1
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Kahali S, Das SK, Kumar R, Gupta K, Kundu R, Bhattacharya B, Nath A, Venkatramani R, Datta A. A water-soluble, cell-permeable Mn(ii) sensor enables visualization of manganese dynamics in live mammalian cells. Chem Sci 2024; 15:10753-10769. [PMID: 39027293 PMCID: PMC11253179 DOI: 10.1039/d4sc00907j] [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: 02/06/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Central roles of Mn2+ ions in immunity, brain function, and photosynthesis necessitate probes for tracking this essential metal ion in living systems. However, developing a cell-permeable, fluorescent sensor for selective imaging of Mn2+ ions in the aqueous cellular milieu has remained a challenge. This is because Mn2+ is a weak binder to ligand-scaffolds and Mn2+ ions quench fluorescent dyes leading to turn-off sensors that are not applicable for in vivo imaging. Sensors with a unique combination of Mn2+ selectivity, μM sensitivity, and response in aqueous media are necessary for not only visualizing labile cellular Mn2+ ions live, but also for measuring Mn2+ concentrations in living cells. No sensor has achieved this combination thus far. Here we report a novel, completely water-soluble, reversible, fluorescent turn-on, Mn2+ selective sensor, M4, with a K d of 1.4 μM for Mn2+ ions. M4 entered cells within 15 min of direct incubation and was applied to image Mn2+ ions in living mammalian cells in both confocal fluorescence intensity and lifetime-based set-ups. The probe was able to visualize Mn2+ dynamics in live cells revealing differential Mn2+ localization and uptake dynamics under pathophysiological versus physiological conditions. In a key experiment, we generated an in-cell Mn2+ response curve for the sensor which allowed the measurement of the endogenous labile Mn2+ concentration in HeLa cells as 1.14 ± 0.15 μM. Thus, our computationally designed, selective, sensitive, and cell-permeable sensor with a 620 nM limit of detection for Mn2+ in water provides the first estimate of endogenous labile Mn2+ levels in mammalian cells.
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Affiliation(s)
- Smitaroopa Kahali
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Sujit Kumar Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Ravinder Kumar
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Kunika Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Rajasree Kundu
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Baivabi Bhattacharya
- Department of Developmental Biology and Genetics, Indian Institute of Science Bangalore 560012 India
| | - Arnab Nath
- Department of Developmental Biology and Genetics, Indian Institute of Science Bangalore 560012 India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Ankona Datta
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
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2
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Kim M, Le MT, Fan L, Campbell C, Sen S, Capdevila DA, Stemmler TL, Giedroc DP. Characterization of the Zinc Uptake Repressor (Zur) from Acinetobacter baumannii. Biochemistry 2024; 63:660-670. [PMID: 38385972 PMCID: PMC11019503 DOI: 10.1021/acs.biochem.3c00679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Bacterial cells tightly regulate the intracellular concentrations of essential transition metal ions by deploying a panel of metal-regulated transcriptional repressors and activators that bind to operator-promoter regions upstream of regulated genes. Like other zinc uptake regulator (Zur) proteins, Acinetobacter baumannii Zur represses transcription of its regulon when ZnII is replete and binds more weakly to DNA when ZnII is limiting. Previous studies established that Zur proteins are homodimeric and harbor at least two metal sites per protomer or four per dimer. CdII X-ray absorption spectroscopy (XAS) of the Cd2Zn2 AbZur metalloderivative with CdII bound to the allosteric sites reveals a S(N/O)3 first coordination shell. Site-directed mutagenesis suggests that H89 and C100 from the N-terminal DNA binding domain and H107 and E122 from the C-terminal dimerization domain comprise the regulatory metal site. KZn for this allosteric site is 6.0 (±2.2) × 1012 M-1 with a functional "division of labor" among the four metal ligands. N-terminal domain ligands H89 and C100 contribute far more to KZn than H107 and E122, while C100S AbZur uniquely fails to bind to DNA tightly as measured by an in vitro transcription assay. The heterotropic allosteric coupling free energy, ΔGc, is negative, consistent with a higher KZn for the AbZur-DNA complex and defining a bioavailable ZnII set-point of ≈6 × 10-14 M. Small-angle X-ray scattering (SAXS) experiments reveal that only the wild-type Zn homodimer undergoes allosteric switching, while the C100S AbZur fails to switch. These data collectively suggest that switching to a high affinity DNA-binding conformation involves a rotation/translation of one protomer relative to the other in a way that is dependent on the integrity of C100. We place these findings in the context of other Zur proteins and Fur family repressors more broadly.
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Affiliation(s)
- Minyong Kim
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - My Tra Le
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Courtney Campbell
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201-2417, United States
| | - Sambuddha Sen
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405 BWE Buenos Aires, Argentina
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201-2417, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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3
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Basak P, Cabelli DE, Chivers PT, Farquhar ER, Maroney MJ. In vitro maturation of NiSOD reveals a role for cytoplasmic histidine in processing and metalation. Metallomics 2023; 15:mfad054. [PMID: 37723610 PMCID: PMC10628968 DOI: 10.1093/mtomcs/mfad054] [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: 06/13/2023] [Accepted: 09/16/2023] [Indexed: 09/20/2023]
Abstract
The importance of cellular low molecular weight ligands in metalloenzyme maturation is largely unexplored. Maturation of NiSOD requires post-translational N-terminal processing of the proenzyme, SodN, by its cognate protease, SodX. Here we provide evidence for the participation of L-histidine in the protease-dependent maturation of nickel-dependent superoxide dismutase (NiSOD) from Streptomyces coelicolor. In vitro studies using purified proteins cloned from S. coelicolor and overexpressed in E. coli support a model where a ternary complex formed between the substrate (SodN), the protease (SodX) and L-Histidine creates a novel Ni-binding site that is capable of the N-terminal processing of SodN and specifically incorporates Ni into the apo-NiSOD product. Thus, L-Histidine serves many of the functions associated with a metallochaperone or, conversely, eliminates the need for a metallochaperone in NiSOD maturation.
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Affiliation(s)
- Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Diane E Cabelli
- Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Erik R Farquhar
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA
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4
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Osman D, Robinson NJ. Protein metalation in a nutshell. FEBS Lett 2023; 597:141-150. [PMID: 36124565 PMCID: PMC10087151 DOI: 10.1002/1873-3468.14500] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 01/14/2023]
Abstract
Metalation, the acquisition of metals by proteins, must avoid mis-metalation with tighter binding metals. This is illustrated by four selected proteins that require different metals: all show similar ranked orders of affinity for bioavailable metals, as described in a universal affinity series (the Irving-Williams series). Crucially, cellular protein metalation occurs in competition with other metal binding sites. The strength of this competition defines the intracellular availability of each metal: its magnitude has been estimated by calibrating a cells' set of DNA-binding, metal-sensing, transcriptional regulators. This has established that metal availabilities (as free energies for forming metal complexes) are maintained to the inverse of the universal series. The tightest binding metals are least available. With these availabilities, correct metalation is achieved.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, University of Durham, UK.,Department of Chemistry, University of Durham, UK
| | - Nigel J Robinson
- Department of Biosciences, University of Durham, UK.,Department of Chemistry, University of Durham, UK
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5
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Choi TS, Tezcan FA. Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. J Am Chem Soc 2022; 144:18090-18100. [PMID: 36154053 PMCID: PMC9949983 DOI: 10.1021/jacs.2c08050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Selective metal binding is a key requirement not only for the functions of natural metalloproteins but also for the potential applications of artificial metalloproteins in heterogeneous environments such as cells and environmental samples. The selection of transition-metal ions through protein design can, in principle, be achieved through the appropriate choice and the precise positioning of amino acids that comprise the primary metal coordination sphere. However, this task is made difficult by the intrinsic flexibility of proteins and the fact that protein design approaches generally lack the sub-Å precision required for the steric selection of metal ions. We recently introduced a flexible/probabilistic protein design strategy (MASCoT) that allows metal ions to search for optimal coordination geometry within a flexible, yet covalently constrained dimer interface. In an earlier proof-of-principle study, we used MASCoT to generate an artificial metalloprotein dimer, (AB)2, which selectively bound CoII and NiII over CuII (as well as other first-row transition-metal ions) through the imposition of a rigid octahedral coordination geometry, thus countering the Irving-Williams trend. In this study, we set out to redesign (AB)2 to examine the applicability of MASCoT to the selective binding of other metal ions. We report here the design and characterization of a new flexible protein dimer, B2, which displays ZnII selectivity over all other tested metal ions including CuII both in vitro and in cellulo. Selective, anti-Irving-Williams ZnII binding by B2 is achieved through the formation of a unique trinuclear Zn coordination motif in which His and Glu residues are rigidly placed in a tetrahedral geometry. These results highlight the utility of protein flexibility in the design and discovery of selective binding motifs.
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6
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Foster AW, Clough SE, Aki Z, Young TR, Clarke AR, Robinson NJ. Metalation calculators for E. coli strain JM109 (DE3): Aerobic, anaerobic and hydrogen peroxide exposed cells cultured in LB media. Metallomics 2022; 14:6657815. [PMID: 35933161 PMCID: PMC9434800 DOI: 10.1093/mtomcs/mfac058] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/24/2022] [Indexed: 11/14/2022]
Abstract
Three web-based calculators, and three analogous spreadsheets, have been generated that predict in vivo metal occupancies of proteins based on known metal affinities. The calculations exploit estimates of the availabilities of the labile buffered pools of different metals inside a cell. Here, metal availabilities have been estimated for a strain of E. coli that is commonly used in molecular biology and biochemistry research, for example in the production of recombinant proteins. Metal availabilities have been examined for cells grown in LB medium aerobically, anaerobically and in response to H2O2 by monitoring the abundance of a selected set of metal-responsive transcripts by qPCR. The selected genes are regulated by DNA-binding metal sensors that have been thermodynamically characterised in related bacterial cells enabling gene expression to be read-out as a function of intracellular metal availabilities expressed as free energies for forming metal complexes. The calculators compare these values with the free energies for forming complexes with the protein of interest, derived from metal affinities, to estimate how effectively the protein can compete with exchangeable binding sites in the intracellular milieu. The calculators then inter-compete the different metals, limiting total occupancy of the site to a maximum stoichiometry of 1, to output percentage occupancies with each metal. In addition to making these new and conditional calculators available, an original purpose of this article was to provide a tutorial which discusses constraints of this approach and presents ways in which such calculators might be exploited in basic and applied research, and in next-generation manufacturing.
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Affiliation(s)
- Andrew W Foster
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Sophie E Clough
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Zeynep Aki
- Advanced Research Computing, Durham University, Durham, UK
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | | | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
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7
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Fakhoury JN, Zhang Y, Edmonds KA, Bringas M, Luebke JL, Gonzalez-Gutierrez G, Capdevila DA, Giedroc DP. Functional asymmetry and chemical reactivity of CsoR family persulfide sensors. Nucleic Acids Res 2021; 49:12556-12576. [PMID: 34755876 PMCID: PMC8643695 DOI: 10.1093/nar/gkab1040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
CstR is a persulfide-sensing member of the functionally diverse copper-sensitive operon repressor (CsoR) superfamily. While CstR regulates the bacterial response to hydrogen sulfide (H2S) and more oxidized reactive sulfur species (RSS) in Gram-positive pathogens, other dithiol-containing CsoR proteins respond to host derived Cu(I) toxicity, sometimes in the same bacterial cytoplasm, but without regulatory crosstalk in cells. It is not clear what prevents this crosstalk, nor the extent to which RSS sensors exhibit specificity over other oxidants. Here, we report a sequence similarity network (SSN) analysis of the entire CsoR superfamily, which together with the first crystallographic structure of a CstR and comprehensive mass spectrometry-based kinetic profiling experiments, reveal new insights into the molecular basis of RSS specificity in CstRs. We find that the more N-terminal cysteine is the attacking Cys in CstR and is far more nucleophilic than in a CsoR. Moreover, our CstR crystal structure is markedly asymmetric and chemical reactivity experiments reveal the functional impact of this asymmetry. Substitution of the Asn wedge between the resolving and the attacking thiol with Ala significantly decreases asymmetry in the crystal structure and markedly impacts the distribution of species, despite adopting the same global structure as the parent repressor. Companion NMR, SAXS and molecular dynamics simulations reveal that the structural and functional asymmetry can be traced to fast internal dynamics of the tetramer. Furthermore, this asymmetry is preserved in all CstRs and with all oxidants tested, giving rise to markedly distinct distributions of crosslinked products. Our exploration of the sequence, structural, and kinetic features that determine oxidant-specificity suggest that the product distribution upon RSS exposure is determined by internal flexibility.
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Affiliation(s)
- Joseph N Fakhoury
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Yifan Zhang
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
| | - Katherine A Edmonds
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Mauro Bringas
- Fundación Instituto Leloir, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - Justin L Luebke
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Giovanni Gonzalez-Gutierrez
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
| | - Daiana A Capdevila
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Fundación Instituto Leloir, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - David P Giedroc
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
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8
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Brawley HN, Lindahl PA. Direct Detection of the Labile Nickel Pool in Escherichia coli: New Perspectives on Labile Metal Pools. J Am Chem Soc 2021; 143:18571-18580. [PMID: 34723500 DOI: 10.1021/jacs.1c08213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nickel serves critical roles in the metabolism of E. coli and many prokaryotes. Many details of nickel trafficking are unestablished, but a nonproteinaceous low-molecular-mass (LMM) labile nickel pool (LNiP) is thought to be involved. The portion of the cell lysate that flowed through a 3 kDa cutoff membrane, which ought to contain this pool, was analyzed by size-exclusion and hydrophilic interaction chromatographies (SEC and HILIC) with detection by inductively coupled plasma (ICP) and electrospray ionization (ESI) mass spectrometries. Flow-through-solutions (FTSs) contained 11-15 μM Ni, which represented most Ni in the cell. Chromatograms exhibited 4 major Ni-detected peaks. MS analysis of FTS and prepared nickel complex standards established that these peaks arose from Ni(II) coordinated to oxidized glutathione, histidine, aspartate, and ATP. Surprisingly, Ni complexes with reduced glutathione or citrate were not members of the LNiP under the conditions examined. Aqueous Ni(II) ions were absent in the FTS. Detected complexes were stable in chelator-free buffer but were disrupted by treatment with 1,10-phenanthroline or citrate. Titrating FTS with additional NiSO4 suggested that the total nickel-binding capacity of cytosol is approximately 20-45 μM. Members of the LNiP are probably in rapid equilibrium. Previously reported binding constants to various metalloregulators may have overestimated the relevant binding strength in the cell because aqueous metal salts were used in those determinations. The LNiP may serve as both a Ni reservoir and buffer, allowing cells to accommodate a range of Ni concentrations. The composition of the LNiP may change with cellular metabolism and nutrient status.
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Affiliation(s)
- Hayley N Brawley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
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9
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Foster AW, Young TR, Chivers PT, Robinson NJ. Protein metalation in biology. Curr Opin Chem Biol 2021; 66:102095. [PMID: 34763208 PMCID: PMC8867077 DOI: 10.1016/j.cbpa.2021.102095] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/08/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022]
Abstract
Inorganic metals supplement the chemical repertoire of organic molecules, especially proteins. This requires the correct metals to associate with proteins at metalation. Protein mismetalation typically occurs when excesses of unbound metals compete for a binding site ex vivo. However, in biology, excesses of metal-binding sites typically compete for limiting amounts of exchangeable metals. Here, we summarise mechanisms of metal homeostasis that sustain optimal metal availabilities in biology. We describe recent progress to understand metalation by comparing the strength of metal binding to a protein versus the strength of binding to competing sites inside cells.
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Affiliation(s)
- Andrew W Foster
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK; Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK; Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Peter T Chivers
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK; Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK; Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
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10
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Calculating metalation in cells reveals CobW acquires Co II for vitamin B 12 biosynthesis while related proteins prefer Zn II. Nat Commun 2021; 12:1195. [PMID: 33608553 PMCID: PMC7895991 DOI: 10.1038/s41467-021-21479-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/25/2021] [Indexed: 02/01/2023] Open
Abstract
Protein metal-occupancy (metalation) in vivo has been elusive. To address this challenge, the available free energies of metals have recently been determined from the responses of metal sensors. Here, we use these free energy values to develop a metalation-calculator which accounts for inter-metal competition and changing metal-availabilities inside cells. We use the calculator to understand the function and mechanism of GTPase CobW, a predicted CoII-chaperone for vitamin B12. Upon binding nucleotide (GTP) and MgII, CobW assembles a high-affinity site that can obtain CoII or ZnII from the intracellular milieu. In idealised cells with sensors at the mid-points of their responses, competition within the cytosol enables CoII to outcompete ZnII for binding CobW. Thus, CoII is the cognate metal. However, after growth in different [CoII], CoII-occupancy ranges from 10 to 97% which matches CobW-dependent B12 synthesis. The calculator also reveals that related GTPases with comparable ZnII affinities to CobW, preferentially acquire ZnII due to their relatively weaker CoII affinities. The calculator is made available here for use with other proteins.
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11
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Osman D, Cooke A, Young TR, Deery E, Robinson NJ, Warren MJ. The requirement for cobalt in vitamin B 12: A paradigm for protein metalation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118896. [PMID: 33096143 PMCID: PMC7689651 DOI: 10.1016/j.bbamcr.2020.118896] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Anastasia Cooke
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK.
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12
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Baksh KA, Zamble DB. Allosteric control of metal-responsive transcriptional regulators in bacteria. J Biol Chem 2020; 295:1673-1684. [PMID: 31857375 PMCID: PMC7008368 DOI: 10.1074/jbc.rev119.011444] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many transition metals are essential trace nutrients for living organisms, but they are also cytotoxic in high concentrations. Bacteria maintain the delicate balance between metal starvation and toxicity through a complex network of metal homeostasis pathways. These systems are coordinated by the activities of metal-responsive transcription factors-also known as metal-sensor proteins or metalloregulators-that are tuned to sense the bioavailability of specific metals in the cell in order to regulate the expression of genes encoding proteins that contribute to metal homeostasis. Metal binding to a metalloregulator allosterically influences its ability to bind specific DNA sequences through a variety of intricate mechanisms that lie on a continuum between large conformational changes and subtle changes in internal dynamics. This review summarizes recent advances in our understanding of how metal sensor proteins respond to intracellular metal concentrations. In particular, we highlight the allosteric mechanisms used for metal-responsive regulation of several prokaryotic single-component metalloregulators, and we briefly discuss current open questions of how metalloregulators function in bacterial cells. Understanding the regulation and function of metal-responsive transcription factors is a fundamental aspect of metallobiochemistry and is important for gaining insights into bacterial growth and virulence.
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Affiliation(s)
- Karina A Baksh
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Deborah B Zamble
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.
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13
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Ha Y, Hu H, Higgins K, Maroney M, Hedman B, Hodgson K, Solomon E. The Electronic Structure of the Metal Active Site Determines the Geometric Structure and Function of the Metalloregulator NikR. Biochemistry 2019; 58:3585-3591. [PMID: 31339709 DOI: 10.1021/acs.biochem.9b00542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NikR is a nickel-responsive metalloregulator protein that controls the level of Ni2+ ions in living cells. Previous studies have shown that NikR can bind a series of first-row transition metal ions but binds to DNA with high affinity only as a Ni2+ complex. To understand this metal selectivity, S K-edge X-ray absorption spectroscopy of NikR bound to different metal ions was used to evaluate the different electronic structures. The experimental results are coupled with density functional theory calculations on relevant models. This study shows that both the Zeff of the metal ion and the donor nature of the ligands determine the electronic structure of the metal site. This impacts the geometric structure of the metal site and thus the conformation of the protein. This contribution of electronic structure to geometric structure can be extended to other metal selective metalloregulators.
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Affiliation(s)
- Yang Ha
- Department of Chemistry , Stanford University , Stanford , California 94035 , United States.,Stanford Synchrotron Radiation Lightsource, SLAC , Stanford University , Menlo Park , California 94025 , United States
| | - Heidi Hu
- Department of Chemistry , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Khadine Higgins
- Department of Chemistry , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Michael Maroney
- Department of Chemistry , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC , Stanford University , Menlo Park , California 94025 , United States
| | - Keith Hodgson
- Department of Chemistry , Stanford University , Stanford , California 94035 , United States.,Stanford Synchrotron Radiation Lightsource, SLAC , Stanford University , Menlo Park , California 94025 , United States
| | - Edward Solomon
- Department of Chemistry , Stanford University , Stanford , California 94035 , United States.,Stanford Synchrotron Radiation Lightsource, SLAC , Stanford University , Menlo Park , California 94025 , United States
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14
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Abstract
Nickel is essential for the survival of many pathogenic bacteria. E. coli and H. pylori require nickel for [NiFe]-hydrogenases. H. pylori also requires nickel for urease. At high concentrations nickel can be toxic to the cell, therefore, nickel concentrations are tightly regulated. Metalloregulators help to maintain nickel concentration in the cell by regulating the expression of the genes associated with nickel import and export. Nickel import into the cell, delivery of nickel to target proteins, and export of nickel from the cell is a very intricate and well-choreographed process. The delivery of nickel to [NiFe]-hydrogenase and urease is complex and involves several chaperones and accessory proteins. A combination of biochemical, crystallographic, and spectroscopic techniques has been utilized to study the structures of these proteins, as well as protein-protein interactions resulting in an expansion of our knowledge regarding how these proteins sense and bind nickel. In this review, recent advances in the field will be discussed, focusing on the metal site structures of nickel bound to metalloregulators and chaperones.
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15
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Witkowska D, Rowińska-Żyrek M. Biophysical approaches for the study of metal-protein interactions. J Inorg Biochem 2019; 199:110783. [PMID: 31349072 DOI: 10.1016/j.jinorgbio.2019.110783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.
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Affiliation(s)
- Danuta Witkowska
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland.
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16
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Molecular Modelling of the Ni(II)-Responsive Synechocystis PCC 6803 Transcriptional Regulator InrS in the Metal Bound Form. INORGANICS 2019. [DOI: 10.3390/inorganics7060076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
InrS (internal nickel-responsive sensor) is a transcriptional regulator found in cyanobacteria that represses the transcription of the nickel exporter NrsD in the apo form and de-represses expression of the exporter upon Ni(II) binding. Although a crystal structure of apo-InrS from Synechocystis PCC 6803 has been reported, no structure of the protein with metal ions bound is available. Here we report the results of a computational study aimed to reconstruct the metal binding site by taking advantage of recent X-ray absorption spectroscopy (XAS) data and to envisage the structural rearrangements occurring upon Ni(II) binding. The modelled Ni(II) binding site shows a square planar geometry consistent with experimental data. The structural details of the conformational changes occurring upon metal binding are also discussed in the framework of trying to rationalize the different affinity of the apo- and holo-forms of the protein for DNA.
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17
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Huang HT, Maroney MJ. Ni(II) Sensing by RcnR Does Not Require an FrmR-Like Intersubunit Linkage. Inorg Chem 2019; 58:13639-13653. [PMID: 31247878 DOI: 10.1021/acs.inorgchem.9b01096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
E. coli RcnR (resistance to cobalt and nickel regulator) is a homotetrameric DNA binding protein that regulates the expression of a Ni(II) and Co(II) exporter (RcnAB) by derepressing expression of rcnA and rcnB in response to binding Co(II) or Ni(II). Prior studies have shown that the cognate metal ions, Ni(II) and Co(II), bind in six-coordinate sites at subunit interfaces and are distinguished from noncognate metals (Cu(I), Cu(II), and Zn(II)) by coordination number and ligand selection. In analogy with FrmR, a formaldehyde-responsive transcriptional regulator in the RcnR/CsoR family, the interfacial site allows the metal ions to "cross-link" the N-terminal domain of one subunit with the invariant Cys35 residue in another, which has been deemed to be key to mediating the allosteric response of the tetrameric protein to metal binding. Through the use of mutagenesis to disconnect one subunit from the metal-mediated cross-link, X-ray absorption spectroscopy (XAS) as a structural probe, LacZ reporter assays, and metal binding studies using isothermal titration calorimetry (ITC), the work presented here shows that neither the interfacial binding site nor the coordination number of Ni(II) is important to the allosteric response to binding of this cognate metal ion. The opposite is found for the other cognate metal ion, Co(II), with respect to the interfacial binding site, suggesting that the molecular mechanisms for transcriptional regulation by the two ions are distinct. The metal binding studies reveal that tight metal binding is maintained in the variant. XAS is further used to demonstrate that His33 is not a ligand for Co(II), Ni(II), or Zn(II) in WT-RcnR. The results are discussed in the context of the overall understanding of the molecular mechanisms of metallosensors.
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18
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Philpott CC, Jadhav S. The ins and outs of iron: Escorting iron through the mammalian cytosol. Free Radic Biol Med 2019; 133:112-117. [PMID: 30321701 DOI: 10.1016/j.freeradbiomed.2018.10.411] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023]
Abstract
Mammalian cells contain thousands of metalloproteins and have evolved sophisticated systems for ensuring that metal cofactors are correctly assembled and delivered to their proper destinations. Equally critical in this process are the strategies to avoid the insertion of the wrong metal cofactor into apo-proteins and to avoid the damage that redox-active metals can catalyze in the cellular milieu. Iron and zinc are the most abundant metal cofactors in cells and iron cofactors include heme, iron-sulfur clusters, and mono- and dinuclear iron centers. Systems for the intracellular trafficking of iron cofactors are being characterized. This review focuses on the trafficking of ferrous iron cofactors in the cytosol of mammalian cells, a process that involves specialized iron-binding proteins, termed iron chaperones, of the poly rC-binding protein family.
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Affiliation(s)
- Caroline C Philpott
- Genetics and Metabolism, Section Liver Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD 20892, United States.
| | - Shyamalagauri Jadhav
- Genetics and Metabolism, Section Liver Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD 20892, United States
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19
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Osman D, Martini MA, Foster AW, Chen J, Scott AJP, Morton RJ, Steed JW, Lurie-Luke E, Huggins TG, Lawrence AD, Deery E, Warren MJ, Chivers PT, Robinson NJ. Bacterial sensors define intracellular free energies for correct enzyme metalation. Nat Chem Biol 2019; 15:241-249. [PMID: 30692683 PMCID: PMC6420079 DOI: 10.1038/s41589-018-0211-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/04/2018] [Indexed: 01/06/2023]
Abstract
There is a challenge for metalloenzymes to acquire their correct metals because some inorganic elements form more stable complexes with proteins than do others. These preferences can be overcome provided some metals are more available than others. However, while the total amount of cellular metal can be readily measured, the available levels of each metal have been more difficult to define. Metal-sensing transcriptional regulators are tuned to the intracellular availabilities of their cognate ions. Here we have determined the standard free energy for metal complex formation to which each sensor, in a set of bacterial metal sensors, is attuned: The less competitive the metal, the less favorable the free energy and hence greater availability to which the cognate allosteric mechanism is tuned. Comparing these free energies with values derived from the metal affinities of a metalloprotein reveals the mechanism of correct metalation exemplified here by a cobalt-chelatase for vitamin B12.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | | | - Andrew W Foster
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Junjun Chen
- Procter and Gamble, Mason Business Center, Cincinnati, OH, USA
| | | | - Richard J Morton
- Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle-upon-Tyne, UK
| | | | | | | | | | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Peter T Chivers
- Department of Biosciences, Durham University, Durham, UK. .,Department of Chemistry, Durham University, Durham, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham, UK. .,Department of Chemistry, Durham University, Durham, UK.
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20
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Stewart LJ, Thaqi D, Kobe B, McEwan AG, Waldron KJ, Djoko KY. Handling of nutrient copper in the bacterial envelope. Metallomics 2019; 11:50-63. [DOI: 10.1039/c8mt00218e] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The insertion of copper into bacterial cuproenzymesin vivodoes not always require a copper-binding metallochaperone – why?
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Affiliation(s)
- Louisa J. Stewart
- Institute for Cell and Molecular Biosciences
- Newcastle University
- Newcastle upon Tyne
- UK
| | - Denis Thaqi
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre
- The University of Queensland
- St Lucia
- Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre
- The University of Queensland
- St Lucia
- Australia
- Institute for Molecular Bioscience
| | - Alastair G. McEwan
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre
- The University of Queensland
- St Lucia
- Australia
| | - Kevin J. Waldron
- Institute for Cell and Molecular Biosciences
- Newcastle University
- Newcastle upon Tyne
- UK
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21
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Das S, Khatua K, Rakshit A, Carmona A, Sarkar A, Bakthavatsalam S, Ortega R, Datta A. Emerging chemical tools and techniques for tracking biological manganese. Dalton Trans 2019; 48:7047-7061. [DOI: 10.1039/c9dt00508k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This frontier article discusses chemical tools and techniques for tracking and imaging Mn ions in biology.
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Affiliation(s)
- Sayani Das
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
| | - Kaustav Khatua
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
| | - Ananya Rakshit
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
| | - Asuncion Carmona
- Chemical Imaging and Speciation
- CENBG
- University of Bordeaux
- UMR 5797
- 33175 Gradignan
| | - Anindita Sarkar
- Department of Biological Chemistry
- University of Michigan
- Ann Arbor
- USA
| | | | - Richard Ortega
- Chemical Imaging and Speciation
- CENBG
- University of Bordeaux
- UMR 5797
- 33175 Gradignan
| | - Ankona Datta
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
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22
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Pal R, Barker ACJ, Hummel D, Pålsson LO. In Vitro and in Cellulo Sensing of Transition Metals Using Time-Resolved Fluorescence Spectroscopy and Microscopy. J Fluoresc 2018; 29:255-263. [PMID: 30588577 PMCID: PMC6428955 DOI: 10.1007/s10895-018-2335-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/11/2018] [Indexed: 12/19/2022]
Abstract
In this work we demonstrate that time domain techniques can be used successfully to monitor realtively weak modulations of the fluorescence in sensing applications. The metal sensing complex Newport Green DCF™ can detect selected transition metals in vivo as well as in vitro. Incremental addition of Ni and/or Zn (in vitro) lead to a substantial reduction in the yield of the fast component in a bi-exponential fluorescence decay (τ1 = 150-250 ps) from 60% to 30-35%. This is rationalised as an inhibition of intra-molecular electron transfer in the NPG sensing complex due to metal complexation. In order to explore this effect in cellulo, NIH 3 T3 mouse skin fibroplast cells were pre-incubated with set levels of Ni and Zn, at a constant concentration of NPG. The fluorescence modulation in cellullo was subsequently studied employing both time-resolved fluorescence microscopy and confocal fluorescence microscopy. In correlation with the in vitro observations, similar effects were observed on the fluorescence decay in cellulo.
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Affiliation(s)
- Robert Pal
- Department of Chemistry, Durham University, Lower Mountjoy, Stockton Road, Durham, DH1 3LE, UK
| | - Abigail C J Barker
- Department of Chemistry, Durham University, Lower Mountjoy, Stockton Road, Durham, DH1 3LE, UK
| | - Daniel Hummel
- Department of Chemistry, Durham University, Lower Mountjoy, Stockton Road, Durham, DH1 3LE, UK
| | - Lars-Olof Pålsson
- Department of Chemistry, Durham University, Lower Mountjoy, Stockton Road, Durham, DH1 3LE, UK.
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23
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Rakshit A, Khatua K, Shanbhag V, Comba P, Datta A. Cu 2+ selective chelators relieve copper-induced oxidative stress in vivo. Chem Sci 2018; 9:7916-7930. [PMID: 30450181 PMCID: PMC6202919 DOI: 10.1039/c8sc04041a] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 09/29/2018] [Indexed: 02/06/2023] Open
Abstract
Copper ions are essential for biological function yet are severely detrimental when present in excess. At the molecular level, copper ions catalyze the production of hydroxyl radicals that can irreversibly alter essential bio-molecules. Hence, selective copper chelators that can remove excess copper ions and alleviate oxidative stress will help assuage copper-overload diseases. However, most currently available chelators are non-specific leading to multiple undesirable side-effects. The challenge is to build chelators that can bind to copper ions with high affinity but leave the levels of essential metal ions unaltered. Here we report the design and development of redox-state selective Cu ion chelators that have 108 times higher conditional stability constants toward Cu2+ compared to both Cu+ and other biologically relevant metal ions. This unique selectivity allows the specific removal of Cu2+ ions that would be available only under pathophysiological metal overload and oxidative stress conditions and provides access to effective removal of the aberrant redox-cycling Cu ion pool without affecting the essential non-redox cycling Cu+ labile pool. We have shown that the chelators provide distinct protection against copper-induced oxidative stress in vitro and in live cells via selective Cu2+ ion chelation. Notably, the chelators afford significant reduction in Cu-induced oxidative damage in Atp7a-/- Menkes disease model cells that have endogenously high levels of Cu ions. Finally, in vivo testing of our chelators in a live zebrafish larval model demonstrate their protective properties against copper-induced oxidative stress.
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Affiliation(s)
- Ananya Rakshit
- Department of Chemical Sciences , Tata Institute of Fundamental Research , 1 Homi Bhabha Road, Colaba , Mumbai-400005 , India .
| | - Kaustav Khatua
- Department of Chemical Sciences , Tata Institute of Fundamental Research , 1 Homi Bhabha Road, Colaba , Mumbai-400005 , India .
| | - Vinit Shanbhag
- Department of Biochemistry , Christopher S. Bond Life Science Center , University of Missouri , Columbia , USA
| | - Peter Comba
- Universität Heidelberg , Anorganisch-Chemisches Institut , Interdisciplinary Center for Scientific Computing , INF 270 , D-69120 Heidelberg , Germany
| | - Ankona Datta
- Department of Chemical Sciences , Tata Institute of Fundamental Research , 1 Homi Bhabha Road, Colaba , Mumbai-400005 , India .
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24
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Gutekunst K, Hoffmann D, Westernströer U, Schulz R, Garbe-Schönberg D, Appel J. In-vivo turnover frequency of the cyanobacterial NiFe-hydrogenase during photohydrogen production outperforms in-vitro systems. Sci Rep 2018; 8:6083. [PMID: 29666458 PMCID: PMC5904137 DOI: 10.1038/s41598-018-24430-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022] Open
Abstract
Cyanobacteria provide all components for sunlight driven biohydrogen production. Their bidirectional NiFe-hydrogenase is resistant against low levels of oxygen with a preference for hydrogen evolution. However, until now it was unclear if its catalytic efficiency can keep pace with the photosynthetic electron transfer rate. We identified NikKLMQO (sll0381-sll0385) as a nickel transporter, which is required for hydrogen production. ICP-MS measurements were used to quantify hydrogenase molecules per cell. We found 400 to 2000 hydrogenase molecules per cell depending on the conditions. In-vivo turnover frequencies of the enzyme ranged from 62 H2/s in the wild type to 120 H2/s in a mutant during photohydrogen production. These frequencies are above maximum in-vivo photosynthetic electron transfer rates of 47 e-/s (equivalent to 24 H2/s). They are also above those of existing in-vitro systems working with unlimited electron supply and show that in-vivo photohydrogen production is limited by electron delivery to the enzyme.
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Affiliation(s)
- Kirstin Gutekunst
- Botanical Institute, Christian-Albrechts-University, 24118, Kiel, Germany
| | - Dörte Hoffmann
- Botanical Institute, Christian-Albrechts-University, 24118, Kiel, Germany
| | | | - Rüdiger Schulz
- Botanical Institute, Christian-Albrechts-University, 24118, Kiel, Germany
| | | | - Jens Appel
- Botanical Institute, Christian-Albrechts-University, 24118, Kiel, Germany.
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25
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Krämer U. Conceptualizing plant systems evolution. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:66-75. [PMID: 29579731 DOI: 10.1016/j.pbi.2018.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/22/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Organisms inhabiting extreme environments are emerging models in systems evolution, enabling us to identify the molecular alterations effecting major phenotypic divergence through comparative approaches. Here I discuss possible physiological mechanisms underlying evolutionary adaptations to extreme environments both theoretically and in relation to experimental observations. Reasoning leads me to the 'conserved steady-state' hypothesis of evolutionary adaptation: Between closely related plants adapted to differently composed soils, the homeostatically controlled steady-state set point cytosolic (buffered) concentrations of mineral ions are conserved. Subsequently, I compare molecular alterations expected to contribute to physiological adaptations with our present knowledge. Key roles of enhanced gene product dosage in plant evolutionary adaptations question the widespread stimulus response-centric paradigm. As a broader implication, co-regulation networks can lack decisive functional network elements. With this article, I hope to stimulate a discussion across research fields and provide an initial conceptual framework for future experimental testing and for quantitative modelling.
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Affiliation(s)
- Ute Krämer
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstraße 150, ND3/30, D-44801 Bochum, Germany.
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26
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Osman D, Foster AW, Chen J, Svedaite K, Steed JW, Lurie-Luke E, Huggins TG, Robinson NJ. Fine control of metal concentrations is necessary for cells to discern zinc from cobalt. Nat Commun 2017; 8:1884. [PMID: 29192165 PMCID: PMC5709419 DOI: 10.1038/s41467-017-02085-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022] Open
Abstract
Bacteria possess transcription factors whose DNA-binding activity is altered upon binding to specific metals, but metal binding is not specific in vitro. Here we show that tight regulation of buffered intracellular metal concentrations is a prerequisite for metal specificity of Zur, ZntR, RcnR and FrmR in Salmonella Typhimurium. In cells, at non-inhibitory elevated concentrations, Zur and ZntR, only respond to Zn(II), RcnR to cobalt and FrmR to formaldehyde. However, in vitro all these sensors bind non-cognate metals, which alters DNA binding. We model the responses of these sensors to intracellular-buffered concentrations of Co(II) and Zn(II) based upon determined abundances, metal affinities and DNA affinities of each apo- and metalated sensor. The cognate sensors are modelled to respond at the lowest concentrations of their cognate metal, explaining specificity. However, other sensors are modelled to respond at concentrations only slightly higher, and cobalt or Zn(II) shock triggers mal-responses that match these predictions. Thus, perfect metal specificity is fine-tuned to a narrow range of buffered intracellular metal concentrations.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.,Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Andrew W Foster
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.,Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Junjun Chen
- Procter and Gamble, Mason Business Center, Cincinnati, OH, 45040, USA
| | - Kotryna Svedaite
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.,Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | | | - Elena Lurie-Luke
- Procter and Gamble, Singapore Innovation Center, Singapore, 138589, Singapore
| | - Thomas G Huggins
- Procter and Gamble, Mason Business Center, Cincinnati, OH, 45040, USA
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK. .,Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
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27
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Carr CE, Foster AW, Maroney MJ. An XAS investigation of the nickel site structure in the transcriptional regulator InrS. J Inorg Biochem 2017; 177:352-358. [PMID: 28844329 PMCID: PMC5741488 DOI: 10.1016/j.jinorgbio.2017.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/10/2017] [Accepted: 08/05/2017] [Indexed: 12/29/2022]
Abstract
InrS (Internal nickel-responsive Sensor) is a transcriptional repressor of the nickel exporter NrsD and de-represses expression of the exporter upon binding Ni(II) ions. Although a crystal structure of apo-InrS has been reported, no structure of the protein with metal ions bound is available. Herein we report the results of metal site structural investigations of Ni(II) and Cu(II) complexes of InrS using X-ray absorption spectroscopy (XAS) that are complementary to data available from the apo-InrS crystal structure, and are consistent with a planar four-coordinate [Ni(His)2(Cys)2] structure, where the ligands are derived from the side chains of His21, Cys53, His78, and Cys82. Coordination of Cu(II) to InrS forms a nearly identical planar four-coordinate complex that is consistent with a simple replacement of the Ni(II) center by Cu(II).
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Affiliation(s)
- Carolyn E Carr
- Chemistry Department, University of Massachusetts Amherst, MA 01003, USA
| | - Andrew W Foster
- Department of Biosciences, Durham University, Durham, UK; Department of Chemistry, Durham University, Durham, UK
| | - Michael J Maroney
- Chemistry Department, University of Massachusetts Amherst, MA 01003, USA; Program in Molecular and Cellular Biology, University of Massachusetts Amherst, MA 01003, USA.
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28
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Metallochaperones and metalloregulation in bacteria. Essays Biochem 2017; 61:177-200. [PMID: 28487396 DOI: 10.1042/ebc20160076] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 12/21/2022]
Abstract
Bacterial transition metal homoeostasis or simply 'metallostasis' describes the process by which cells control the intracellular availability of functionally required metal cofactors, from manganese (Mn) to zinc (Zn), avoiding both metal deprivation and toxicity. Metallostasis is an emerging aspect of the vertebrate host-pathogen interface that is defined by a 'tug-of-war' for biologically essential metals and provides the motivation for much recent work in this area. The host employs a number of strategies to starve the microbial pathogen of essential metals, while for others attempts to limit bacterial infections by leveraging highly competitive metals. Bacteria must be capable of adapting to these efforts to remodel the transition metal landscape and employ highly specialized metal sensing transcriptional regulators, termed metalloregulatory proteins,and metallochaperones, that allocate metals to specific destinations, to mediate this adaptive response. In this essay, we discuss recent progress in our understanding of the structural mechanisms and metal specificity of this adaptive response, focusing on energy-requiring metallochaperones that play roles in the metallocofactor active site assembly in metalloenzymes and metallosensors, which govern the systems-level response to metal limitation and intoxication.
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