
Abstract
Abstract Copper is essential in cells as a cofactor for key redox enzymes. Bacteria have acquired molecular components that sense, uptake, distribute, and expel copper ensuring that cuproenzymes are metallated and steady-state metal levels are maintained. Toward preventing deleterious reactions, proteins bind copper ions with high affinities and transfer the metal via ligand exchange, warranting that copper ions are always complexed. Consequently, the directional copper distribution within cell compartments and across cell membranes requires specific dynamic interactions and metal exchange between cognate holo-apo protein partners. These metal exchange reactions are determined by thermodynamic and kinetics parameters and influenced by mass action. Then, copper distribution can be conceptualized as a molecular system of singular interacting elements that maintain a physiological copper homeostasis. This review focuses on the impact of copper high-affinity binding and exchange reactions on the homeostatic mechanisms, the conceptual models to describe the cell as a homeostatic system, the various molecule functions that contribute to copper homeostasis, and the alternative system architectures responsible for copper homeostasis in model bacteria. Graphical Abstract ![]()
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Affiliation(s)
- Lorena Novoa-Aponte
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St, Worcester, MA, 01605, USA.,Genetics and Metabolism Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St, Worcester, MA, 01605, USA.
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8
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Keren-Paz A, Maan H, Karunker I, Olender T, Kapishnikov S, Dersch S, Kartvelishvily E, Wolf SG, Gal A, Graumann PL, Kolodkin-Gal I. The roles of intracellular and extracellular calcium in Bacillus subtilis biofilms. iScience 2022; 25:104308. [PMID: 35663026 PMCID: PMC9160756 DOI: 10.1016/j.isci.2022.104308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/26/2022] [Accepted: 04/22/2022] [Indexed: 11/06/2022] Open
Abstract
In nature, bacteria reside in biofilms– multicellular differentiated communities held together by an extracellular matrix. This work identified a novel subpopulation—mineral-forming cells—that is essential for biofilm formation in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by the inhibition of calcium uptake. Our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes. The orchestrated formation of calcite scaffolds supports the morphogenesis of microbial biofilms A novel subpopulation—mineral-forming cells—is essential for biofilm formation This subpopulation contains an intracellular calcium-accumulating niche, supporting the formation of calcium carbonate Intracellular calcium homeostasis and calcium export are associated with a functional biofilm macrostructure
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Affiliation(s)
- Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Iris Karunker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Kapishnikov
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Simon Dersch
- Centre for Synthetic Microbiology (SYNMIKRO), Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Sharon G Wolf
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Peter L Graumann
- Centre for Synthetic Microbiology (SYNMIKRO), Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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9
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Khan M, Kamran M, Kadi RH, Hassan MM, Elhakem A, Sakit ALHaithloul HA, Soliman MH, Mumtaz MZ, Ashraf M, Shamim S. Harnessing the Potential of Bacillus altitudinis MT422188 for Copper Bioremediation. Front Microbiol 2022; 13:878000. [PMID: 35663894 PMCID: PMC9161743 DOI: 10.3389/fmicb.2022.878000] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/05/2022] [Indexed: 12/08/2022] Open
Abstract
The contamination of heavy metals is a cause of environmental concern across the globe, as their increasing levels can pose a significant risk to our natural ecosystems and public health. The present study was aimed to evaluate the ability of a copper (Cu)-resistant bacterium, characterized as Bacillus altitudinis MT422188, to remove Cu from contaminated industrial wastewater. Optimum growth was observed at 37°C, pH 7, and 1 mm phosphate, respectively. Effective concentration 50 (EC50), minimum inhibitory concentration (MIC), and cross-heavy metal resistance pattern were observed at 5.56 mm, 20 mm, and Ni > Zn > Cr > Pb > Ag > Hg, respectively. Biosorption of Cu by live and dead bacterial cells in its presence and inhibitors 1 and 2 (DNP and DCCD) was suggestive of an ATP-independent efflux system. B. altitudinis MT422188 was also able to remove 73 mg/l and 82 mg/l of Cu at 4th and 8th day intervals from wastewater, respectively. The presence of Cu resulted in increased GR (0.004 ± 0.002 Ug−1FW), SOD (0.160 ± 0.005 Ug−1FW), and POX (0.061 ± 0.004 Ug−1FW) activity. Positive motility (swimming, swarming, twitching) and chemotactic behavior demonstrated Cu as a chemoattractant for the cells. Metallothionein (MT) expression in the presence of Cu was also observed by SDS-PAGE. Adsorption isotherm and pseudo-kinetic-order studies suggested Cu biosorption to follow Freundlich isotherm as well as second-order kinetic model, respectively. Thermodynamic parameters such as Gibbs free energy (∆G°), change in enthalpy (∆H° = 10.431 kJ/mol), and entropy (∆S° = 0.0006 kJ/mol/K) depicted the biosorption process to a feasible, endothermic reaction. Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), and Energy-Dispersive X-Ray Spectroscopy (EDX) analyses revealed the physiochemical and morphological changes in the bacterial cell after biosorption, indicating interaction of Cu ions with its functional groups. Therefore, these features suggest the potentially effective role of B. altitudinis MT422188 in Cu bioremediation.
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Affiliation(s)
- Maryam Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Kamran
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Roqayah H. Kadi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohamed M. Hassan
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
- *Correspondence: Mohamed M. Hassan,
| | - Abeer Elhakem
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | | | - Mona H. Soliman
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
- Biology Department, Faculty of Science, Taibah University, Al-Sharm, Yanbu El-Bahr, Saudi Arabia
| | - Muhammad Zahid Mumtaz
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Saba Shamim
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
- Saba Shamim,
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10
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Damle MS, Singh AN, Peters SC, Szalai VA, Fisher OS. The YcnI protein from Bacillus subtilis contains a copper-binding domain. J Biol Chem 2021; 297:101078. [PMID: 34400169 PMCID: PMC8424229 DOI: 10.1016/j.jbc.2021.101078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022] Open
Abstract
Bacteria require a precise balance of copper ions to ensure that essential cuproproteins are fully metalated while also avoiding copper-induced toxicity. The Gram-positive bacterium Bacillus subtilis maintains appropriate copper homeostasis in part through the ycn operon. The ycn operon comprises genes encoding three proteins: the putative copper importer YcnJ, the copper-dependent transcriptional repressor YcnK, and the uncharacterized Domain of Unknown Function 1775 (DUF1775) containing YcnI. DUF1775 domains are found across bacterial phylogeny, and bioinformatics analyses indicate that they frequently neighbor domains implicated in copper homeostasis and transport. Here, we investigated whether YcnI can interact with copper and, using electron paramagnetic resonance and inductively coupled plasma-MS, found that this protein can bind a single Cu(II) ion. We determine the structure of both the apo and copper-bound forms of the protein by X-ray crystallography, uncovering a copper-binding site featuring a unique monohistidine brace ligand set that is highly conserved among DUF1775 domains. These data suggest a possible role for YcnI as a copper chaperone and that DUF1775 domains in other bacterial species may also function in copper homeostasis.
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Affiliation(s)
- Madhura S Damle
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Aarshi N Singh
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Stephen C Peters
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Veronika A Szalai
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania, USA.
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11
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Alotaibi BS, Khan M, Shamim S. Unraveling the Underlying Heavy Metal Detoxification Mechanisms of Bacillus Species. Microorganisms 2021; 9:1628. [PMID: 34442707 PMCID: PMC8402239 DOI: 10.3390/microorganisms9081628] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 12/26/2022] Open
Abstract
The rise of anthropogenic activities has resulted in the increasing release of various contaminants into the environment, jeopardizing fragile ecosystems in the process. Heavy metals are one of the major pollutants that contribute to the escalating problem of environmental pollution, being primarily introduced in sensitive ecological habitats through industrial effluents, wastewater, as well as sewage of various industries. Where heavy metals like zinc, copper, manganese, and nickel serve key roles in regulating different biological processes in living systems, many heavy metals can be toxic even at low concentrations, such as mercury, arsenic, cadmium, chromium, and lead, and can accumulate in intricate food chains resulting in health concerns. Over the years, many physical and chemical methods of heavy metal removal have essentially been investigated, but their disadvantages like the generation of chemical waste, complex downstream processing, and the uneconomical cost of both methods, have rendered them inefficient,. Since then, microbial bioremediation, particularly the use of bacteria, has gained attention due to the feasibility and efficiency of using them in removing heavy metals from contaminated environments. Bacteria have several methods of processing heavy metals through general resistance mechanisms, biosorption, adsorption, and efflux mechanisms. Bacillus spp. are model Gram-positive bacteria that have been studied extensively for their biosorption abilities and molecular mechanisms that enable their survival as well as their ability to remove and detoxify heavy metals. This review aims to highlight the molecular methods of Bacillus spp. in removing various heavy metals ions from contaminated environments.
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Affiliation(s)
- Badriyah Shadid Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Maryam Khan
- Institute of Molecular Biology and Biotechnology (IMBB), Defence Road Campus, The University of Lahore, Lahore 55150, Pakistan;
| | - Saba Shamim
- Institute of Molecular Biology and Biotechnology (IMBB), Defence Road Campus, The University of Lahore, Lahore 55150, Pakistan;
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12
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Molecular Insights into the Copper-Sensitive Operon Repressor in Acidithiobacillus caldus. Appl Environ Microbiol 2021; 87:e0066021. [PMID: 34085855 DOI: 10.1128/aem.00660-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The copper-sensitive operon repressor (CsoR) family, which is the main Cu(I)-sensing family, is widely distributed and regulates regulons involved in detoxification in response to extreme copper stress (a general range of ≥3 g/liter copper ions). Here, we identified CsoR in hyper-copper-resistant Acidithiobacillus caldus (CsoRAc), an organism used in the bioleaching process of copper ores. CsoRAc possesses highly conserved Cu(I) ligands and structures within the CsoR family members. Transcriptional analysis assays indicated that the promoter (PIII) of csoR was active but weakly responsive to copper in Escherichia coli. Copper titration assays gave a stoichiometry of 0.8 mol Cu(I) per apo-CsoRAc monomer in vitro combined with atomic absorption spectroscopy analysis. CuI-CsoRAc and apo-CsoRAc share essentially identical secondary structures and assembly states, as demonstrated by circular dichroism spectra and size exclusion chromatography profiles. The average dissociation constants (KD = 2.26 × 10-18 M and 0.53 × 10-15 M) and Cu(I) binding affinity of apo-CsoRAc were estimated by bathocuproine disulfonate (BCS) and bicinchoninic acid (BCA) competition assays, respectively. Site-directed mutations of conserved Cu(I) ligands in CsoRAc did not significantly alter the secondary structure or assembly state. Competition assays showed that mutants had the same order of magnitude of Cu(I) binding affinity as apo-CsoRAc. Moreover, apo-CsoRAc could bind to the DNA fragment P08430 in vitro, although with low affinity. Finally, a working model was developed to illustrate putative copper resistance mechanisms in A. caldus. IMPORTANCE Research on copper resistance among various species has attracted considerable interest. However, due to the lack of effective and reproducible genetic tools, few studies regarding copper resistance have been reported for A. caldus. Here, we characterized a major Cu(I)-sensing family protein, CsoRAc, which binds Cu(I) with an attomolar affinity higher than that of the Cu(I)-specific chelator bathocuproine disulfonate. In particular, CsoR family proteins were identified only in A. caldus, rather than A. ferrooxidans and A. thiooxidans, which are both used for bioleaching. Meanwhile, A. caldus harbored more copper resistance determinants and a relatively full-scale regulatory system involved in copper homeostasis. These observations suggested that A. caldus may play an essential role in the application of engineered strains with higher copper resistance in the near future.
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Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch HG. Cu Homeostasis in Bacteria: The Ins and Outs. MEMBRANES 2020; 10:E242. [PMID: 32962054 PMCID: PMC7558416 DOI: 10.3390/membranes10090242] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.
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Affiliation(s)
- Andreea Andrei
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
- Fakultät für Biologie, Albert-Ludwigs Universität Freiburg; Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yavuz Öztürk
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Juna Rauch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | - Dorian Marckmann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
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Rules of Expansion: an Updated Consensus Operator Site for the CopR-CopY Family of Bacterial Copper Exporter System Repressors. mSphere 2020; 5:5/3/e00411-20. [PMID: 32461276 PMCID: PMC7253601 DOI: 10.1128/msphere.00411-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Many Gram-positive bacteria respond to copper stress by upregulating a copper export system controlled by a copper-sensitive repressor, CopR-CopY. The previous operator sequence for this family of proteins had been identified as TACANNTGTA. Here, using several recombinant proteins and mutations in various DNA fragments, we define those 10 bases as necessary but not sufficient for binding and in doing so, refine the cop operon operator to the 16-base sequence RNYKACANNTGTMRNY. Due to the sheer number of repressors that have been said to bind to the original 10 bases, including many antibiotic resistance repressors such as BlaI and MecI, we feel that this study highlights the need to reexamine many of these sites of the past and use added stringency for verifying operators in the future. Copper is broadly toxic to bacteria. As such, bacteria have evolved specialized copper export systems (cop operons) often consisting of a DNA-binding/copper-responsive regulator (which can be a repressor or activator), a copper chaperone, and a copper exporter. For those bacteria using DNA-binding copper repressors, few studies have examined the regulation of this operon regarding the operator DNA sequence needed for repressor binding. In Streptococcus pneumoniae (the pneumococcus), CopY is the copper repressor for the cop operon. Previously, homologs of pneumococcal CopY have been characterized to bind a 10-base consensus sequence T/GACANNTGTA known as the cop box. Using this motif, we sought to determine whether genes outside the cop operon are also regulated by the CopY repressor, which was previously shown in Lactococcus lactis. We found that S. pneumoniae CopY did not bind to cop operators upstream of these candidate genes in vitro. During this process, we found that the cop box sequence is necessary but not sufficient for CopY binding. Here, we propose an updated operator sequence for the S. pneumoniaecop operon to be ATTGACAAATGTAGAT binding CopY with a dissociation constant (Kd) of ∼28 nM. We demonstrate strong cross-species interaction between some CopY proteins and CopY operators, suggesting strong evolutionary conservation. Taken together with our binding studies and bioinformatics data, we propose the consensus operator RNYKACANNYGTMRNY for the bacterial CopR-CopY copper repressor homologs. IMPORTANCE Many Gram-positive bacteria respond to copper stress by upregulating a copper export system controlled by a copper-sensitive repressor, CopR-CopY. The previous operator sequence for this family of proteins had been identified as TACANNTGTA. Here, using several recombinant proteins and mutations in various DNA fragments, we define those 10 bases as necessary but not sufficient for binding and in doing so, refine the cop operon operator to the 16-base sequence RNYKACANNTGTMRNY. Due to the sheer number of repressors that have been said to bind to the original 10 bases, including many antibiotic resistance repressors such as BlaI and MecI, we feel that this study highlights the need to reexamine many of these sites of the past and use added stringency for verifying operators in the future.
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15
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Dysregulation of Magnesium Transport Protects Bacillus subtilis against Manganese and Cobalt Intoxication. J Bacteriol 2020; 202:JB.00711-19. [PMID: 31964700 DOI: 10.1128/jb.00711-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
Transition metals are essential for life but are toxic when in excess. Metal ion intoxication may result from the mismetallation of essential metal-dependent enzymes with a noncognate metal. To begin to identify enzymes and processes that are susceptible to mismetallation, we have selected for strains with increased resistance to Mn(II) and Co(II). In Bacillus subtilis, cells lacking the MntR metalloregulator are exquisitely sensitive to Mn(II) but can easily become resistant by acquiring mutations affecting the MntH Mn(II) importer. Using transposon mutagenesis, and starting with an mntR mntH strain, we recovered mariner insertions that inactivated the mpfA gene encoding a putative Mg(II) efflux system. Loss of MpfA leads to elevated intracellular Mg(II), increased sensitivity to high Mg(II), and reduced Mn(II) sensitivity. Consistently, we also recovered an insertion disrupting the mgtE riboswitch, which normally restricts expression of the major Mg(II) importer. These results suggest that Mn(II) intoxication results from disruption of a Mg(II)-dependent enzyme or process. Mutations that inactivate MpfA were also recovered in a selection for Co(II) resistance beginning with sensitized strains lacking the major Co(II) efflux pump, CzcD. Since both Mn(II) and Co(II) may mismetallate iron-dependent enzymes, we repeated the selections under conditions of iron depletion imposed by expression of the Listeria monocytogenes FrvA iron exporter. Under conditions of iron depletion, a wider variety of suppressor mutations were recovered, but they still point to a central role for Mg(II) in maintaining metal ion homeostasis.IMPORTANCE Cellular metal ion homeostasis is tightly regulated. When metal ion levels are imbalanced, or when one metal is at toxic levels, enzymes may bind to the wrong metal cofactor. Enzyme mismetallation can impair metabolism, lead to new and deleterious reactions, and cause cell death. Beginning with Bacillus subtilis strains genetically sensitized to metal intoxication through loss of efflux or by lowering intracellular iron, we identified mutations that suppress the deleterious effects of excess Mn(II) or Co(II). For both metals, mutations in mpfA, encoding a Mg(II) efflux pump, suppressed toxicity. These mutant strains have elevated intracellular Mg(II), suggesting that Mg(II)-dependent processes are very sensitive to disruption by transition metals.
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16
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Xing C, Chen J, Zheng X, Chen L, Chen M, Wang L, Li X. Functional metagenomic exploration identifies novel prokaryotic copper resistance genes from the soil microbiome. Metallomics 2020; 12:387-395. [PMID: 31942889 DOI: 10.1039/c9mt00273a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Functional metagenomics is a premise-free approach for exploring metal resistance genes, enabling more profound effects on the development of bioremediation tools than pure culture based selection. Six soil metagenomic libraries were screened for copper (Cu) resistance genes in the current study through conventional functional genomics. Clones from the six metagenomic libraries were randomly selected from solid medium supplied with Cu, resulting in 411 Cu resistance clones. Thirty-five clones with the strongest Cu resistance were sequenced and 12 unique sequences harboring 25 putative open reading frames were obtained. It is inferred by bioinformatic analysis that putative genes carried by these recombinant plasmids probably function in the pathways of responding to Cu stress, including energy metabolism, integral components of membrane, ion transport/chelation, protein/amino acid metabolism, carbohydrate/fatty acid metabolism, signal transduction and DNA binding. The sequenced clones were re-transformed into Escherichia coli strain DH5α, and the host's biomass and the metal sorption under Cu stress were subsequently determined. The results showed that the biomass of eight of the clones was significantly increased, whereas four of them were significantly reduced. A negative correlation (R = 0.86) was found between the biomass and Cu sorption capacity. The 12 positive clones were further transferred into a Cu-sensitive E. coli strain (ΔCopA), among which nine restored the host's Cu resistance substantially. The Cu resistant genes explored in this study by functional metagenomics possess a potential capacity for developing novel bioremediation strategies, and the findings imply a vast diversity of microbial Cu resistance genetic factors in soil yet to be discovered.
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Affiliation(s)
- Chao Xing
- Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
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17
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The Disulfide Stress Response and Protein S-thioallylation Caused by Allicin and Diallyl Polysulfanes in Bacillus subtilis as Revealed by Transcriptomics and Proteomics. Antioxidants (Basel) 2019; 8:antiox8120605. [PMID: 31795512 PMCID: PMC6943732 DOI: 10.3390/antiox8120605] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
Garlic plants (Allium sativum L.) produce antimicrobial compounds, such as diallyl thiosulfinate (allicin) and diallyl polysulfanes. Here, we investigated the transcriptome and protein S-thioallylomes under allicin and diallyl tetrasulfane (DAS4) exposure in the Gram-positive bacterium Bacillus subtilis. Allicin and DAS4 caused a similar thiol-specific oxidative stress response, protein and DNA damage as revealed by the induction of the OhrR, PerR, Spx, YodB, CatR, HypR, AdhR, HxlR, LexA, CymR, CtsR, and HrcA regulons in the transcriptome. At the proteome level, we identified, in total, 108 S-thioallylated proteins under allicin and/or DAS4 stress. The S-thioallylome includes enzymes involved in the biosynthesis of surfactin (SrfAA, SrfAB), amino acids (SerA, MetE, YxjG, YitJ, CysJ, GlnA, YwaA), nucleotides (PurB, PurC, PyrAB, GuaB), translation factors (EF-Tu, EF-Ts, EF-G), antioxidant enzymes (AhpC, MsrB), as well as redox-sensitive MarR/OhrR and DUF24-family regulators (OhrR, HypR, YodB, CatR). Growth phenotype analysis revealed that the low molecular weight thiol bacillithiol, as well as the OhrR, Spx, and HypR regulons, confer protection against allicin and DAS4 stress. Altogether, we show here that allicin and DAS4 cause a strong oxidative, disulfide and sulfur stress response in the transcriptome and widespread S-thioallylation of redox-sensitive proteins in B. subtilis. The results further reveal that allicin and polysulfanes have similar modes of actions and thiol-reactivities and modify a similar set of redox-sensitive proteins by S-thioallylation.
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18
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Lee J, Dennison C. Cytosolic Copper Binding by a Bacterial Storage Protein and Interplay with Copper Efflux. Int J Mol Sci 2019; 20:ijms20174144. [PMID: 31450649 PMCID: PMC6747150 DOI: 10.3390/ijms20174144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 01/06/2023] Open
Abstract
Escherichia coli has a well-characterized copper (Cu) transporting ATPase (CopA) that removes this potentially toxic metal ion from the cytosol. Growth of the strain lacking CopA (ΔcopA) is inhibited above 0.5 mM Cu, whilst a similar effect does not occur in wild type (WT) E. coli until over 2.5 mM Cu. Limited expression of CopA can restore growth to WT levels in ΔcopAE. coli in the presence of Cu. To study the influence of a bacterial cytosolic Cu storage protein (Csp3) on how E. coli handles Cu, the protein from Bacillus subtilis (BsCsp3) has been overexpressed in the WT and ΔcopA strains. BsCsp3 can protect both strains from Cu toxicity, promoting growth at up to ~1.5 and ~3.5 mM Cu, respectively. Higher levels of Csp3 expression are needed to provide resistance to Cu toxicity in ΔcopAE. coli. At 1.5 mM Cu, BsCsp3 purified from ΔcopAE. coli binds up to approximately four equivalents of Cu(I) per monomer. A similar number of Cu(I) equivalents can be bound by BsCsp3 purified from WT E. coli also grown at 1.5 mM Cu, a concentration that does not cause toxicity in this strain. Much lower amounts of BsCsp3 are produced in WT E. coli grown in the presence of 3.4 mM Cu, but the protein still counteracts toxicity and is almost half loaded with Cu(I). Csp3s can protect E. coli from Cu toxicity by sequestering cuprous ions in the cytosol. This appears to include an ability to acquire and withhold Cu(I) from the main efflux system in a heterologous host.
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Affiliation(s)
- Jaeick Lee
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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19
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Rosario-Cruz Z, Eletsky A, Daigham NS, Al-Tameemi H, Swapna GVT, Kahn PC, Szyperski T, Montelione GT, Boyd JM. The copBL operon protects Staphylococcus aureus from copper toxicity: CopL is an extracellular membrane-associated copper-binding protein. J Biol Chem 2019; 294:4027-4044. [PMID: 30655293 PMCID: PMC6422080 DOI: 10.1074/jbc.ra118.004723] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/08/2019] [Indexed: 12/22/2022] Open
Abstract
As complications associated with antibiotic resistance have intensified, copper (Cu) is attracting attention as an antimicrobial agent. Recent studies have shown that copper surfaces decrease microbial burden, and host macrophages use Cu to increase bacterial killing. Not surprisingly, microbes have evolved mechanisms to tightly control intracellular Cu pools and protect against Cu toxicity. Here, we identified two genes (copB and copL) encoded within the Staphylococcus aureus arginine-catabolic mobile element (ACME) that we hypothesized function in Cu homeostasis. Supporting this hypothesis, mutational inactivation of copB or copL increased copper sensitivity. We found that copBL are co-transcribed and that their transcription is increased during copper stress and in a strain in which csoR, encoding a Cu-responsive transcriptional repressor, was mutated. Moreover, copB displayed genetic synergy with copA, suggesting that CopB functions in Cu export. We further observed that CopL functions independently of CopB or CopA in Cu toxicity protection and that CopL from the S. aureus clone USA300 is a membrane-bound and surface-exposed lipoprotein that binds up to four Cu+ ions. Solution NMR structures of the homologous Bacillus subtilis CopL, together with phylogenetic analysis and chemical-shift perturbation experiments, identified conserved residues potentially involved in Cu+ coordination. The solution NMR structure also revealed a novel Cu-binding architecture. Of note, a CopL variant with defective Cu+ binding did not protect against Cu toxicity in vivo Taken together, these findings indicate that the ACME-encoded CopB and CopL proteins are additional factors utilized by the highly successful S. aureus USA300 clone to suppress copper toxicity.
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Affiliation(s)
- Zuelay Rosario-Cruz
- From the Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901
| | - Alexander Eletsky
- the Department of Chemistry, State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, New York 14260, and
| | - Nourhan S Daigham
- the Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - Hassan Al-Tameemi
- From the Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901
| | - G V T Swapna
- the Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - Peter C Kahn
- From the Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901
| | - Thomas Szyperski
- the Department of Chemistry, State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, New York 14260, and
| | - Gaetano T Montelione
- the Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854,
- the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - Jeffrey M Boyd
- From the Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901,
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Draft Genome Sequence of Pseudarthrobacter sp. Strain AG30, Isolated from a Gold and Copper Mine in China. Microbiol Resour Announc 2018; 7:MRA01329-18. [PMID: 30533765 PMCID: PMC6256500 DOI: 10.1128/mra.01329-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 11/20/2022] Open
Abstract
Here, we report the features and draft genome sequence of Pseudarthrobacter sp. strain AG30, isolated from the Zijin gold and copper mine in China. Here, we report the features and draft genome sequence of Pseudarthrobacter sp. strain AG30, isolated from the Zijin gold and copper mine in China. The genome size of Pseudarthrobacter sp. AG30 was 4,618,494 bp, with a G+C content of 66.2%. Interesting genes and operons putatively conferring resistance to copper and arsenic were identified.
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21
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Mass spectrometric studies of Cu(I)-binding to the N-terminal domains of B. subtilis CopA and influence of bacillithiol. J Inorg Biochem 2018; 190:24-30. [PMID: 30342352 DOI: 10.1016/j.jinorgbio.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/20/2022]
Abstract
CopA is a Cu(I)-exporting transmembrane P1B-type ATPase from Bacillus subtilis. It contains two N-terminal cytoplasmic domains, CopAab, which bind Cu(I) with high affinity and to form higher-order complexes with multiple Cu(I) ions. To determine the precise nature of these species, electrospray ionisation mass spectrometry (ESI-MS) under non-denaturing conditions was employed. Up to 1 Cu per CopAab resulted in Cu coordination to one or both CopAab domains. At >1 Cu/CopAab, two distinct dimeric charge state envelopes were observed, corresponding to distinct conformations, each with Cu6(CopAab)2 as its major form. The influence of the physiologically relevant low molecular weight thiol bacillithiol (BSH) on Cu(I)-binding to CopAab was assessed. Dimeric CopAab persisted in the presence of BSH, with previously undetected Cu7(CopAab)2 and Cu6(CopAab)2(BSH) forms apparent.
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22
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Purves J, Thomas J, Riboldi GP, Zapotoczna M, Tarrant E, Andrew PW, Londoño A, Planet PJ, Geoghegan JA, Waldron KJ, Morrissey JA. A horizontally gene transferred copper resistance locus confers hyper-resistance to antibacterial copper toxicity and enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in macrophages. Environ Microbiol 2018. [PMID: 29521441 PMCID: PMC5947656 DOI: 10.1111/1462-2920.14088] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Excess copper is highly toxic and forms part of the host innate immune system's antibacterial arsenal, accumulating at sites of infection and acting within macrophages to kill engulfed pathogens. We show for the first time that a novel, horizontally gene transferred copper resistance locus (copXL), uniquely associated with the SCCmec elements of the highly virulent, epidemic, community acquired methicillin resistant Staphylococcus aureus (CA-MRSA) USA300, confers copper hyper-resistance. These genes are additional to existing core genome copper resistance mechanisms, and are not found in typical S. aureus lineages, but are increasingly identified in emerging pathogenic isolates. Our data show that CopX, a putative P1B-3 -ATPase efflux transporter, and CopL, a novel lipoprotein, confer copper hyper-resistance compared to typical S. aureus strains. The copXL genes form an operon that is tightly repressed in low copper environments by the copper regulator CsoR. Significantly, CopX and CopL are important for S. aureus USA300 intracellular survival within macrophages. Therefore, the emergence of new S. aureus clones with the copXL locus has significant implications for public health because these genes confer increased resistance to antibacterial copper toxicity, enhancing bacterial fitness by altering S. aureus interaction with innate immunity.
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Affiliation(s)
- Joanne Purves
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Jamie Thomas
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gustavo P Riboldi
- Institute for Cell & Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Marta Zapotoczna
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Ireland
| | - Emma Tarrant
- Institute for Cell & Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Peter W Andrew
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester, LE1 9HN, UK
| | | | - Paul J Planet
- Department of Pediatrics, Columbia University, New York, NY, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joan A Geoghegan
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Ireland
| | - Kevin J Waldron
- Institute for Cell & Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Julie A Morrissey
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
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23
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Abstract
Copper is essential for most organisms as a cofactor for key enzymes involved in fundamental processes such as respiration and photosynthesis. However, copper also has toxic effects in cells, which is why eukaryotes and prokaryotes have evolved mechanisms for safe copper handling. A new family of bacterial proteins uses a Cys-rich four-helix bundle to safely store large quantities of Cu(I). The work leading to the discovery of these proteins, their properties and physiological functions, and how their presence potentially impacts the current views of bacterial copper handling and use are discussed in this review.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
| | - Sholto David
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Jaeick Lee
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
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24
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Vincent M, Duval RE, Hartemann P, Engels-Deutsch M. Contact killing and antimicrobial properties of copper. J Appl Microbiol 2018; 124:1032-1046. [PMID: 29280540 DOI: 10.1111/jam.13681] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/06/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022]
Abstract
With the emergence of antibiotic resistance, the interest for antimicrobial agents has recently increased again in public health. Copper was recognized in 2008 by the United States Environmental Protection Agency (EPA) as the first metallic antimicrobial agent. This led to many investigations of the various properties of copper as an antibacterial, antifungal and antiviral agent. This review summarizes the latest findings about 'contact killing', the mechanism of action of copper nanoparticles and the different ways micro-organisms develop resistance to copper.
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Affiliation(s)
- M Vincent
- CNRS, LEMTA, UMR 7563, Vandœuvre-lès-Nancy, France.,Université de Lorraine, LEMTA, UMR 7563, Vandœuvre-lès Nancy, France
| | - R E Duval
- CNRS, UMR 7565, SRSMC, Vandœuvre-lès-Nancy, France.,Université de Lorraine, UMR 7565, SRSMC, Nancy, France.,ABC Platform®, Nancy, France
| | - P Hartemann
- Faculté de Médecine, EA 7298, ERAMBO, DESP, Vandœuvre-lès-Nancy, France
| | - M Engels-Deutsch
- CNRS, LEMTA, UMR 7563, Vandœuvre-lès-Nancy, France.,Université de Lorraine, LEMTA, UMR 7563, Vandœuvre-lès Nancy, France.,Faculté de Médecine, EA 7298, ERAMBO, DESP, Vandœuvre-lès-Nancy, France
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25
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Copper Chaperone CupA and Zinc Control CopY Regulation of the Pneumococcal cop Operon. mSphere 2017; 2:mSphere00372-17. [PMID: 29062896 PMCID: PMC5646241 DOI: 10.1128/msphere.00372-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/27/2017] [Indexed: 01/08/2023] Open
Abstract
As mechanisms of copper toxicity are emerging, bacterial processing of intracellular copper, specifically inside Streptococcus pneumoniae, remains unclear. In this study, we investigated two proteins encoded by the copper export operon: the repressor, CopY, and the copper chaperone, CupA. Zinc suppressed transcription of the copper export operon by increasing the affinity of CopY for DNA. Furthermore, CupA was able to chelate copper from CopY not bound to DNA and reduce it from Cu2+ to Cu1+. This reduced copper state is essential for bacterial copper export via CopA. In view of the fact that innate immune cells use copper to kill pathogenic bacteria, understanding the mechanisms of copper export could expose new small-molecule therapeutic targets that could work synergistically with copper against pathogenic bacteria. Any metal in excess can be toxic; therefore, metal homeostasis is critical to bacterial survival. Bacteria have developed specialized metal import and export systems for this purpose. For broadly toxic metals such as copper, bacteria have evolved only export systems. The copper export system (cop operon) usually consists of the operon repressor, the copper chaperone, and the copper exporter. In Streptococcus pneumoniae, the causative agent of pneumonia, otitis media, sepsis, and meningitis, little is known about operon regulation. This is partly due to the S. pneumoniae repressor, CopY, and copper chaperone, CupA, sharing limited homology to proteins of putative related function and confirmed established systems. In this study, we examined CopY metal crosstalk, CopY interactions with CupA, and how CupA can control the oxidation state of copper. We found that CopY bound zinc and increased the DNA-binding affinity of CopY by roughly an order of magnitude over that of the apo form of CopY. Once copper displaced zinc in CopY, resulting in operon activation, CupA chelated copper from CopY. After copper was acquired from CopY or other sources, if needed, CupA facilitated the reduction of Cu2+ to Cu1+, which is the exported copper state. Taken together, these data show novel mechanisms for copper processing in S. pneumoniae. IMPORTANCE As mechanisms of copper toxicity are emerging, bacterial processing of intracellular copper, specifically inside Streptococcus pneumoniae, remains unclear. In this study, we investigated two proteins encoded by the copper export operon: the repressor, CopY, and the copper chaperone, CupA. Zinc suppressed transcription of the copper export operon by increasing the affinity of CopY for DNA. Furthermore, CupA was able to chelate copper from CopY not bound to DNA and reduce it from Cu2+ to Cu1+. This reduced copper state is essential for bacterial copper export via CopA. In view of the fact that innate immune cells use copper to kill pathogenic bacteria, understanding the mechanisms of copper export could expose new small-molecule therapeutic targets that could work synergistically with copper against pathogenic bacteria.
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26
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Quintana J, Novoa-Aponte L, Argüello JM. Copper homeostasis networks in the bacterium Pseudomonas aeruginosa. J Biol Chem 2017; 292:15691-15704. [PMID: 28760827 DOI: 10.1074/jbc.m117.804492] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/21/2017] [Indexed: 11/06/2022] Open
Abstract
Bacterial copper (Cu+) homeostasis enables both precise metallation of diverse cuproproteins and control of variable metal levels. To this end, protein networks mobilize Cu+ to cellular targets with remarkable specificity. However, the understanding of these processes is rather fragmented. Here, we use genome-wide transcriptomic analysis by RNA-Seq to characterize the response of Pseudomonas aeruginosa to external 0.5 mm CuSO4, a condition that did not generate pleiotropic effects. Pre-steady-state (5-min) and steady-state (2-h) Cu+ fluxes resulted in distinct transcriptome landscapes. Cells quickly responded to Cu2+ stress by slowing down metabolism. This was restored once steady state was reached. Specific Cu+ homeostasis genes were strongly regulated in both conditions. Our system-wide analysis revealed induction of three Cu+ efflux systems (a P1B-ATPase, a porin, and a resistance-nodulation-division (RND) system) and of a putative Cu+-binding periplasmic chaperone and the unusual presence of two cytoplasmic CopZ proteins. Both CopZ chaperones could bind Cu+ with high affinity. Importantly, novel transmembrane transporters probably mediating Cu+ influx were among those largely repressed upon Cu+ stress. Compartmental Cu+ levels appear independently controlled; the cytoplasmic Cu+ sensor CueR controls cytoplasmic chaperones and plasma membrane transporters, whereas CopR/S responds to periplasmic Cu+ Analysis of ΔcopR and ΔcueR mutant strains revealed a CopR regulon composed of genes involved in periplasmic Cu+ homeostasis and its putative DNA recognition sequence. In conclusion, our study establishes a system-wide model of a network of sensors/regulators, soluble chaperones, and influx/efflux transporters that control the Cu+ levels in P. aeruginosa compartments.
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Affiliation(s)
- Julia Quintana
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Lorena Novoa-Aponte
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - José M Argüello
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
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27
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Abstract
Bacteria require iron for growth, with only a few reported exceptions. In many environments, iron is a limiting nutrient for growth and high affinity uptake systems play a central role in iron homeostasis. However, iron can also be detrimental to cells when it is present in excess, particularly under aerobic conditions where its participation in Fenton chemistry generates highly reactive hydroxyl radicals. Recent results have revealed a critical role for iron efflux transporters in protecting bacteria from iron intoxication. Systems that efflux iron are widely distributed amongst bacteria and fall into several categories: P1B-type ATPases, cation diffusion facilitator (CDF) proteins, major facilitator superfamily (MFS) proteins, and membrane bound ferritin-like proteins. Here, we review the emerging role of iron export in both iron homeostasis and as part of the adaptive response to oxidative stress.
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Affiliation(s)
- Hualiang Pi
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.
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28
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Antimicrobial resistance and its association with tolerance to heavy metals in agriculture production. Food Microbiol 2017; 64:23-32. [DOI: 10.1016/j.fm.2016.12.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 11/20/2022]
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29
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Saha RP, Samanta S, Patra S, Sarkar D, Saha A, Singh MK. Metal homeostasis in bacteria: the role of ArsR-SmtB family of transcriptional repressors in combating varying metal concentrations in the environment. Biometals 2017; 30:459-503. [PMID: 28512703 DOI: 10.1007/s10534-017-0020-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 05/09/2017] [Indexed: 02/02/2023]
Abstract
Bacterial infections cause severe medical problems worldwide, resulting in considerable death and loss of capital. With the ever-increasing rise of antibiotic-resistant bacteria and the lack of development of new antibiotics, research on metal-based antimicrobial therapy has now gained pace. Metal ions are essential for survival, but can be highly toxic to organisms if their concentrations are not strictly controlled. Through evolution, bacteria have acquired complex metal-management systems that allow them to acquire metals that they need for survival in different challenging environments while evading metal toxicity. Metalloproteins that controls these elaborate systems in the cell, and linked to key virulence factors, are promising targets for the anti-bacterial drug development. Among several metal-sensory transcriptional regulators, the ArsR-SmtB family displays greatest diversity with several distinct metal-binding and nonmetal-binding motifs that have been characterized. These prokaryotic metolloregulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of metal ions by directly binding to the regulatory regions of DNA, while derepression results from direct binding of metal ions by these homodimeric proteins. Many bacteria, e.g., Mycobacterium tuberculosis, Bacillus anthracis, etc., have evolved to acquire multiple metal-sensory motifs which clearly demonstrate the importance of regulating concentrations of multiple metal ions. Here, we discussed the mechanisms of how ArsR-SmtB family regulates the intracellular bioavailability of metal ions both inside and outside of the host. Knowledge of the metal-challenges faced by bacterial pathogens and their survival strategies will enable us to develop the next generation drugs.
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Affiliation(s)
- Rudra P Saha
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India.
| | - Saikat Samanta
- Department of Microbiology, School of Science, Adamas University, Kolkata, 700126, India
| | - Surajit Patra
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
| | - Diganta Sarkar
- Department of Biotechnology, Techno India University, Kolkata, 700091, India
| | - Abinit Saha
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
| | - Manoj Kumar Singh
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
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30
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Foster AW, Pernil R, Patterson CJ, Scott AJP, Pålsson LO, Pal R, Cummins I, Chivers PT, Pohl E, Robinson NJ. A tight tunable range for Ni(II) sensing and buffering in cells. Nat Chem Biol 2017; 13:409-414. [PMID: 28166209 PMCID: PMC5365139 DOI: 10.1038/nchembio.2310] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/01/2016] [Indexed: 11/08/2022]
Abstract
The metal affinities of metal-sensing transcriptional regulators co-vary with cellular metal concentrations over more than 12 orders of magnitude. To understand the cause of this relationship, we determined the structure of the Ni(II) sensor InrS and then created cyanobacteria (Synechocystis PCC 6803) in which transcription of genes encoding a Ni(II) exporter and a Ni(II) importer were controlled by InrS variants with weaker Ni(II) affinities. Variant strains were sensitive to elevated nickel and contained more nickel, but the increase was small compared with the change in Ni(II) affinity. All of the variant sensors retained the allosteric mechanism that inhibits DNA binding following metal binding, but a response to nickel in vivo was observed only when the sensitivity was set to respond in a relatively narrow (less than two orders of magnitude) range of nickel concentrations. Thus, the Ni(II) affinity of InrS is attuned to cellular metal concentrations rather than the converse.
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Affiliation(s)
- Andrew W. Foster
- Department of Biosciences, Durham University, DH1 3LE, UK
- Department of Chemistry, Durham University, DH1 3LE, UK
| | - Rafael Pernil
- Department of Biosciences, Durham University, DH1 3LE, UK
- Department of Chemistry, Durham University, DH1 3LE, UK
| | - Carl J. Patterson
- Department of Biosciences, Durham University, DH1 3LE, UK
- Department of Chemistry, Durham University, DH1 3LE, UK
| | | | | | - Robert Pal
- Department of Chemistry, Durham University, DH1 3LE, UK
| | - Ian Cummins
- Department of Biosciences, Durham University, DH1 3LE, UK
| | - Peter T. Chivers
- Department of Biosciences, Durham University, DH1 3LE, UK
- Department of Chemistry, Durham University, DH1 3LE, UK
| | - Ehmke Pohl
- Department of Biosciences, Durham University, DH1 3LE, UK
- Department of Chemistry, Durham University, DH1 3LE, UK
| | - Nigel J. Robinson
- Department of Biosciences, Durham University, DH1 3LE, UK
- Department of Chemistry, Durham University, DH1 3LE, UK
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31
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Vita N, Landolfi G, Baslé A, Platsaki S, Lee J, Waldron KJ, Dennison C. Bacterial cytosolic proteins with a high capacity for Cu(I) that protect against copper toxicity. Sci Rep 2016; 6:39065. [PMID: 27991525 PMCID: PMC5171941 DOI: 10.1038/srep39065] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/16/2016] [Indexed: 01/23/2023] Open
Abstract
Bacteria are thought to avoid using the essential metal ion copper in their cytosol due to its toxicity. Herein we characterize Csp3, the cytosolic member of a new family of bacterial copper storage proteins from Methylosinus trichosporium OB3b and Bacillus subtilis. These tetrameric proteins possess a large number of Cys residues that point into the cores of their four-helix bundle monomers. The Csp3 tetramers can bind a maximum of approximately 80 Cu(I) ions, mainly via thiolate groups, with average affinities in the (1–2) × 1017 M−1 range. Cu(I) removal from these Csp3s by higher affinity potential physiological partners and small-molecule ligands is very slow, which is unexpected for a metal-storage protein. In vivo data demonstrate that Csp3s prevent toxicity caused by the presence of excess copper. Furthermore, bacteria expressing Csp3 accumulate copper and are able to safely maintain large quantities of this metal ion in their cytosol. This suggests a requirement for storing copper in this compartment of Csp3-producing bacteria.
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Affiliation(s)
- Nicolas Vita
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gianpiero Landolfi
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Semeli Platsaki
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jaeick Lee
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kevin J Waldron
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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32
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Regulation of the Cobalt/Nickel Efflux Operon dmeRF in Agrobacterium tumefaciens and a Link between the Iron-Sensing Regulator RirA and Cobalt/Nickel Resistance. Appl Environ Microbiol 2016; 82:4732-4742. [PMID: 27235438 DOI: 10.1128/aem.01262-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/20/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Agrobacterium tumefaciens C58 genome harbors an operon containing the dmeR (Atu0890) and dmeF (Atu0891) genes, which encode a transcriptional regulatory protein belonging to the RcnR/CsoR family and a metal efflux protein belonging to the cation diffusion facilitator (CDF) family, respectively. The dmeRF operon is specifically induced by cobalt and nickel, with cobalt being the more potent inducer. Promoter-lacZ transcriptional fusion, an electrophoretic mobility shift assay, and DNase I footprinting assays revealed that DmeR represses dmeRF transcription through direct binding to the promoter region upstream of dmeR A strain lacking dmeF showed increased accumulation of intracellular cobalt and nickel and exhibited hypersensitivity to these metals; however, this strain displayed full virulence, comparable to that of the wild-type strain, when infecting a Nicotiana benthamiana plant model under the tested conditions. Cobalt, but not nickel, increased the expression of many iron-responsive genes and reduced the induction of the SoxR-regulated gene sodBII Furthermore, control of iron homeostasis via RirA is important for the ability of A. tumefaciens to cope with cobalt and nickel toxicity. IMPORTANCE The molecular mechanism of the regulation of dmeRF transcription by DmeR was demonstrated. This work provides evidence of a direct interaction of apo-DmeR with the corresponding DNA operator site in vitro The recognition site for apo-DmeR consists of 10-bp AT-rich inverted repeats separated by six C bases (5'-ATATAGTATACCCCCCTATAGTATAT-3'). Cobalt and nickel cause DmeR to dissociate from the dmeRF promoter, which leads to expression of the metal efflux gene dmeF This work also revealed a connection between iron homeostasis and cobalt/nickel resistance in A. tumefaciens.
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33
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Hobbs ET, Pereira T, O’Neill PK, Erill I. A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. Algorithms Mol Biol 2016; 11:19. [PMID: 27398089 PMCID: PMC4938975 DOI: 10.1186/s13015-016-0082-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/30/2016] [Indexed: 11/13/2022] Open
Abstract
Background Metagenomics enables the analysis of bacterial population composition and the study of emergent population features, such as shared metabolic pathways. Recently, we have shown that metagenomics datasets can be leveraged to characterize population-wide transcriptional regulatory networks, or meta-regulons, providing insights into how bacterial populations respond collectively to specific triggers. Here we formalize a Bayesian inference framework to analyze the composition of transcriptional regulatory networks in metagenomes by determining the probability of regulation of orthologous gene sequences. We assess the performance of this approach on synthetic datasets and we validate it by analyzing the copper-homeostasis network of Firmicutes species in the human gut microbiome. Results Assessment on synthetic datasets shows that our method provides a robust and interpretable metric for assessing putative regulation by a transcription factor on sets of promoter sequences mapping to an orthologous gene cluster. The inference framework integrates the regulatory contribution of secondary sites and can discern false positives arising from multiple instances of a clonal sequence. Posterior probabilities for orthologous gene clusters decline sharply when less than 20 % of mapped promoters have binding sites, but we introduce a sensitivity adjustment procedure to speed up computation that enhances regulation assessment in heterogeneous ortholog clusters. Analysis of the copper-homeostasis regulon governed by CsoR in the human gut microbiome Firmicutes reveals that CsoR controls itself and copper-translocating P-type ATPases, but not CopZ-type copper chaperones. Our analysis also indicates that CsoR frequently targets promoters with dual CsoR-binding sites, suggesting that it exploits higher-order binding conformations to fine-tune its activity. Conclusions We introduce and validate a method for the analysis of transcriptional regulatory networks from metagenomic data that enables inference of meta-regulons in a systematic and interpretable way. Validation of this method on the CsoR meta-regulon of gut microbiome Firmicutes illustrates the usefulness of the approach, revealing novel properties of the copper-homeostasis network in poorly characterized bacterial species and putting forward evidence of new mechanisms of DNA binding for this transcriptional regulator. Our approach will enable the comparative analysis of regulatory networks across metagenomes, yielding novel insights into the evolution of transcriptional regulatory networks. Electronic supplementary material The online version of this article (doi:10.1186/s13015-016-0082-8) contains supplementary material, which is available to authorized users.
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34
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Marcus SA, Sidiropoulos SW, Steinberg H, Talaat AM. CsoR Is Essential for Maintaining Copper Homeostasis in Mycobacterium tuberculosis. PLoS One 2016; 11:e0151816. [PMID: 26999439 PMCID: PMC4801387 DOI: 10.1371/journal.pone.0151816] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022] Open
Abstract
Mycobacterium tuberculosis, a pathogen infecting one third of the world population, faces numerous challenges within the host, including high levels of copper. We have previously shown that M. tuberculosis CsoR is a copper inducible transcriptional regulator. Here we examined the hypothesis that csoR is necessary for maintaining copper homeostasis and surviving under various stress conditions. With an unmarked csoR knockout strain, we were able to characterize the role of csoR in M. tuberculosis as it faced copper and host stress. Growth under high levels of copper demonstrated that M. tuberculosis survives copper stress significantly better in the absence of csoR. Yet under minimal levels of copper, differential expression analysis revealed that the loss of csoR results in a cell wide hypoxia-type stress response with the induction of the DosR regulon. Despite the stress placed on M. tuberculosis by the loss of csoR, survival of the knockout strain was increased compared to wild type during the early chronic stages of mouse infection, suggesting that csoR could play an active role in modulating M. tuberculosis fitness within the host. Overall, analysis of CsoR provided an increased understanding of the M. tuberculosis copper response with implications for other intracellular pathogens harboring CsoR.
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Affiliation(s)
- Sarah A. Marcus
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sarah W. Sidiropoulos
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Howard Steinberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Adel M. Talaat
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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35
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Abstract
Copper (Cu) is an essential trace element for all aerobic organisms. It functions as a cofactor in enzymes that catalyze a wide variety of redox reactions due to its ability to cycle between two oxidation states, Cu(I) and Cu(II). This same redox property of copper has the potential to cause toxicity if copper homeostasis is not maintained. Studies suggest that the toxic properties of copper are harnessed by the innate immune system of the host to kill bacteria. To counter such defenses, bacteria rely on copper tolerance genes for virulence within the host. These discoveries suggest bacterial copper intoxication is a component of host nutritional immunity, thus expanding our knowledge of the roles of copper in biology. This review summarizes our current understanding of copper tolerance in bacteria, and the extent to which these pathways contribute to bacterial virulence within the host.
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Affiliation(s)
- Erik Ladomersky
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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36
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Mancini S, Kumar R, Abicht HK, Fischermeier E, Solioz M. Copper resistance and its regulation in the sulfate-reducing bacterium Desulfosporosinus sp. OT. MICROBIOLOGY-SGM 2016; 162:684-693. [PMID: 26873027 DOI: 10.1099/mic.0.000256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Desulfosporosinus sp. OT is a Gram-positive, acidophilic sulfate-reducing firmicute isolated from copper tailings sediment in the Norilsk mining-smelting area in Siberia and represents the first Desulfosporosinus species whose genome has been sequenced. Desulfosporosinus sp. OT is exceptionally copper resistant, which made it of interest to study the resistance mechanism. It possesses a copUAZ operon which is shown here to be involved in copper resistance. The copU gene encodes a CsoR-type homotetrameric repressor. By electrophoretic mobility shift assay, it was shown that CopU binds to the operator/promoter region of the copUAZ operon in the absence of copper and is released from the DNA by Cu+ or Ag+, implying that CopU regulates the operon in a copper/silver-dependent manner. DOT_CopA is a P1B-type ATPase related to other characterized, bacterial copper ATPases. When expressed in a copper-sensitive Escherichia coli ΔcopA mutant, it restores copper resistance to WT levels. His-tagged DOT_CopA was expressed from a plasmid in E. coli and purified by Ni-NTA affinity chromatography. The purified enzyme was most active in the presence of Cu(I) and bacterial phospholipids. These findings indicate that the copUAZ operon confers copper resistance to Desulfosporosinus sp. OT, but do not per se explain the basis of the high copper resistance of this strain.
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Affiliation(s)
- Stefano Mancini
- Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Ranjeet Kumar
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Helge K Abicht
- Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | | | - Marc Solioz
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia.,Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
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37
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Fukuhara T, Kobayashi K, Kanayama Y, Enomoto SI, Kondo T, Tsunekawa N, Nemoto M, Ogasawara N, Inagaki K, Tamura T. Identification and characterization of the zosA gene involved in copper uptake in Bacillus subtilis 168. Biosci Biotechnol Biochem 2015; 80:600-9. [PMID: 26566138 DOI: 10.1080/09168451.2015.1107462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
DL-Penicillamine, a copper-specific metal chelator, remarkably suppressed the growth of Bacillus subtilis 168 when added to a synthetic medium under Cu(2+) limitation. DNA microarray and screening of 2,602 knockout mutants showed that the zosA gene was de-repressed in the presence of 0.1% dl-penicillamine, and that the zosA mutant was sensitive to dl-penicillamine medium. The zosA mutant delayed the growth under Cu-limitation even without the chelator, and the sensitivity to dl-penicillamine was reversed by induction using 0.3 mM IPTG and the Pspac promoter inserted directly upstream of the zosA gene. Furthermore, the zosA mutant showed elevated tolerance of excessive Cu(2+) but not of excessive Zn(2+) added to LB and synthetic media. Homology modeling of the ZosA protein suggested that the protein can fold itself into essential domains for constituting a metal transporting ATPase. Our study suggests that zosA is a candidate gene involved in copper uptake.
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Affiliation(s)
- Takahiro Fukuhara
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan
| | - Kazuo Kobayashi
- b Graduate School of Information Science , Nara Institute of Science & Technology , Ikoma , Japan
| | - Yousuke Kanayama
- c Laboratory of Multiple Molecular Imaging Research , Center for Molecular Imaging Science, RIKEN Kobe Institute , Hyogo , Japan
| | - Shu-ichi Enomoto
- c Laboratory of Multiple Molecular Imaging Research , Center for Molecular Imaging Science, RIKEN Kobe Institute , Hyogo , Japan
| | - Taeko Kondo
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan
| | - Naoki Tsunekawa
- d Institute of Molecular and Cellular Biosciences , The University of Tokyo , Tokyo , Japan
| | - Michiko Nemoto
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan
| | - Naotake Ogasawara
- b Graduate School of Information Science , Nara Institute of Science & Technology , Ikoma , Japan
| | - Kenji Inagaki
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan
| | - Takashi Tamura
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan.,e PRESTO, Japan Science and Technology Agency , Tokyo , Japan
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38
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Porto TV, Hough MA, Worrall JAR. Structural insights into conformational switching in the copper metalloregulator CsoR from Streptomyces lividans. ACTA ACUST UNITED AC 2015; 71:1872-8. [PMID: 26327377 DOI: 10.1107/s1399004715013012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/06/2015] [Indexed: 11/10/2022]
Abstract
Copper-sensitive operon repressors (CsoRs) act to sense cuprous ions and bind them with a high affinity under copper stress in many bacteria. The binding of copper(I) leads to a conformational change in their homotetramer structure, causing disassembly of the operator DNA-CsoR complex and evoking a transcriptional response. Atomic-level structural insight into the conformational switching mechanism between the apo and metal-bound states is lacking. Here, a new X-ray crystal structure of the CsoR from Streptomyces lividans is reported and compared with a previously reported S. lividans CsoR X-ray structure crystallized under different conditions. Based on evidence from this new X-ray structure, it is revealed that the conformational switching between states centres on a concertina effect at the C-terminal end of each α2 helix in the homotetramer. This drives the Cys104 side chain, a copper(I)-ligating residue, into a position enabling copper(I) coordination and as a result disrupts the α2-helix geometry, leading to a compacting and twisting of the homotetramer structure. Strikingly, the conformational switching induces a redistribution of electrostatic surface potential on the tetrameric DNA-binding face, which in the copper(I)-bound state would no longer favour interaction with the mode of operator DNA binding.
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Affiliation(s)
- Tatiana V Porto
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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39
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Osman D, Piergentili C, Chen J, Chakrabarti B, Foster AW, Lurie-Luke E, Huggins TG, Robinson NJ. Generating a Metal-responsive Transcriptional Regulator to Test What Confers Metal Sensing in Cells. J Biol Chem 2015; 290:19806-22. [PMID: 26109070 PMCID: PMC4528141 DOI: 10.1074/jbc.m115.663427] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/06/2022] Open
Abstract
FrmR from Salmonella enterica serovar typhimurium (a CsoR/RcnR-like transcriptional de-repressor) is shown to repress the frmRA operator-promoter, and repression is alleviated by formaldehyde but not manganese, iron, cobalt, nickel, copper, or Zn(II) within cells. In contrast, repression by a mutant FrmRE64H (which gains an RcnR metal ligand) is alleviated by cobalt and Zn(II). Unexpectedly, FrmR was found to already bind Co(II), Zn(II), and Cu(I), and moreover metals, as well as formaldehyde, trigger an allosteric response that weakens DNA affinity. However, the sensory metal sites of the cells' endogenous metal sensors (RcnR, ZntR, Zur, and CueR) are all tighter than FrmR for their cognate metals. Furthermore, the endogenous metal sensors are shown to out-compete FrmR. The metal-sensing FrmRE64H mutant has tighter metal affinities than FrmR by approximately 1 order of magnitude. Gain of cobalt sensing by FrmRE64H remains enigmatic because the cobalt affinity of FrmRE64H is substantially weaker than that of the endogenous cobalt sensor. Cobalt sensing requires glutathione, which may assist cobalt access, conferring a kinetic advantage. For Zn(II), the metal affinity of FrmRE64H approaches the metal affinities of cognate Zn(II) sensors. Counter-intuitively, the allosteric coupling free energy for Zn(II) is smaller in metal-sensing FrmRE64H compared with nonsensing FrmR. By determining the copies of FrmR and FrmRE64H tetramers per cell, then estimating promoter occupancy as a function of intracellular Zn(II) concentration, we show how a modest tightening of Zn(II) affinity, plus weakened DNA affinity of the apoprotein, conspires to make the relative properties of FrmRE64H (compared with ZntR and Zur) sufficient to sense Zn(II) inside cells.
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Affiliation(s)
- Deenah Osman
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Cecilia Piergentili
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Junjun Chen
- Procter and Gamble, Mason Business Centre, Cincinnati, Ohio 45040, and
| | - Buddhapriya Chakrabarti
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Andrew W Foster
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Elena Lurie-Luke
- Life Sciences Open Innovation, London Innovation Centre, Procter and Gamble Technical Centres, Ltd., Egham TW20 9NW, United Kingdom
| | - Thomas G Huggins
- Procter and Gamble, Mason Business Centre, Cincinnati, Ohio 45040, and
| | - Nigel J Robinson
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom,
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40
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Hirooka K. Transcriptional response machineries of Bacillus subtilis conducive to plant growth promotion. Biosci Biotechnol Biochem 2015; 78:1471-84. [PMID: 25209494 DOI: 10.1080/09168451.2014.943689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Bacillus subtilis collectively inhabits the rhizosphere, where it contributes to the promotion of plant growth, although it does not have a direct symbiotic relationship to plants as observed in the case of rhizobia between leguminous plants. As rhizobia sense the flavonoids released from their host roots through the NodD transcriptional factor, which triggers transcription of the nod genes involved in the symbiotic processes, we supposed that B. subtilis utilizes certain flavonoids as signaling molecules to perceive and adapt to the rhizospheric environment that it is in. Our approaches to identify the flavonoid-responsive transcriptional regulatory system from B. subtilis resulted in the findings that three transcriptional factors (LmrA/QdoR, YetL, and Fur) are responsive to flavonoids, with the modes of action being different from each other. We also revealed a unique regulatory system by two transcriptional factors, YcnK and CsoR, for copper homeostasis in B. subtilis. In this review, we summarize the molecular mechanisms of these regulatory systems with the relevant information and discuss their physiological significances in the mutually beneficial interaction between B. subtilis and plants, considering the possibility of their application for plant cultivation.
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Affiliation(s)
- Kazutake Hirooka
- a Department of Biotechnology, Faculty of Life Science and Biotechnology , Fukuyama University , Fukuyama , Hiroshima , Japan
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41
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Zhao Z, Zhou Z, Li L, Xian X, Ke X, Chen M, Zhang Y. A copper-responsive gene cluster is required for copper homeostasis and contributes to oxidative resistance in Deinococcus radiodurans R1. MOLECULAR BIOSYSTEMS 2015; 10:2607-16. [PMID: 25030084 DOI: 10.1039/c4mb00320a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Excess copper is toxic to organisms, and therefore, copper homeostasis is important for the limitation of its cellular levels. However, copper homeostasis has not been studied to date in the bacteria Deinococcus radiodurans R1, which exhibits extreme resistance to various environmental stresses. We have identified a copper-responsive gene cluster that encodes CopA, which is a copper-transporting P1-type ATPase, CopZ, which is a copper metallochaperone, and CsoR, which is a copper-sensing repressor. Copper induces the transcription of genes in this cluster. Mutants lacking copA exhibited reduced copper resistance and the overaccumulation of copper compared with the wild-type strain. Additionally, both in the absence and presence of copper, the copZ mutation increased the expression of copA and led to the accumulation of lower levels of copper compared with the wild type. The bioinformatic analysis showed that CsoR in D. radiodurans R1 shares high sequence similarity and identity with the CsoR of Mycobacterium tuberculosis and Bacillus subtilis. We also demonstrated through DNase I footprinting and electrophoretic mobility shift assays that CsoR binds to the promoter of the cluster and that copper ions eliminate this interaction. This implies that CsoR is the repressor of this cluster and that CopA, CopZ and CsoR participate in the regulation of copper homeostasis. Our data also indicate that after treatment with H2O2 and cumene hydroperoxide, the viability of the copA mutants was significantly reduced. This suggests that copper homeostasis plays an important role in oxidative resistance in D. radiodurans R1.
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Affiliation(s)
- Zhongchao Zhao
- China University of Mining and Technology (Beijing), Beijing 100083, China.
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42
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Chang FMJ, Martin JE, Giedroc DP. Electrostatic occlusion and quaternary structural ion pairing are key determinants of Cu(I)-mediated allostery in the copper-sensing operon repressor (CsoR). Biochemistry 2015; 54:2463-72. [PMID: 25798654 DOI: 10.1021/acs.biochem.5b00154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The copper-sensing operon repressor (CsoR) is an all-α-helical disc-shaped D2-symmetric homotetramer that forms a 2:1 tetramer/DNA operator complex and represses the expression of copper-resistance genes in a number of bacteria. A previous bioinformatics analysis of CsoR-family repressors distributes Cu(I)-sensing CsoRs in four of seven distinct clades on the basis of global sequence similarity. In this work, we define energetically important determinants of DNA binding in the apo-state (ΔΔGbind), and for allosteric negative coupling of Cu(I) binding to DNA binding (ΔΔGc) in a model clade IV CsoR from Geobacillus thermodenitrificans (Gt) of known structure, by selectively targeting for mutagenesis those charged residues uniquely conserved in clade IV CsoRs. These include a folded N-terminal "tail" and a number of Cu(I)-sensor and clade-specific residues that when mapped onto a model of Cu(I)-bound Gt CsoR define a path across one face of the tetramer. We find that Cu(I)-binding prevents formation of the 2:1 "sandwich" complex rather than DNA binding altogether. Folding of the N-terminal tail (residues R18, E22, R74) upon Cu-binding to the periphery of the tetramer inhibits assembly of the 2:1 apoprotein-DNA complex. In contrast, Ala substitution of residues that surround the central "hole" (R65, K101) in the tetramer, as well R48, impact DNA binding. We also identify a quaternary structural ion-pair, E73-K101″, that crosses the tetramer interface, charge-reversal of which restores DNA binding activity, allosteric regulation by Cu(I), and transcriptional derepression by Cu(I) in cells. These findings suggest an "electrostatic occlusion" model, in which basic residues important for DNA binding and/or allostery become sequestered via ion-pairing specifically in the Cu(I)-bound state, and this aids in copper-dependent disassembly of a repression complex.
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Affiliation(s)
- Feng-Ming James Chang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Julia E Martin
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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43
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Copper homeostasis-related genes in three separate transcriptional units regulated by CsoR in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2015; 99:3505-17. [DOI: 10.1007/s00253-015-6373-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 12/23/2014] [Accepted: 12/28/2014] [Indexed: 10/24/2022]
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44
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Hobman JL, Crossman LC. Bacterial antimicrobial metal ion resistance. J Med Microbiol 2014; 64:471-497. [PMID: 25418738 DOI: 10.1099/jmm.0.023036-0] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/17/2014] [Indexed: 01/23/2023] Open
Abstract
Metals such as mercury, arsenic, copper and silver have been used in various forms as antimicrobials for thousands of years with until recently, little understanding of their mode of action. The discovery of antibiotics and new organic antimicrobial compounds during the twentieth century saw a general decline in the clinical use of antimicrobial metal compounds, with the exception of the rediscovery of the use of silver for burns treatments and niche uses for other metal compounds. Antibiotics and new antimicrobials were regarded as being safer for the patient and more effective than the metal-based compounds they supplanted. Bacterial metal ion resistances were first discovered in the second half of the twentieth century. The detailed mechanisms of resistance have now been characterized in a wide range of bacteria. As the use of antimicrobial metals is limited, it is legitimate to ask: are antimicrobial metal resistances in pathogenic and commensal bacteria important now? This review details the new, rediscovered and 'never went away' uses of antimicrobial metals; examines the prevalence and linkage of antimicrobial metal resistance genes to other antimicrobial resistance genes; and examines the evidence for horizontal transfer of these genes between bacteria. Finally, we discuss the possible implications of the widespread dissemination of these resistances on re-emergent uses of antimicrobial metals and how this could impact upon the antibiotic resistance problem.
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Affiliation(s)
- Jon L Hobman
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Lisa C Crossman
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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45
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Chang FMJ, Coyne HJ, Cubillas C, Vinuesa P, Fang X, Ma Z, Ma D, Helmann JD, García-de los Santos A, Wang YX, Dann CE, Giedroc DP. Cu(I)-mediated allosteric switching in a copper-sensing operon repressor (CsoR). J Biol Chem 2014; 289:19204-17. [PMID: 24831014 DOI: 10.1074/jbc.m114.556704] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The copper-sensing operon repressor (CsoR) is representative of a major Cu(I)-sensing family of bacterial metalloregulatory proteins that has evolved to prevent cytoplasmic copper toxicity. It is unknown how Cu(I) binding to tetrameric CsoRs mediates transcriptional derepression of copper resistance genes. A phylogenetic analysis of 227 DUF156 protein members, including biochemically or structurally characterized CsoR/RcnR repressors, reveals that Geobacillus thermodenitrificans (Gt) CsoR characterized here is representative of CsoRs from pathogenic bacilli Listeria monocytogenes and Bacillus anthracis. The 2.56 Å structure of Cu(I)-bound Gt CsoR reveals that Cu(I) binding induces a kink in the α2-helix between two conserved copper-ligating residues and folds an N-terminal tail (residues 12-19) over the Cu(I) binding site. NMR studies of Gt CsoR reveal that this tail is flexible in the apo-state with these dynamics quenched upon Cu(I) binding. Small angle x-ray scattering experiments on an N-terminally truncated Gt CsoR (Δ2-10) reveal that the Cu(I)-bound tetramer is hydrodynamically more compact than is the apo-state. The implications of these findings for the allosteric mechanisms of other CsoR/RcnR repressors are discussed.
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Affiliation(s)
- Feng-Ming James Chang
- From the Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102
| | - H Jerome Coyne
- From the Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102
| | - Ciro Cubillas
- the Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, México, 04510
| | - Pablo Vinuesa
- the Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, México, 04510
| | - Xianyang Fang
- the Structural Biophysics Laboratory, Center for Cancer Research, NCI-National Institutes of Health, Frederick, Maryland 21702-1201, and
| | - Zhen Ma
- the Department of Microbiology, Cornell University, Ithaca, New York 14853-8101
| | - Dejian Ma
- From the Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102
| | - John D Helmann
- the Department of Microbiology, Cornell University, Ithaca, New York 14853-8101
| | - Alejandro García-de los Santos
- the Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, México, 04510
| | - Yun-Xing Wang
- the Structural Biophysics Laboratory, Center for Cancer Research, NCI-National Institutes of Health, Frederick, Maryland 21702-1201, and
| | - Charles E Dann
- From the Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102
| | - David P Giedroc
- From the Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102,
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46
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Foster AW, Pernil R, Patterson CJ, Robinson NJ. Metal specificity of cyanobacterial nickel-responsive repressor InrS: cells maintain zinc and copper below the detection threshold for InrS. Mol Microbiol 2014; 92:797-812. [PMID: 24666373 PMCID: PMC4235346 DOI: 10.1111/mmi.12594] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 12/25/2022]
Abstract
InrS is a Ni(II)-responsive, CsoR/RcnR-like, DNA-binding transcriptional repressor of the nrsD gene, but the Ni(II) co-ordination sphere of InrS is unlike Ni(II)-RcnR. We show that copper and Zn(II) also bind tightly to InrS and in vitro these ions also impair InrS binding to the nrsD operator-promoter. InrS does not respond to Zn(II) (or copper) in vivo after 48 h, when Zn(II) sensor ZiaR responds, but InrS transiently responds (1 h) to both metals. InrS conserves only one (of two) second co-ordination shell residues of CsoR (Glu98 in InrS). The allosteric mechanism of InrS is distinct from Cu(I)-CsoR and conservation of deduced second shell residues better predicts metal specificity than do the metal ligands. The allosteric mechanism of InrS permits greater promiscuity in vitro than CsoR. The factors dictating metal-selectivity in vivo are that KNi(II) and ΔGCNi(II)-InrS·DNA are sufficiently high, relative to other metal sensors, for InrS to detect Ni(II), while the equivalent parameters for copper may be insufficient for copper-sensing in S ynechocystis (at 48 h). InrS KZn(II) (5.6 × 10−13 M) is comparable to the sensory sites of ZiaR (and Zur), but ΔGCZn(II)-InrS·DNA is less than ΔGCZn(II)-ZiaR·DNA implying that relative to other sensors, ΔGCZn(II)-Sensor·DNA rather than KZn(II) determines the final detection threshold for Zn(II).
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Affiliation(s)
- Andrew W Foster
- Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK
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47
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Antelmann H, Hecker M, Zuber P. Proteomic signatures uncover thiol-specific electrophile resistance mechanisms inBacillus subtilis. Expert Rev Proteomics 2014; 5:77-90. [DOI: 10.1586/14789450.5.1.77] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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48
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Higgins KA, Giedroc D. Insights into Protein Allostery in the CsoR/RcnR Family of Transcriptional Repressors. CHEM LETT 2014; 43:20-25. [PMID: 24695963 DOI: 10.1246/cl.130965] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CsoR/RcnR transcriptional repressors adopt a disc-shaped, all α-helical dimer of dimers tetrameric architecture, with a four-helix bundle the key structural feature of the dimer. Individual members of this large family of repressors coordinate Cu(I) or Ni(II)/Co(II) or perform cysteine sulfur chemistry in mitigating the effects of metal or metabolite toxicity, respectively. Here we highlight recent insights into the functional diversity of this fascinating family of repressors.
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Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA
| | - David Giedroc
- Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA
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49
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Argüello JM, Raimunda D, Padilla-Benavides T. Mechanisms of copper homeostasis in bacteria. Front Cell Infect Microbiol 2013; 3:73. [PMID: 24205499 PMCID: PMC3817396 DOI: 10.3389/fcimb.2013.00073] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 10/17/2013] [Indexed: 01/27/2023] Open
Abstract
Copper is an important micronutrient required as a redox co-factor in the catalytic centers of enzymes. However, free copper is a potential hazard because of its high chemical reactivity. Consequently, organisms exert a tight control on Cu(+) transport (entry-exit) and traffic through different compartments, ensuring the homeostasis required for cuproprotein synthesis and prevention of toxic effects. Recent studies based on biochemical, bioinformatics, and metalloproteomics approaches, reveal a highly regulated system of transcriptional regulators, soluble chaperones, membrane transporters, and target cuproproteins distributed in the various bacterial compartments. As a result, new questions have emerged regarding the diversity and apparent redundancies of these components, their irregular presence in different organisms, functional interactions, and resulting system architectures.
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Affiliation(s)
- José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute Worcester, MA, USA
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50
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Tan BG, Vijgenboom E, Worrall JAR. Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans. Nucleic Acids Res 2013; 42:1326-40. [PMID: 24121681 PMCID: PMC3902906 DOI: 10.1093/nar/gkt902] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. The copper sensitive operon repressor (CsoR) family is widely distributed in bacteria and controls the expression of copper efflux systems. CsoR operator sites consist of G-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. Here, we use a structurally characterized CsoR from Streptomyces lividans (CsoRSl) together with three specific operator targets to reveal the salient features pertaining to the mechanism of DNA binding. We reveal that CsoRSl binds to its operator site through a 2-fold axis of symmetry centred on a conserved 5′-TAC/GTA-3′ inverted repeat. Operator recognition is stringently dependent not only on electropositive residues but also on a conserved polar glutamine residue. Thermodynamic and circular dichroic signatures of the CsoRSl–DNA interaction suggest selectivity towards the A-DNA-like topology of the G-tracts at the operator site. Such properties are enhanced on protein binding thus enabling the symmetrical binding of two CsoRSl tetramers. Finally, differential binding modes may exist in operator sites having more than one 5′-TAC/GTA-3′ inverted repeat with implications in vivo for a mechanism of modular control.
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Affiliation(s)
- Benedict G Tan
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK and Molecular Biotechnology, Institute of Biology Leiden, Sylvius Laboratory, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands
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