1
|
Schürmann J, Fischer MA, Herzberg M, Reemtsma T, Strommenger B, Werner G, Schuster CF, Layer-Nicolaou F. The genes mgtE and spoVG are involved in zinc tolerance of Staphylococcus aureus. Appl Environ Microbiol 2024; 90:e0045324. [PMID: 38752746 PMCID: PMC11218649 DOI: 10.1128/aem.00453-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 06/19/2024] Open
Abstract
Metals are essential for all living organisms, but the type of metal and its concentration determines its action. Even low concentrations of metals may have toxic effects on organisms and therefore exhibit antimicrobial activities. In this study, we investigate the evolutionary adaptation processes of Staphylococcus aureus to metals and common genes for metal tolerance. Laboratory and clinical isolates were treated with manganese, cobalt, zinc, or nickel metal salts to generate growth-adapted mutants. After growth in medium supplemented with zinc, whole-genome sequencing identified, among others, two genes, mgtE (SAUSA300_0910), a putative magnesium transporter and spoVG (SAUSA300_0475), a global transcriptional regulator, as hot spots for stress-induced single-nucleotide polymorphisms (SNPs). SNPs in mgtE were also detected in mutants treated with high levels of cobalt or nickel salts. To investigate the effect of these genes on metal tolerance, deletion mutants and complementation strains in an S. aureus USA300 LAC* laboratory strain were generated. Both, the mgtE and spoVG deletion strains were more tolerant to cobalt, manganese, and zinc. The mgtE mutant was also more tolerant to nickel exposure. Inductively coupled plasma mass spectrometry analysis demonstrated that the mgtE deletion mutant accumulated less intracellular zinc than the wild type, explaining increased tolerance. From these results, we conclude that mgtE gene inactivation increases zinc tolerance presumably due to reduced uptake of zinc. For the SpoVG mutant, no direct effect on the intracellular zinc concentration was detected, indicating toward different pathways to increase tolerance. Importantly, inactivation of these genes offers a growth advantage in environments containing certain metals, pointing toward a common tolerance mechanism. IMPORTANCE Staphylococcus aureus is an opportunistic pathogen causing tremendous public health burden and high mortality in invasive infections. Treatment is becoming increasingly difficult due to antimicrobial resistances. The use of metals in animal husbandry and aquaculture to reduce bacterial growth and subsequent acquisition of metal resistances has been shown to co-select for antimicrobial resistance. Therefore, understanding adaptive mechanisms that help S. aureus to survive metal exposure is essential. Using a screening approach, we were able to identify two genes encoding the transporter MgtE and the transcriptional regulator SpoVG, which conferred increased tolerance to specific metals such as zinc when inactivated. Further testing showed that the deletion of mgtE leads to reduced intracellular zinc levels, suggesting a role in zinc uptake. The accumulation of mutations in these genes when exposed to other metals suggests that inactivation of these genes could be a common mechanism for intrinsic tolerance to certain metals.
Collapse
Affiliation(s)
- Jacqueline Schürmann
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Martin A. Fischer
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Martin Herzberg
- Department Environmental Analytical Chemistry, Helmholtz-Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Thorsten Reemtsma
- Department Environmental Analytical Chemistry, Helmholtz-Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Birgit Strommenger
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Christopher F. Schuster
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer-Nicolaou
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Zinc-Responsive Regulator Zur Regulates Zinc Homeostasis, Secondary Metabolism, and Morphological Differentiation in Streptomyces avermitilis. Appl Environ Microbiol 2022; 88:e0027822. [PMID: 35323024 DOI: 10.1128/aem.00278-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Zinc is an essential cofactor for many metal enzymes and transcription regulators. Zn2+ availability has long been known to affect antibiotic production and morphological differentiation of Streptomyces species. However, the molecular mechanism whereby zinc regulates these processes remains unclear. We investigated the regulatory roles of the zinc-sensing regulator Zur in Streptomyces avermitilis. Our findings demonstrate that Zur plays an essential role in maintaining zinc homeostasis by repressing the expression of the zinc uptake system ZnuACB and alternative non-zinc-binding ribosomal proteins and promoting the expression of zinc exporter ZitB. Deletion of the zur gene resulted in decreased production of avermectin and oligomycin and delayed morphological differentiation, and these parameters were restored close to wild-type levels in a zur-complemented strain. Zur bound specifically to Zur box in the promoter regions of avermectin pathway-specific activator gene aveR, oligomycin polyketide synthase gene olmA1, and filipin biosynthetic pathway-specific regulatory genes pteR and pteF. Analyses by reverse transcription quantitative PCR and luciferase reporter systems indicated that Zur directly activates the transcription of these genes, i.e., that Zur directly activates biosynthesis of avermectin and oligomycin. Zur positively regulated morphological development by repressing the transcription of differentiation-related genes ssgB and minD2. Our findings, taken together, demonstrate that Zur in S. avermitilis directly controls zinc homeostasis, biosynthesis of avermectin and oligomycin, and morphological differentiation. IMPORTANCE Biosynthesis of secondary metabolites and morphological differentiation in bacteria are affected by environmental signals. The molecular mechanisms whereby zinc availability affects secondary metabolism and morphological differentiation remain poorly understood. We identified several new target genes of the zinc response regulator Zur in Streptomyces avermitilis, the industrial producer of avermectin. Zur was found to directly and positively control avermectin production, oligomycin production, and morphological differentiation in response to extracellular Zn2+ levels. Our findings clarify the regulatory functions of Zur in Streptomyces, which involve linking environmental Zn2+ status with control of antibiotic biosynthetic pathways and morphological differentiation.
Collapse
|
5
|
Mikhaylina A, Scott L, Scanlan DJ, Blindauer CA. A metallothionein from an open ocean cyanobacterium removes zinc from the sensor protein controlling its transcription. J Inorg Biochem 2022; 230:111755. [DOI: 10.1016/j.jinorgbio.2022.111755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 10/19/2022]
|
6
|
Jacquiod S, Nunes I, Brejnrod A, Hansen MA, Holm PE, Johansen A, Brandt KK, Priemé A, Sørensen SJ. Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages. MICROBIOME 2018; 6:223. [PMID: 30545417 PMCID: PMC6292020 DOI: 10.1186/s40168-018-0606-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/25/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon coupled to shotgun mRNA sequencing) to study the legacy effects of a century-long soil copper (Cu) pollution on microbial activity and composition, as well as its effect on the capacity of the microbial community to react to temporal fluctuations. RESULTS Despite evidence of microbial adaptation (e.g., iron homeostasis and avoidance/resistance strategies), increased heterogeneity and richness loss in transcribed gene pools were observed with increasing soil Cu, together with an unexpected predominance of phage mRNA signatures. Apparently, phage activation was either triggered directly by Cu, or indirectly via enhanced expression of DNA repair/SOS response systems in Cu-exposed bacteria. Even though total soil carbon and nitrogen had accumulated with increasing Cu, a reduction in temporally induced mRNA functions was observed. Microbial temporal response groups (TRGs, groups of microbes with a specific temporal response) were heavily affected by Cu, both in abundance and phylogenetic composition. CONCLUSION Altogether, results point toward a Cu-mediated "decoupling" between environmental fluctuations and microbial activity, where Cu-exposed microbes stopped fulfilling their expected contributions to soil functioning relative to the control. Nevertheless, some functions remained active in February despite Cu, concomitant with an increase in phage mRNA signatures, highlighting that somehow, microbial activity is still happening under these adverse conditions.
Collapse
Affiliation(s)
- Samuel Jacquiod
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Agroécologie, AgroSup Dijon, INRA, Univ Bourgogne Franche-Comté, 17 rue Sully, 21000, Dijon, France
| | - Inês Nunes
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Present address: Microbe Technology Department, Novozymes A/S, Krogshoejvej 36, 2880, Bagsværd, Denmark
| | - Asker Brejnrod
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Present address: Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
| | - Martin A Hansen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Peter E Holm
- Present address: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Anders Johansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Kristian K Brandt
- Present address: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Anders Priemé
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
| |
Collapse
|
7
|
Choi SH, Lee KL, Shin JH, Cho YB, Cha SS, Roe JH. Zinc-dependent regulation of zinc import and export genes by Zur. Nat Commun 2017; 8:15812. [PMID: 28598435 PMCID: PMC5472717 DOI: 10.1038/ncomms15812] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 05/04/2017] [Indexed: 12/21/2022] Open
Abstract
In most bacteria, zinc depletion is sensed by Zur, whereas the surplus is sensed by different regulators to achieve zinc homeostasis. Here we present evidence that zinc-bound Zur not only represses genes for zinc acquisition but also induces the zitB gene encoding a zinc exporter in Streptomyces coelicolor, a model actinobacteria. Zinc-dependent gene regulation by Zur occurs in two phases. At sub-femtomolar zinc concentrations (phase I), dimeric Zur binds to the Zur-box motif immediately upstream of the zitB promoter, resulting in low zitB expression. At the same time, Zur represses genes for zinc uptake. At micromolar zinc concentrations (phase II), oligomeric Zur binding with footprint expansion upward from the Zur box results in high zitB induction. Our findings reveal a mode of zinc-dependent gene activation that uses a single metalloregulator to control genes for both uptake and export over a wide range of zinc concentrations. Zinc homeostasis in most bacteria is achieved by a set of regulators, each responding to a certain level of intracellular zinc. Here the authors show that, in Streptomyces coelicolor, the Zur regulator modulates the expression of genes for zinc import and export over a large range of zinc concentrations.
Collapse
Affiliation(s)
- Seung-Hwan Choi
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Kang-Lok Lee
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Jung-Ho Shin
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Yoo-Bok Cho
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jung-Hye Roe
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| |
Collapse
|
8
|
Carr CE, Musiani F, Huang HT, Chivers PT, Ciurli S, Maroney MJ. Glutamate Ligation in the Ni(II)- and Co(II)-Responsive Escherichia coli Transcriptional Regulator, RcnR. Inorg Chem 2017; 56:6459-6476. [PMID: 28517938 DOI: 10.1021/acs.inorgchem.7b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli RcnR (resistance to cobalt and nickel regulator, EcRcnR) is a metal-responsive repressor of the genes encoding the Ni(II) and Co(II) exporter proteins RcnAB by binding to PRcnAB. The DNA binding affinity is weakened when the cognate ions Ni(II) and Co(II) bind to EcRcnR in a six-coordinate site that features a (N/O)5S ligand donor-atom set in distinct sites: while both metal ions are bound by the N terminus, Cys35, and His64, Co(II) is additionally bound by His3. On the other hand, the noncognate Zn(II) and Cu(I) ions feature a lower coordination number, have a solvent-accessible binding site, and coordinate protein ligands that do not include the N-terminal amine. A molecular model of apo-EcRcnR suggested potential roles for Glu34 and Glu63 in binding Ni(II) and Co(II) to EcRcnR. The roles of Glu34 and Glu63 in metal binding, metal selectivity, and function were therefore investigated using a structure/function approach. X-ray absorption spectroscopy was used to assess the structural changes in the Ni(II), Co(II), and Zn(II) binding sites of Glu → Ala and Glu → Cys variants at both positions. The effect of these structural alterations on the regulation of PrcnA by EcRcnR in response to metal binding was explored using LacZ reporter assays. These combined studies indicate that while Glu63 is a ligand for both metal ions, Glu34 is a ligand for Co(II) but possibly not for Ni(II). The Glu34 variants affect the structure of the cognate metal sites, but they have no effect on the transcriptional response. In contrast, the Glu63 variants affect both the structure and transcriptional response, although they do not completely abolish the function of EcRcnR. The structure of the Zn(II) site is not significantly perturbed by any of the glutamic acid variations. The spectroscopic and functional data obtained on the mutants were used to calculate models of the metal-site structures of EcRcnR bound to Ni(II), Co(II), and Zn(II). The results are interpreted in terms of a switch mechanism, in which a subset of the metal-binding ligands is responsible for the allosteric response required for DNA release.
Collapse
Affiliation(s)
- Carolyn E Carr
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Hsin-Ting Huang
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University , Durham DH1 3LE, United Kingdom
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| |
Collapse
|
9
|
Chandrangsu P, Rensing C, Helmann JD. Metal homeostasis and resistance in bacteria. Nat Rev Microbiol 2017; 15:338-350. [PMID: 28344348 DOI: 10.1038/nrmicro.2017.15] [Citation(s) in RCA: 406] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal ions are essential for many reactions, but excess metals can be toxic. In bacteria, metal limitation activates pathways that are involved in the import and mobilization of metals, whereas excess metals induce efflux and storage. In this Review, we highlight recent insights into metal homeostasis, including protein-based and RNA-based sensors that interact directly with metals or metal-containing cofactors. The resulting transcriptional response to metal stress takes place in a stepwise manner and is reinforced by post-transcriptional regulatory systems. Metal limitation and intoxication by the host are evolutionarily ancient strategies for limiting bacterial growth. The details of the resulting growth restriction are beginning to be understood and seem to be organism-specific.
Collapse
Affiliation(s)
- Pete Chandrangsu
- Department of Microbiology, Cornell University, Wing Hall, 123 Wing Drive, Ithaca, New York 14853, USA
| | - Christopher Rensing
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.,Department of Agricultural Resource and Environment, College of Resources and the Environment, Fujian Agriculture &Forestry University, Boxbue Building, 15 Shangxiadian Road, Cangshan District, Fuzhou, Fujian 350002, China.,J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Wing Hall, 123 Wing Drive, Ithaca, New York 14853, USA
| |
Collapse
|
10
|
Entropy redistribution controls allostery in a metalloregulatory protein. Proc Natl Acad Sci U S A 2017; 114:4424-4429. [PMID: 28348247 DOI: 10.1073/pnas.1620665114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Allosteric communication between two ligand-binding sites in a protein is a central aspect of biological regulation that remains mechanistically unclear. Here we show that perturbations in equilibrium picosecond-nanosecond motions impact zinc (Zn)-induced allosteric inhibition of DNA binding by the Zn efflux repressor CzrA (chromosomal zinc-regulated repressor). DNA binding leads to an unanticipated increase in methyl side-chain flexibility and thus stabilizes the complex entropically; Zn binding redistributes these motions, inhibiting formation of the DNA complex by restricting coupled fast motions and concerted slower motions. Allosterically impaired CzrA mutants are characterized by distinct nonnative fast internal dynamics "fingerprints" upon Zn binding, and DNA binding is weakly regulated. We demonstrate the predictive power of the wild-type dynamics fingerprint to identify key residues in dynamics-driven allostery. We propose that driving forces arising from dynamics can be harnessed by nature to evolve new allosteric ligand specificities in a compact molecular scaffold.
Collapse
|
11
|
Martin JE, Edmonds KA, Bruce KE, Campanello GC, Eijkelkamp BA, Brazel EB, McDevitt CA, Winkler ME, Giedroc DP. The zinc efflux activator SczA protects Streptococcus pneumoniae serotype 2 D39 from intracellular zinc toxicity. Mol Microbiol 2017; 104:636-651. [PMID: 28249108 DOI: 10.1111/mmi.13654] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2017] [Indexed: 12/19/2022]
Abstract
Zinc is an essential trace element that serves as a catalytic cofactor in metalloenzymes and a structural element in proteins involved in general metabolism and cellular defenses of pathogenic bacteria. Despite its importance, high zinc levels can impair cellular processes, inhibiting growth of many pathogenic bacteria, including the major respiratory pathogen Streptococcus pneumoniae. Zinc intoxication is prevented in S. pneumoniae by expression of the zinc exporter CzcD, whose expression is activated by the novel TetR-family transcriptional zinc-sensing regulator SczA. How zinc bioavailability triggers activation of SczA is unknown. It is shown here through functional studies in S. pneumoniae that an unannotated homodimeric TetR from S. agalactiae (PDB 3KKC) is the bona fide zinc efflux regulator SczA, and binds two zinc ions per protomer. Mutagenesis analysis reveals two metal binding sites, termed A and B, located on opposite sides of the SczA C-terminal regulatory domain. In vivo, the A- and B-site SczA mutant variants impact S. pneumoniae resistance to zinc toxicity and survival in infected macrophages. A model is proposed for S. pneumoniae SczA function in which both A- and B-sites were required for transcriptional activation of czcD expression, with the A-site serving as the evolutionarily conserved intracellular sensing site in SczAs.
Collapse
Affiliation(s)
- Julia E Martin
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7005, USA
| | - Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7005, USA
| | - Kevin E Bruce
- Department of Biology, Indiana University, Bloomington, IN, 47405-7005, USA
| | | | - Bart A Eijkelkamp
- Research Centre for Infectious Diseases, School of Biological Sciences, the University of Adelaide, SA, 5005, Australia
| | - Erin B Brazel
- Research Centre for Infectious Diseases, School of Biological Sciences, the University of Adelaide, SA, 5005, Australia
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, the University of Adelaide, SA, 5005, Australia
| | - Malcolm E Winkler
- Department of Biology, Indiana University, Bloomington, IN, 47405-7005, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7005, USA
| |
Collapse
|
12
|
Wątły J, Potocki S, Rowińska-Żyrek M. Zinc Homeostasis at the Bacteria/Host Interface-From Coordination Chemistry to Nutritional Immunity. Chemistry 2016; 22:15992-16010. [DOI: 10.1002/chem.201602376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry; University of Wroclaw; F. Joliot-Curie 14 50-383 Wroclaw Poland
| | - Sławomir Potocki
- Faculty of Chemistry; University of Wroclaw; F. Joliot-Curie 14 50-383 Wroclaw Poland
| | | |
Collapse
|
13
|
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: 18] [Impact Index Per Article: 2.0] [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.
Collapse
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,
| |
Collapse
|
14
|
Szunyogh D, Gyurcsik B, Larsen FH, Stachura M, Thulstrup PW, Hemmingsen L, Jancsó A. Zn(II) and Hg(II) binding to a designed peptide that accommodates different coordination geometries. Dalton Trans 2015; 44:12576-88. [PMID: 26040991 DOI: 10.1039/c5dt00945f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Designed metal ion binding peptides offer a variety of applications in both basic science as model systems of more complex metalloproteins, and in biotechnology, e.g. in bioremediation of toxic metal ions, biomining or as artificial enzymes. In this work a peptide (HS: Ac-SCHGDQGSDCSI-NH2) has been specifically designed for binding of both Zn(II) and Hg(II), i.e. metal ions with different preferences in terms of coordination number, coordination geometry, and to some extent ligand composition. It is demonstrated that HS accommodates both metal ions, and the first coordination sphere, metal ion exchange between peptides, and speciation are characterized as a function of pH using UV-absorption-, synchrotron radiation CD-, (1)H-NMR-, and PAC-spectroscopy as well as potentiometry. Hg(II) binds to the peptide with very high affinity in a {HgS2} coordination geometry, bringing together the two cysteinates close to each end of the peptide in a loop structure. Despite the high affinity, Hg(II) is kinetically labile, exchanging between peptides on the subsecond timescale, as indicated by line broadening in (1)H-NMR. The Zn(II)-HS system displays more complex speciation, involving monomeric species with coordinating cysteinates, histidine, and a solvent water molecule, as well as HS-Zn(II)-HS complexes. In summary, the HS peptide displays conformational flexibility, contains many typical metal ion binding groups, and is able to accommodate metal ions with different structural and ligand preferences with high affinity. As such, the HS peptide may be a scaffold offering binding of a variety of metal ions, and potentially serve for metal ion sequestration in biotechnological applications.
Collapse
Affiliation(s)
- Dániel Szunyogh
- MTA-SZTE Bioinorganic Chemistry Research Group, Dóm tér 7, Szeged, H-6720, Hungary
| | | | | | | | | | | | | |
Collapse
|
15
|
Abstract
The metal binding preferences of most metalloproteins do not match their metal requirements. Thus, metallation of an estimated 30% of metalloenzymes is aided by metal delivery systems, with ∼ 25% acquiring preassembled metal cofactors. The remaining ∼ 70% are presumed to compete for metals from buffered metal pools. Metallation is further aided by maintaining the relative concentrations of these pools as an inverse function of the stabilities of the respective metal complexes. For example, magnesium enzymes always prefer to bind zinc, and these metals dominate the metalloenzymes without metal delivery systems. Therefore, the buffered concentration of zinc is held at least a million-fold below magnesium inside most cells.
Collapse
Affiliation(s)
- Andrew W Foster
- From the Department of Chemistry and School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Deenah Osman
- From the Department of Chemistry and School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Nigel J Robinson
- From the Department of Chemistry and School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| |
Collapse
|
16
|
Ma Z, Chandrangsu P, Helmann TC, Romsang A, Gaballa A, Helmann JD. Bacillithiol is a major buffer of the labile zinc pool in Bacillus subtilis. Mol Microbiol 2014; 94:756-70. [PMID: 25213752 DOI: 10.1111/mmi.12794] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2014] [Indexed: 02/06/2023]
Abstract
Intracellular zinc levels are tightly regulated since zinc is an essential cofactor for numerous enzymes, yet can be toxic when present in excess. The majority of intracellular zinc is tightly associated with proteins and is incorporated during synthesis from a poorly defined pool of kinetically labile zinc. In Bacillus subtilis, this labile pool is sensed by equilibration with the metalloregulator Zur, as an indication of zinc sufficiency, and by CzrA, as an indication of zinc excess. Here, we demonstrate that the low-molecular-weight thiol bacillithiol (BSH) serves as a major buffer of the labile zinc pool. Upon shift to conditions of zinc excess, cells transiently accumulate zinc in a low-molecular-weight pool, and this accumulation is largely dependent on BSH. Cells lacking BSH are more sensitive to zinc stress, and they induce zinc efflux at lower external zinc concentrations. Thiol reactive agents such as diamide and cadmium induce zinc efflux by interfering with the Zn-buffering function of BSH. Our data provide new insights into intracellular zinc buffering and may have broad relevance given the presence of BSH in pathogens and the proposed role of zinc sequestration in innate immunity.
Collapse
Affiliation(s)
- Zhen Ma
- Department of Microbiology, Cornell University, Ithaca, NY, USA; Dupont Corporation, Wilmington, DE, USA
| | | | | | | | | | | |
Collapse
|
17
|
Trepreau J, Grosse C, Mouesca JM, Sarret G, Girard E, Petit-Haertlein I, Kuennemann S, Desbourdes C, de Rosny E, Maillard AP, Nies DH, Covès J. Metal sensing and signal transduction by CnrX from Cupriavidus metallidurans CH34: role of the only methionine assessed by a functional, spectroscopic, and theoretical study. Metallomics 2014; 6:263-73. [PMID: 24154823 DOI: 10.1039/c3mt00248a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
When CnrX, the periplasmic sensor protein in the CnrYXH transmembrane signal transduction complex of Cupriavidus metallidurans CH34, binds the cognate metal ions Ni(II) or Co(II), the ECF-type sigma factor CnrH is made available in the cytoplasm for the RNA-polymerase to initiate transcription at the cnrYp and cnrCp promoters. Ni(II) or Co(II) are sensed by a metal-binding site with a N3O2S coordination sphere with octahedral geometry, where S stands for the thioether sulfur of the only methionine (Met123) residue of CnrX. The M123A-CnrX derivative has dramatically reduced signal propagation in response to metal sensing while the X-ray structure of Ni-bound M123A-CnrXs showed that the metal-binding site was not affected by the mutation. Ni(II) remained six-coordinate in M123A-CnrXs, with a water molecule replacing the sulfur as the sixth ligand. H32A-CnrXs, the soluble model of the wild-type membrane-anchored CnrX, was compared to the double mutants H32A-M123A-CnrXs and H32A-M123C-CnrXs to spectroscopically evaluate the role of this unique ligand in the binding site of Ni or Co. The Co- and Ni-bound forms of the protein display unusually blue-shifted visible spectra. TD-DFT calculations using structure-based models allowed identification and assignment of the electronic transitions of Co-bound form of the protein and its M123A derivative. Among them, the signature of the S-Co transition is distinguishable in the shoulder at 530 nm. In vitro affinity measurements point out the crucial role of Met123 in the selectivity for Ni or Co, and in vivo data support the conclusion that Met123 is a trigger of the signal transduction.
Collapse
Affiliation(s)
- Juliette Trepreau
- Institut de Biologie Structurale, UMR 5075 CNRS-CEA-UJF-Grenoble-1, 6 Rue Jules Horowitz, 38042 Grenoble, France.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Chakravorty DK, Merz KM. Studying allosteric regulation in metal sensor proteins using computational methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:181-218. [PMID: 25443958 DOI: 10.1016/bs.apcsb.2014.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this chapter, we describe advances made in understanding the mechanism of allosteric regulation of DNA operator binding in the ArsR/SmtB family of metal-sensing proteins using computational methods. The paradigm, zinc-sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Here, we discuss studies that helped to characterize a metal ion-mediated hydrogen-bonding pathway (HBP) that plays a dominant role in the allosteric mechanism of DNA operator binding in these proteins. The chapter discusses computational methods used to provide a molecular basis for the large conformational motions and allosteric coupling free energy (~6kcal/mol) associated with Zn(II) binding in CzrA. We present an accurate and convenient means by which to include metal ions in the nuclear magnetic resonance (NMR) structure determination process using molecular dynamics (MD) constrained by NMR-derived data. The method provides a realistic and physically viable description of the metal-binding site(s) and has potentially broad applicability in the structure determination of metal ion-bound proteins, protein folding, and metal template protein-design studies. Finally, our simulations provide strong support for a proposed HBP that physically connects the metal-binding residue, His97, to the DNA-binding interface through the αR helix that is present only in the Zn(II)-bound state. We find the interprotomer hydrogen bond interaction to be significantly stronger (~8kcal/mol) at functional allosteric metal-binding sites compared to the apo proteins. This interaction works to overcome the considerable disorder at these hydrogen-bonding sites in apo protein and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. This interaction is found to be considerably weaker in nonresponsive metal-binding sites. These findings suggest a conserved functional role of metal-mediated second-shell coordination hydrogen bonds at allosterically responsive sites in zinc-sensing transcription regulators.
Collapse
Affiliation(s)
- Dhruva K Chakravorty
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA.
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
19
|
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).
Collapse
Affiliation(s)
- Andrew W Foster
- Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK
| | | | | | | |
Collapse
|
20
|
Lisher JP, Higgins KA, Maroney MJ, Giedroc DP. Physical characterization of the manganese-sensing pneumococcal surface antigen repressor from Streptococcus pneumoniae. Biochemistry 2013; 52:7689-701. [PMID: 24067066 DOI: 10.1021/bi401132w] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Transition metals, including manganese, are required for the proper virulence and persistence of many pathogenic bacteria. In Streptococcus pneumoniae (Spn), manganese homeostasis is controlled by a high-affinity Mn(II) uptake complex, PsaBCA, and a constitutively expressed efflux transporter, MntE. psaBCA expression is transcriptionally regulated by the DtxR/MntR family metalloregulatory protein pneumococcal surface antigen repressor (PsaR) in Spn. Here, we present a comprehensive analysis of the metal and DNA binding properties of PsaR. PsaR is a homodimer in the absence and presence of metals and binds two manganese or zinc atoms per protomer (four per dimer) in two pairs of structurally distinct sites, termed site 1 and site 2. Site 1 is likely filled with Zn(II) in vivo (K(Zn1) ≥ 10¹³ M⁻¹; K(Mn1) ≈ 10⁸ M⁻¹). The Zn(II)-site 1 complex adopts a pentacoordinate geometry as determined by X-ray absorption spectroscopy containing a single cysteine and appears to be analogous to the Cd(II) site observed in Streptococcus gordonii ScaR. Site 1 is necessary but not sufficient for full positive allosteric activation of DNA operator binding by metals as measured by ΔGc, the allosteric coupling free energy, because site 1 mutants show an intermediate ΔGc. Site 2 is the primary regulatory site and governs specificity for Mn(II) over Zn(II) in PsaR, where ΔGc(Zn,Mn) >> ΔGc(Zn,Zn) despite the fact that Zn(II) binds site 2 with an affinity 40-fold higher than that of Mn(II); i.e., K(Zn2) > K(Mn2). Mutational studies reveal that Asp7 in site 2 is a critical ligand for Mn(II)-dependent allosteric activation of DNA binding. These findings are discussed in the context of other well-studied DtxR/MntR Mn(II)/Fe(II) metallorepressors.
Collapse
Affiliation(s)
- John P Lisher
- Department of Chemistry and ‡Interdisciplinary Graduate Program in Biochemistry, Indiana University , Bloomington, Indiana 47405-7102, United States
| | | | | | | |
Collapse
|
21
|
Chakravorty DK, Wang B, Lee CW, Guerra AJ, Giedroc DP, Merz KM. Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. JOURNAL OF BIOMOLECULAR NMR 2013; 56:125-137. [PMID: 23609042 PMCID: PMC3773525 DOI: 10.1007/s10858-013-9729-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/10/2013] [Indexed: 06/02/2023]
Abstract
Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.
Collapse
Affiliation(s)
- Dhruva K. Chakravorty
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
| | - Bing Wang
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
| | - Chul Won Lee
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Alfredo J. Guerra
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Kenneth M. Merz
- Department of Chemistry and the Quantum Theory Project, 2238 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435, United States
| |
Collapse
|
22
|
Campanello GC, Ma Z, Grossoehme NE, Guerra AJ, Ward BP, Dimarchi RD, Ye Y, Dann CE, Giedroc DP. Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family. J Mol Biol 2013; 425:1143-57. [PMID: 23353829 DOI: 10.1016/j.jmb.2013.01.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/13/2013] [Accepted: 01/16/2013] [Indexed: 11/18/2022]
Abstract
The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97' NH(ε2)...O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A "cavity" introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, -T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression.
Collapse
|
23
|
Chakravorty DK, Parker TM, Guerra AJ, Sherrill CD, Giedroc DP, Merz KM. Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins. J Am Chem Soc 2012; 135:30-3. [PMID: 23214972 DOI: 10.1021/ja309170g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A metal-mediated interprotomer hydrogen bond has been implicated in the allosteric mechanism of DNA operator binding in several metal-sensing proteins. Using computational methods, we investigate the energetics of such zinc-mediated interactions in members of the ArsR/SmtB family of proteins (CzrA, SmtB, CadC, and NmtR) and the MarR family zinc-uptake repressor AdcR, which feature similar interactions, but in sites that differ widely in their allosteric responsiveness. We provide novel structural insight into previously uncharacterized allosteric forms of these proteins using computational methodologies. We find this metal-mediated interaction to be significantly stronger (∼8 kcal/mol) at functional allosteric metal binding sites compared to a nonresponsive site (CadC) and the apo-proteins. Simulations of the apo-proteins further reveal that the high interaction energy works to overcome the considerable disorder at these hydrogen-bonding sites and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. These findings suggest a conserved functional role of metal-mediated second coordination shell hydrogen bonds at allosterically responsive sites in zinc-sensing transcription regulators.
Collapse
Affiliation(s)
- Dhruva K Chakravorty
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, United States
| | | | | | | | | | | |
Collapse
|
24
|
Higgins KA, Hu HQ, Chivers PT, Maroney MJ. Effects of select histidine to cysteine mutations on transcriptional regulation by Escherichia coli RcnR. Biochemistry 2012; 52:84-97. [PMID: 23215580 DOI: 10.1021/bi300886q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RcnR metalloregulator represses the transcription of the Co(II) and Ni(II) exporter, RcnAB. Previous studies have shown that Co(II) and Ni(II) bind to RcnR in six-coordinate sites, resulting in derepression. Here, the roles of His60, His64, and His67 in specific metal recognition are examined. His60 and His64 correspond to ligands that are important for Cu(I) binding in the homologous Cu(I)-responsive metalloregulator, CsoR. These residues are known to be functionally important in RcnR transcriptional regulation. X-ray absorption spectroscopy (XAS) was used to examine the structure of bound cognate and noncognate metal ions, and lacZ reporter assays were used to assess the transcription of rcnA in response to metal binding in the three His → Cys mutations, H60C, H64C, and H67C. These studies confirm that both Ni(II) and Co(II) use His64 as a ligand. H64C-RcnR is also the only known mutant that retains a Co(II) response while eliminating the response to Ni(II) binding. XAS data indicate that His60 and His67 are potential Co(II) ligands. The effects of the mutations of His60, His64, and His67 on the structures of the noncognate metal ions [Zn(II) and Cu(I)] reveal that these residues have distinctive roles in binding noncognate metals. None of the His → Cys mutants in RcnR confer any response to Cu(I) binding, including H64C-RcnR, where the ligands involved in Cu(I) binding in CsoR are present. These data indicate that while the secondary, tertiary, and quaternary structures of CsoR and RcnR are quite similar, small changes in primary sequence reveal that the specific mechanisms involved in metal recognition are quite different.
Collapse
Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | | | | |
Collapse
|
25
|
Krizkova S, Jilkova E, Krejcova L, Cernei N, Hynek D, Ruttkay-Nedecky B, Sochor J, Kynicky J, Adam V, Kizek R. Rapid superparamagnetic-beads-based automated immunoseparation of Zn-proteins fromStaphylococcus aureuswith nanogram yield. Electrophoresis 2012; 34:224-34. [DOI: 10.1002/elps.201200234] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 08/14/2012] [Accepted: 09/01/2012] [Indexed: 01/13/2023]
Affiliation(s)
| | - Eva Jilkova
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno; Czech Republic
| | - Ludmila Krejcova
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno; Czech Republic
| | - Natalia Cernei
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno; Czech Republic
| | | | | | | | | | | | | |
Collapse
|
26
|
Osman D, Patterson CJ, Bailey K, Fisher K, Robinson NJ, Rigby SEJ, Cavet JS. The copper supply pathway to aSalmonellaCu,Zn-superoxide dismutase (SodCII) involves P1B-type ATPase copper efflux and periplasmic CueP. Mol Microbiol 2012; 87:466-77. [DOI: 10.1111/mmi.12107] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2012] [Indexed: 11/26/2022]
Affiliation(s)
- Deenah Osman
- Life Sciences; Michael Smith Building; University of Manchester; Manchester; M13 9PT; UK
| | - Carl J. Patterson
- The Biophysical Sciences Institute; Department of Chemistry; School of Biological and Biomedical Sciences; University of Durham; Durham; DH1 3LE; UK
| | - Kathryn Bailey
- Life Sciences; Michael Smith Building; University of Manchester; Manchester; M13 9PT; UK
| | - Karl Fisher
- Life Sciences; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street; Manchester; M1 7DN; UK
| | - Nigel J. Robinson
- The Biophysical Sciences Institute; Department of Chemistry; School of Biological and Biomedical Sciences; University of Durham; Durham; DH1 3LE; UK
| | - Stephen E. J. Rigby
- Life Sciences; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street; Manchester; M1 7DN; UK
| | - Jennifer S. Cavet
- Life Sciences; Michael Smith Building; University of Manchester; Manchester; M13 9PT; UK
| |
Collapse
|
27
|
Guerra AJ, Giedroc DP. Metal site occupancy and allosteric switching in bacterial metal sensor proteins. Arch Biochem Biophys 2012; 519:210-22. [PMID: 22178748 PMCID: PMC3312040 DOI: 10.1016/j.abb.2011.11.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/23/2011] [Accepted: 11/29/2011] [Indexed: 12/22/2022]
Abstract
All prokaryotes encode a panel of metal sensor or metalloregulatory proteins that govern the expression of genes that allows an organism to quickly adapt to toxicity or deprivation of both biologically essential transition metal ions, e.g., Zn, Cu, Fe, and heavy metal pollutants. As such, metal sensor proteins can be considered arbiters of intracellular transition metal bioavailability and thus potentially control the metallation state of the metalloproteins in the cell. Metal sensor proteins are specialized allosteric proteins that regulate transcription as a result direct binding of one or two cognate metal ions, to the exclusion of all others. In most cases, the binding of the cognate metal ion induces a structural change in a protein oligomer that either activates or inhibits operator DNA binding. A quantitative measure of the degree to which a particular metal drives metalloregulation of operator DNA-binding is the allosteric coupling free energy, ΔGc. In this review, we summarize recent work directed toward understanding metal occupancy and metal selectivity of these allosteric switches in selected families of metal sensor proteins and examine the structural origins of ΔGc in the functional context a thermodynamic "set-point" model of intracellular metal homeostasis.
Collapse
Affiliation(s)
- Alfredo J. Guerra
- Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN USA 47405-7102
| | - David P. Giedroc
- Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN USA 47405-7102
| |
Collapse
|
28
|
Lee CW, Chakravorty DK, Chang FMJ, Reyes-Caballero H, Ye Y, Merz KM, Giedroc DP. Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery. Biochemistry 2012; 51:2619-29. [PMID: 22394357 DOI: 10.1021/bi3001402] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mycobacterium tuberculosis is an obligate human respiratory pathogen that encodes approximately 10 arsenic repressor (ArsR) family regulatory proteins that allow the organism to respond to a wide range of changes in its immediate microenvironment. How individual ArsR repressors have evolved to respond to selective stimuli is of intrinsic interest. The Ni(II)/Co(II)-specific repressor NmtR and related actinomycete nickel sensors harbor a conserved N-terminal α-NH(2)-Gly2-His3-Gly4 sequence. Here, we present the solution structure of homodimeric apo-NmtR and show that the core of the molecule adopts a typical winged-helix ArsR repressor (α1-α2-α3-αR-β1-β2-α5) "open conformation" that is similar to that of the related zinc sensor Staphylococcus aureus CzrA, but harboring long, flexible N-terminal (residues 2-16) and C-terminal (residues 109-120) extensions. Binding of Ni(II) to the regulatory sites induces strong paramagnetic broadening of the α5 helical region and the extreme N-terminal tail to residue 10. Ratiometric pulse chase amidination mass spectrometry reveals that the rate of amidination of the α-amino group of Gly2 is strongly attenuated in the Ni(II) complex relative to the apo state and noncognate Zn(II) complex. Ni(II) binding also induces dynamic disorder on the microsecond to millisecond time scale of key DNA interacting regions that likely contributes to the negative regulation of DNA binding by Ni(II). Molecular dynamics simulations and quantum chemical calculations reveal that NmtR readily accommodates a distal Ni(II) hexacoordination model involving the α-amine and His3 of the N-terminal region and α5 residues Asp91', His93', His104, and His107, which collectively define a new metal sensing site configuration in ArsR family regulators.
Collapse
Affiliation(s)
- Chul Won Lee
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | | | | | | | | | | | | |
Collapse
|
29
|
Chakravorty DK, Wang B, Lee CW, Giedroc DP, Merz KM. Simulations of allosteric motions in the zinc sensor CzrA. J Am Chem Soc 2012; 134:3367-76. [PMID: 22007899 PMCID: PMC3288340 DOI: 10.1021/ja208047b] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The zinc sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Zn(II) binding induces a quaternary structural switch from a "closed" conformation to a more "open" conformation, reducing the DNA binding affinity by 4 orders of magnitude. In this study, we use classical molecular dynamics and quantum mechanical/molecular mechanical molecular dynamics simulations to investigate the molecular basis for the large conformational motions and allosteric coupling free energy (~6 kcal/mol) associated with Zn(II) binding. Our simulations successfully capture the closed to open allosteric switching in DNA bound CzrA on Zn(II) binding. They reveal that zinc binding quenches global conformational sampling by CzrA, whereas DNA binding enhances the mobility of residues in the allosteric metal binding sites. These findings are in close agreement with experiments. We also identify networks of residues involved in correlated and anticorrelated motions that connect the metal binding and DNA binding sites. Our analysis of the essential dynamics shows metal ion binding to be the primary driving force for the quaternary structural change in CzrA. We also show that Zn(II) binding limits the conformational space sampled by CzrA and causes the electrostatic surface potential at the DNA binding interface to become less favorable toward DNA binding. Finally, our simulations provide strong support for a proposed hydrogen-bonding pathway that physically connects the metal binding residue, His97, to the DNA binding interface through the αR helix that is present only in the Zn(II)-bound state. Overall, our simulations provide molecular-level insights into the mechanism of allosteric regulation by CzrA and demonstrate the importance of protein motion in its biological activity.
Collapse
Affiliation(s)
- Dhruva K. Chakravorty
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435
| | - Bing Wang
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435
| | - Chul Won Lee
- Department of Chemistry, University of Indiana, Bloomington, IN 47405-7102
| | - David P. Giedroc
- Department of Chemistry, University of Indiana, Bloomington, IN 47405-7102
| | - Kenneth M. Merz
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435
| |
Collapse
|
30
|
Abstract
The intracellular availability of all biologically required transition metal ions in bacteria, e.g., Zn, Cu, Fe, as well as the detoxification of nonbiological heavy metal pollutants, is controlled at the molecular level by a panel of metalloregulatory or "metal sensor" proteins. Metal sensor proteins are specialized allosteric proteins that regulate the transcription of genes linked to transition metal homeostasis as a result of direct binding of a single metal ion or two closely related metal ions, to the exclusion of all others. In many cases, the binding of the cognate metal ion induces a structural change in a metal sensor oligomer that either activates or inhibits operator DNA binding. A quantitative measure of the degree to which a particular metal drives metalloregulation of transcription is the allosteric coupling-free energy, ΔG(c). In this chapter, we outline detailed spectroscopically derived methods for measuring metal binding affinity, K(Me), as well as ΔG(c) independent of K(Me), presented in the context of a simple coupled equilibrium scheme. Studies carried out in this way provide quantitative insights into the degree to which a particular metal ion is capable of driving allosteric switching, and via ligand substitution, the extent to which individual coordination bonds establish structural linkage of allosteric metal and operator DNA-binding sites.
Collapse
|
31
|
Reyes-Caballero H, Lee CW, Giedroc DP. Mycobacterium tuberculosis NmtR harbors a nickel sensing site with parallels to Escherichia coli RcnR. Biochemistry 2011; 50:7941-52. [PMID: 21819125 DOI: 10.1021/bi200737a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis NmtR is a Ni(II)/Co(II)-sensing metalloregulatory protein from the extensively studied ArsR/SmtB family. Two Ni(II) ions bind to the NmtR dimer to form octahedral coordination complexes with the following stepwise binding affinities: K(Ni1) = (1.2 ± 0.1) × 10(10) M(-1), and K(Ni2) = (0.7 ± 0.4) × 10(10) M(-1) (pH 7.0). A glutamine scanning mutagenesis approach reveals that Asp91, His93, His104, and His107, all contained within the C-terminal α5 helix, and His3 as part of the conserved α-NH(2)-Gly2-His3-Gly4 motif at the N-terminus make significant contributions to the magnitude of K(Ni). In contrast, substitution of residues from the C-terminal region, His109, Asp114, and His116, previously implicated in Ni(II) binding and metalloregulation in cells, gives rise to wild-type K(Ni) and Ni(II)-dependent allosteric coupling free energies. Interestingly, deletion of residues 112-120 from the C-terminal region (Δ111 NmtR) reduces the Ni(II) binding stoichiometry to one per dimer and greatly reduces Ni(II) responsiveness. H3Q and Δ111 NmtRs also show clear perturbations in the rank order of metal responsiveness to Ni(II), Co(II), and Zn(II) that is distinct from that of wild-type NmtR. (15)N relaxation experiments with apo-NmtR reveal that both N-terminal (residues 2-14) and C- terminal (residues 110-120) regions are unstructured in solution, and this property likely dictates the metal specificity profile characteristic of the Ni(II) sensor NmtR relative to other ArsR family regulators.
Collapse
|
32
|
Ma Z, Gabriel SE, Helmann JD. Sequential binding and sensing of Zn(II) by Bacillus subtilis Zur. Nucleic Acids Res 2011; 39:9130-8. [PMID: 21821657 PMCID: PMC3241647 DOI: 10.1093/nar/gkr625] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacillus subtilis Zur (BsZur) represses high-affinity zinc-uptake systems and alternative ribosomal proteins in response to zinc replete conditions. Sequence alignments and structural studies of related Fur family proteins suggest that BsZur may contain three zinc-binding sites (sites 1–3). Mutational analyses confirm the essential structural role of site 1, while mutants affected in sites 2 and 3 retain partial repressor function. Purified BsZur binds a maximum of two Zn(II) per monomer at site 1 and site 2. Site 3 residues are important for dimerization, but do not directly bind Zn(II). Analyses of metal-binding affinities reveals negative cooperativity between the two site 2 binding events in each dimer. DNA-binding studies indicate that BsZur is sequentially activated from an inactive dimer (Zur2:Zn2) to a partially active asymmetric dimer (Zur2:Zn3), and finally to the fully zinc-loaded active form (Zur2:Zn4). BsZur with a C84S mutation in site 2 forms a Zur2:Zn3 form with normal metal- and DNA-binding affinities but is impaired in formation of the Zur2:Zn4 high affinity DNA-binding state. This mutant retains partial repressor activity in vivo, thereby supporting a model in which stepwise activation by zinc serves to broaden the physiological response to a wider range of metal concentrations.
Collapse
Affiliation(s)
- Zhen Ma
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | | | | |
Collapse
|
33
|
Reyes-Caballero H, Campanello GC, Giedroc DP. Metalloregulatory proteins: metal selectivity and allosteric switching. Biophys Chem 2011; 156:103-14. [PMID: 21511390 DOI: 10.1016/j.bpc.2011.03.010] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 03/29/2011] [Accepted: 03/29/2011] [Indexed: 01/13/2023]
Abstract
Prokaryotic organisms have evolved the capacity to quickly adapt to a changing and challenging microenvironment in which the availability of both biologically required and non-essential transition metal ions can vary dramatically. In all bacteria, a panel of metalloregulatory proteins controls the expression of genes encoding membrane transporters and metal trafficking proteins that collectively manage metal homeostasis and resistance. These "metal sensors" are specialized allosteric proteins, in which the direct binding of a specific or small number of "cognate" metal ion(s) drives a conformational change in the regulator that allosterically activates or inhibits operator DNA binding, or alternatively, distorts the promoter structure thereby converting a poor promoter to a strong one. In this review, we discuss our current understanding of the features that control metal specificity of the allosteric response in these systems, and the role that structure, thermodynamics and conformational dynamics play in mediating allosteric activation or inhibition of DNA binding.
Collapse
|
34
|
Choi SS, Chivers PT, Berg DE. Point mutations in Helicobacter pylori's fur regulatory gene that alter resistance to metronidazole, a prodrug activated by chemical reduction. PLoS One 2011; 6:e18236. [PMID: 21464913 PMCID: PMC3064673 DOI: 10.1371/journal.pone.0018236] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 02/23/2011] [Indexed: 02/08/2023] Open
Abstract
Background Helicobacter pylori's Fur regulatory protein controls transcription of dozens of genes in response to iron availability, acidity and oxidative stress, and affects the vigor of infection and severity of disease. It is unusual among Fur family proteins in being active both when iron-loaded and iron-free. Metholodolgy/Principal Findings We tested if H. pylori fur mutations could affect resistance to metronidazole (Mtz), an anti-H. pylori prodrug rendered bactericidal by chemical reduction. Point mutations were made by PCR in DNA containing fur and a downstream chloramphenicol resistance gene, and were placed in the H. pylori chromosome by transformation of a fur-deletion (Δfur) strain. Several substitutions affecting H. pylori Fur's ∼10 residue N terminal arm, which has no counterpart in prototype (E. coli-type) Fur proteins, increased Mtz resistance, as did mutations affecting the region between DNA binding and dimerization domains. Three types of mutations decreased resistance more than did Δfur: substitutions affecting the N-terminal arm; substitutions affecting the metal binding pocket; and nonsense mutations that resulted in a truncated Fur protein with no C-terminal dimerization domain. Most metal binding pocket mutations were obtained only in fur genes with additional inactivating mutations, and thus seemed deleterious or lethal because they. Conclusions/Significance These results establish that H. pylori Fur's distinctive N terminal arm is functional, and more generally illustrate that point mutations can confer informative phenotypes, distinct from those conferred by null mutations. We propose that fur mutations can affect Mtz susceptibility by altering the balance among Fur's several competing activities, and thereby the expression of genes that control cellular redox potential or elimination of bactericidal Mtz activation products. Further analyses of selected mutants should provide insights into Fur interactions with other cellular components, metabolic circuitry, and how H. pylori thrives in its special gastric niche.
Collapse
Affiliation(s)
- Sung Sook Choi
- Department of Molecular Microbiology, Washington University Medical School, St Louis, Missouri, United States of America
| | - Peter T. Chivers
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St Louis, Missouri, United States of America
| | - Douglas E. Berg
- Department of Molecular Microbiology, Washington University Medical School, St Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
35
|
Reyes-Caballero H, Guerra AJ, Jacobsen FE, Kazmierczak KM, Cowart D, Koppolu UMK, Scott RA, Winkler ME, Giedroc DP. The metalloregulatory zinc site in Streptococcus pneumoniae AdcR, a zinc-activated MarR family repressor. J Mol Biol 2010; 403:197-216. [PMID: 20804771 DOI: 10.1016/j.jmb.2010.08.030] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 08/14/2010] [Accepted: 08/16/2010] [Indexed: 12/11/2022]
Abstract
Streptococcus pneumoniae D39 AdcR (adhesin competence repressor) is the first metal-sensing member of the MarR (multiple antibiotic resistance repressor) family to be characterized. Expression profiling with a ΔadcR strain grown in liquid culture (brain-heart infusion) under microaerobic conditions revealed upregulation of 13 genes, including adcR and adcCBA, encoding a high-affinity ABC uptake system for zinc, and genes encoding cell-surface zinc-binding pneumococcal histidine triad (Pht) proteins and AdcAII (Lmb, laminin binding). The ΔadcR, H108Q and H112Q adcR mutant allelic strains grown in 0.2 mM Zn(II) exhibit a slow-growth phenotype and an approximately twofold increase in cell-associated Zn(II). Apo- and Zn(II)-bound AdcR are homodimers in solution and binding to a 28-mer DNA containing an adc operator is strongly stimulated by Zn(II) with K(DNA-Zn)=2.4 × 10(8) M(-1) (pH 6.0, 0.2 M NaCl, 25 °C). AdcR binds two Zn(II) per dimer, with stepwise Zn(II) affinities K(Zn1) and K(Zn2) of ≥10(9) M(-1) at pH 6.0 and ≥10(12) M(-1) at pH 8.0, and one to three lower affinity Zn(II) depending on the pH. X-ray absorption spectroscopy of the high-affinity site reveals a pentacoordinate N/O complex and no cysteine coordination, the latter finding corroborated by wild type-like functional properties of C30A AdcR. Alanine substitution of conserved residues His42 in the DNA-binding domain, and His108 and His112 in the C-terminal regulatory domain, abolish high-affinity Zn(II) binding and greatly reduce Zn(II)-activated binding to DNA. NMR studies reveal that these mutants adopt the same folded conformation as dimeric wild type apo-AdcR, but fail to conformationally switch upon Zn(II) binding. These studies implicate His42, His108 and H112 as metalloregulatory zinc ligands in S. pneumoniae AdcR.
Collapse
|
36
|
Wang Y, Kendall J, Cavet JS, Giedroc DP. Elucidation of the functional metal binding profile of a Cd(II)/Pb(II) sensor CmtR(Sc) from Streptomyces coelicolor. Biochemistry 2010; 49:6617-26. [PMID: 20586430 DOI: 10.1021/bi100490u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal homeostasis and resistance in bacteria is maintained by a panel of metal-sensing transcriptional regulators that collectively control transition metal availability and mediate resistance to heavy metal xenobiotics, including As(III), Cd(II), Pb(II), and Hg(II). The ArsR family constitutes a superfamily of metal sensors that appear to conform to the same winged helical, homodimeric fold, that collectively "sense" a wide array of beneficial metal ions and heavy metal pollutants. The genomes of many actinomycetes, including the soil dwelling bacterium Streptomyces coelicolor and the human pathogen Mycobacterium tuberculosis, encode over ten ArsR family regulators, most of unknown function. Here, we present the characterization of a homologue of M. tuberculosis CmtR (CmtR(Mtb)) from S. coelicolor, denoted CmtR(Sc). We show that CmtR(Sc), in contrast to CmtR(Mtb), binds two monomer mol equivalents of Pb(II) or Cd(II) to form two pairs of sulfur-rich coordination complexes per dimer. Metal site 1 conforms exactly to the alpha4C site previously characterized in CmtR(Mtb) while metal site 2 is coordinated by a C-terminal vicinal thiolate pair, Cys110 and Cys111. Biological assays reveal that only Cd(II) and, to a lesser extent, Pb(II) mediate transcriptional derepression in the heterologous host Mycobacterium smegmatis in a way that requires metal site 1. In contrast, mutagenesis of metal site 2 ligands Cys110 or Cys111 significantly reduces Cd(II) responsiveness, with no detectable effect on Pb(II) sensing. The implications of these findings on the ability to predict metal specificity and function from metal-site signatures in the primary structure of ArsR family proteins are discussed.
Collapse
Affiliation(s)
- Yun Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
| | | | | | | |
Collapse
|
37
|
Ma Z, Cowart DM, Ward BP, Arnold RJ, DiMarchi RD, Zhang L, George GN, Scott RA, Giedroc DP. Unnatural amino acid substitution as a probe of the allosteric coupling pathway in a mycobacterial Cu(I) sensor. J Am Chem Soc 2010; 131:18044-5. [PMID: 19928961 DOI: 10.1021/ja908372b] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Cu(I) sensor Mycobacterium tuberculosis CsoR is a founding member of a new metalloregulatory protein family. Here we show that two "atom" substitutions of the Nepsilon2 face of a Cu(I) coordinating histidine-61 allosterically uncouple Cu(I) and DNA binding, with no effect on Cu(I) binding affinity and coordination structure. A model analogous to the allosteric switch mechanism in Staphylococcus aureus CzrA, a zinc sensor protein with a completely different fold, is proposed.
Collapse
Affiliation(s)
- Zhen Ma
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Grossoehme NE, Giedroc DP. Energetics of allosteric negative coupling in the zinc sensor S. aureus CzrA. J Am Chem Soc 2010; 131:17860-70. [PMID: 19995076 DOI: 10.1021/ja906131b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The linked equilibria of an allosterically regulated protein are defined by the structures, residue-specific dynamics and global energetics of interconversion among all relevant allosteric states. Here, we use isothermal titration calorimetry (ITC) to probe the global thermodynamics of allosteric negative regulation of the binding of the paradigm ArsR-family zinc sensing repressor Staphylococcus aureus CzrA to the czr DNA operator (CzrO) by Zn(2+). Zn(2+) binds to the two identical binding sites on the free CzrA homodimer in two discernible steps. A larger entropic driving force Delta(-TDeltaS) of -4.7 kcal mol(-1) and a more negative DeltaC(p) characterize the binding of the first Zn(2+) relative to the second. These features suggest a modest structural transition in forming the Zn(1) state followed by a quenching of the internal dynamics on filling the second zinc site, which collectively drive homotropic negative cooperativity of Zn(2+) binding (Delta(DeltaG) = 1.8 kcal mol(-1)). Negative homotropic cooperativity also characterizes Zn(2+) binding to the CzrA*CzrO complex (Delta(DeltaG) = 1.3 kcal mol(-1)), although the underlying energetics are vastly different, with homotropic Delta(DeltaH) and Delta(-TDeltaS) values both small and slightly positive. In short, Zn(2+) binding to the complex fails to induce a large structural or dynamical change in the CzrA bound to the operator. The strong heterotropic negative linkage in this system (DeltaG(c)(t) = 6.3 kcal mol(-1)) therefore derives from the vastly different structures of the apo-CzrA and CzrA*CzrO reference states (DeltaH(c)(t) = 9.4 kcal mol(-1)) in a way that is reinforced by a global rigidification of the allosterically inhibited Zn(2) state off the DNA (TDeltaS(c)(t) = -3.1 kcal mol(-1), i.e., DeltaS(c)(t) > 0). The implications of these findings for other metalloregulatory proteins are discussed.
Collapse
|
39
|
Iwig JS, Chivers PT. Coordinating intracellular nickel-metal-site structure-function relationships and the NikR and RcnR repressors. Nat Prod Rep 2010; 27:658-67. [PMID: 20442957 DOI: 10.1039/b906683g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metalloregulator function requires both sensitivity and selectivity to ensure metal-specific activity without interfering with intracellular metal trafficking pathways. Here, we examine the role of metal coordination geometry in the function of NikR and RcnR, two widely conserved nickel-responsive regulators that are both present in E. coli. The available data suggest an emerging trend in which coordination number is linked to metal-binding affinity, and thus regulatory function. The differences in coordination geometry also suggest that the kinetic mechanisms of metal-association and dissociation will contribute to metalloregulator function. We also discuss ways in which the ligand binding properties of metalloregulators may be tuned to alter the regulatory response.
Collapse
Affiliation(s)
- Jeffrey S Iwig
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, USA
| | | |
Collapse
|
40
|
Arunkumar AI, Campanello GC, Giedroc DP. Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state. Proc Natl Acad Sci U S A 2009; 106:18177-82. [PMID: 19822742 PMCID: PMC2775347 DOI: 10.1073/pnas.0905558106] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus CzrA is a zinc-dependent transcriptional repressor from the ubiquitous ArsR family of metal sensor proteins. Zn(II) binds to a pair of intersubunit C-terminal alpha5-sensing sites, some 15 A distant from the DNA-binding interface, and allosterically inhibits DNA binding. This regulation is characterized by a large allosteric coupling free energy (DeltaGc) of approximately +6 kcal mol(-1), the molecular origin of which is poorly understood. Here, we report the solution quaternary structure of homodimeric CzrA bound to a palindromic 28-bp czr operator, a structure that provides an opportunity to compare the two allosteric "end" states of an ArsR family sensor. Zn(II) binding drives a quaternary structural switch from a "closed" DNA-binding state to a low affinity "open" conformation as a result of a dramatic change in the relative orientations of the winged helical DNA binding domains within the dimer. Zn(II) binding also effectively quenches both rapid and intermediate timescale internal motions of apo-CzrA while stabilizing the native state ensemble. In contrast, DNA binding significantly enhances protein motions in the allosteric sites and reduces the stability of the alpha5 helices as measured by H-D solvent exchange. This study reveals how changes in the global structure and dynamics drive a long-range allosteric response in a large subfamily of bacterial metal sensor proteins, and provides insights on how other structural classes of ArsR sensor proteins may be regulated by metal binding.
Collapse
Affiliation(s)
- Alphonse I. Arunkumar
- Department of Chemistry, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405-7102
| | - Gregory C. Campanello
- Department of Chemistry, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405-7102
| | - David P. Giedroc
- Department of Chemistry, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405-7102
| |
Collapse
|
41
|
Ma Z, Jacobsen FE, Giedroc DP. Coordination chemistry of bacterial metal transport and sensing. Chem Rev 2009; 109:4644-81. [PMID: 19788177 PMCID: PMC2783614 DOI: 10.1021/cr900077w] [Citation(s) in RCA: 433] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zhen Ma
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128 USA
| | - Faith E. Jacobsen
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
| |
Collapse
|
42
|
Ma Z, Cowart DM, Scott RA, Giedroc DP. Molecular insights into the metal selectivity of the copper(I)-sensing repressor CsoR from Bacillus subtilis. Biochemistry 2009; 48:3325-34. [PMID: 19249860 DOI: 10.1021/bi900115w] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacillus subtilis CsoR (Bsu CsoR) is a copper-sensing transcriptional repressor that regulates the expression of the copZA operon encoding a copper chaperone and a Cu efflux P-type ATPase, respectively. Bsu CsoR is a homologue of Mycobacterium tuberculosis CsoR (Mtb CsoR), representative of a large Cu(I)-sensing regulatory protein family. We show here that Bsu CsoR binds approximately 1 mol equiv of Cu(I) per monomer in vitro with an affinity >or=10(21) M(-1). X-ray absorption spectroscopy shows Cu(I) adopts a trigonal S(2)N coordination like Mtb CsoR. Both apo and Cu(I)-bound Bsu CsoR are stable tetramers in the low micromolar monomer concentration range by sedimentation velocity and equilibrium ultracentrifugation. Apo-Bsu CsoR binds to a pseudopalindromic 30 bp copZA operator-promoter DNA with a stoichiometry of two tetramers per DNA and stepwise affinities of K(1)(apo) = 3.1(+/-0.8) x 10(7) M(-1) and K(2)(apo) = 8.3 (+/-2.2) x 10(7) M(-1) (0.4 M NaCl, 25 degrees C, pH 6.5). Cu(I) Bsu CsoR binds to the same DNA with greatly reduced affinities, K(1)(Cu) = 2.9(+/-0.4) x 10(6) M(-1) and K(2)(Cu) <or= 1.0 x 10(5) M(-1) consistent with a copper-dependent derepression model. This Cu-dependent regulation is abrogated by a "second shell" Glu90-to-Ala substitution. Bsu CsoR binds Ni(II) with very high affinity but forms a non-native coordination geometry, as does Co(II) and likely Zn(II); none of these metals strongly regulates copZA operator DNA binding in vitro. The implications of these findings on the specificity of metal-sensing sites in CsoR/RcnR proteins are discussed.
Collapse
Affiliation(s)
- Zhen Ma
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA
| | | | | | | |
Collapse
|
43
|
Liu T, Chen X, Ma Z, Shokes J, Hemmingsen L, Scott RA, Giedroc DP. A Cu(I)-sensing ArsR family metal sensor protein with a relaxed metal selectivity profile. Biochemistry 2008; 47:10564-75. [PMID: 18795800 DOI: 10.1021/bi801313y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ArsR (or ArsR/SmtB) family metalloregulatory homodimeric repressors collectively respond to a wide range of metal ion inducers in regulating homeostasis and resistance of essential and nonessential metal ions in bacteria. BxmR from the cyanobacterium Osciliatoria brevis is the first characterized ArsR protein that senses both Cu (I)/Ag (I) and divalent metals Zn (II)/Cd (II) in cells by regulating the expression of a P-type ATPase efflux pump (Bxa1) and an intracellular metallothionein (BmtA). We show here that both pairs of predicted alpha3N and alpha5 sites bind metal ions, but with distinct physicochemical and functional metal specificities. Inactivation of the thiophilic alpha3N site via mutation (C77S) abolishes regulation by both Cd (II) and Cu (I), while Zn (II) remains a potent allosteric negative effector of operator/promoter binding (Delta G c >or= +3.2 kcal mol (-1)). In contrast, alpha5 site mutant retains regulation by all four metal ions, albeit with a smaller coupling free energy (Delta G c approximately +1.7 (+/-0.1) kcal mol (-1)). Unlike the other metals ions, the BxmR dimer binds 4 mol equiv of Cu (I) to form an alpha3N binuclear Cu (I) 2S 4 cluster by X-ray absorption spectroscopy. BxmR is thus distinguishable from other closely related ArsR family sensors, in having evolved a metalloregulatory alpha3N site that can adopt an expanded range of coordination chemistries while maintaining redundancy in the response to Zn (II). The evolutionary implications of these findings for the ArsR metal sensor family are discussed.
Collapse
Affiliation(s)
- Tong Liu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
| | | | | | | | | | | | | |
Collapse
|
44
|
Iwig JS, Leitch S, Herbst RW, Maroney MJ, Chivers PT. Ni(II) and Co(II) sensing by Escherichia coli RcnR. J Am Chem Soc 2008; 130:7592-606. [PMID: 18505253 DOI: 10.1021/ja710067d] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli RcnR and Mycobacterium tuberculosis CsoR are the founding members of a recently identified, large family of bacterial metal-responsive DNA-binding proteins. RcnR controls the expression of the metal efflux protein RcnA only in response to Ni(II) and Co(II) ions. Here, the interaction of Ni(II) and Co(II) with wild-type and mutant RcnR proteins is examined to understand how these metals function as allosteric effectors. Both metals bind to RcnR with nanomolar affinity and stabilize the protein to denaturation. X-ray absorption and electron paramagnetic resonance spectroscopies reveal six-coordinate high-spin sites for each metal that contains a thiolate ligand. Experimental data support a tripartite N-terminal coordination motif (NH2-Xaa-NH-His) that is common for both metals. However, the Ni(II)- and Co(II)-RcnR complexes are shown to differ in the remaining coordination environment. Each metal coordinates a conserved Cys ligand but with distinct M-S distances. Co(II)-thiolate coordination has not been observed previously in Ni(II)-/Co(II)-responsive metalloregulators. The ability of RcnR to recruit ligands from the N-terminal region of the protein distinguishes it from CsoR, which uses a lower coordination geometry to bind Cu(I). These studies facilitate comparisons between Ni(II)-RcnR and NikR, the other Ni(II)-responsive transcriptional regulator in E. coli, to provide a better understanding how different nickel levels are sensed in E. coli. The characterization of the Ni(II)- and Co(II)-binding sites in RcnR, in combination with bioinformatics analysis of all RcnR/CsoR family members, identified a four amino acid fingerprint that likely defines ligand-binding specificity, leading to an emerging picture of the similarities and differences between different classes of RcnR/CsoR proteins.
Collapse
Affiliation(s)
- Jeffrey S Iwig
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, Saint Louis, Missouri 63110, USA
| | | | | | | | | |
Collapse
|
45
|
Liu T, Reyes-Caballero H, Li C, Scott RA, Giedroc DP. Multiple metal binding domains enhance the Zn(II) selectivity of the divalent metal ion transporter AztA. Biochemistry 2007; 46:11057-68. [PMID: 17824670 PMCID: PMC3561713 DOI: 10.1021/bi7006367] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Transition metal-transporting P1B-type CPx ATPases play crucial roles in mediating metal homeostasis and resistance in all cells. The degree to which N-terminal metal binding domains (MBDs) confer metal specificity to the transporter is unclear. We show that the two MBDs of the Zn/Cd/Pb effluxing pump Anabaena AztA are functionally nonequivalent, but only with respect to zinc resistance. Inactivation of the a-MBD largely abrogates resistance to high intracellular Zn(II) levels, whereas inactivation of the b-MBD is not as deleterious. In contrast, inactivation of either the a- or b-MBD has little measurable impact on Cd(II) and Pb(II) resistance. The membrane proximal b-MBD binds Zn(II) with a higher affinity than the distal N-terminal a-MBD. Facile Zn(II)-specific intermolecular transfer from the a-MBD to the higher-affinity b-MBD is readily observed by 1H-15N HSQC spectroscopy. Unlike Zn(II), Cd(II) and Pb(II) form saturated 1:1 S4 or S3(O/N) complexes with AztAaHbH, where a single metal ion bridges the two MBDs. We propose that the tandem MBDs enhance Zn(II)-specific transport, while stabilizing a non-native inter-MBD Cd/Pb cross-linked structure that is a poor substrate and/or regulator for the transporter.
Collapse
Affiliation(s)
| | | | | | | | - David P. Giedroc
- To whom correspondence should be addressed: Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405-7102. Telephone: (812) 856-5449. Fax: (812) 855-8300.
| |
Collapse
|
46
|
Iranzo O, Cabello C, Pecoraro V. Heterochromia in Designed Metallopeptides: Geometry-Selective Binding of CdII in a De Novo Peptide. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701729] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
47
|
Arunkumar AI, Pennella MA, Kong X, Giedroc DP. Resonance assignments of the metal sensor CzrA in the apo-, Zn2- and DNA-bound (42 kDa) states. BIOMOLECULAR NMR ASSIGNMENTS 2007; 1:99-101. [PMID: 19636838 DOI: 10.1007/s12104-007-9027-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 06/13/2007] [Accepted: 06/15/2007] [Indexed: 05/28/2023]
Abstract
Zn/Co binding to homodimeric CzrA de-represses transcription of the czr (cobalt zinc resistance) operon in Staphylococcus aureus. Essentially complete backbone and stereospecific methyl group resonance assignments for apo-, Zn2 and a 42 kDa apo-CzrA-DNA complex are presented.
Collapse
Affiliation(s)
- Alphonse I Arunkumar
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | | | | | | |
Collapse
|
48
|
Banci L, Bertini I, Cantini F, Ciofi-Baffoni S, Cavet JS, Dennison C, Graham AI, Harvie DR, Robinson NJ. NMR structural analysis of cadmium sensing by winged helix repressor CmtR. J Biol Chem 2007; 282:30181-8. [PMID: 17599915 DOI: 10.1074/jbc.m701119200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CmtR from Mycobacterium tuberculosis is a winged helical DNA-binding repressor of the ArsR-SmtB metal-sensing family that senses cadmium and lead. Cadmium-CmtR is a dimer with the metal bound to Cys-102 from the C-terminal region of one subunit and two Cys associated with helix alphaR from the other subunit, forming a symmetrical pair of cadmium-binding sites. This is a significant novelty in the ArsR-SmtB family. The structure of the dimer could be solved at 312 K. The apoprotein at the same temperature is still a dimer, but it experiences a large conformational exchange at the dimer interface and within each monomer. This is monitored by an overall decrease of the number of nuclear Overhauser effects and by an increase of H(2)O-D(2)O exchange rates, especially at the dimeric interface, in the apo form with respect to the cadmium-bound state. The C-terminal tail region is completely unstructured in both apo and cadmium forms but becomes less mobile in the cadmium-bound protein due to the recruitment of Cys-102 as a metal-ligand. DNA binds to the apo dimer with a ratio 1:3 at millimolar concentration. Addition of cadmium to the apo-CmtR-DNA complex causes DNA detachment, restoring the NMR spectrum of free cadmium-CmtR. Cadmium binding across the dimer interface impairs DNA association by excluding the apo-conformers suited to bind DNA.
Collapse
Affiliation(s)
- Lucia Banci
- Department of Chemistry and Centro Risonanze Magnetiche, University of Florence, Via Luigi Sacconi 6, Florence 50019, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Giedroc DP, Arunkumar AI. Metal sensor proteins: nature's metalloregulated allosteric switches. Dalton Trans 2007:3107-20. [PMID: 17637984 DOI: 10.1039/b706769k] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metalloregulatory proteins control the expression of genes that allow organisms to quickly adapt to chronic toxicity or deprivation of both biologically essential metal ions and heavy metal pollutants found in their microenvironment. Emerging evidence suggests that metal ion homeostasis and resistance defines an important tug-of-war in human host-bacterial pathogen interactions. This adaptive response originates with the formation of "metal receptor" complexes of exquisite selectivity. In this perspective, we summarize consensus structural features of metal sensing coordination complexes and the evolution of distinct metal selectivities within seven characterized metal sensor protein families. In addition, we place recent efforts to understand the structural basis of metal-induced allosteric switching of these metalloregulatory proteins in a thermodynamic framework, and review the degree to which coordination chemistry drives changes in protein structure and dynamics in selected metal sensor systems. New insights into how metal sensor proteins function in the complex intracellular milieu of the cytoplasm of cells will require a more sophisticated understanding of the "metallome" and will benefit greatly from ongoing collaborative efforts in bioinorganic, biophysical and analytical chemistry, structural biology and microbiology.
Collapse
Affiliation(s)
- David P Giedroc
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA.
| | | |
Collapse
|
50
|
Iranzo O, Cabello C, Pecoraro VL. Heterochromia in designed metallopeptides: geometry-selective binding of CdII in a de novo peptide. Angew Chem Int Ed Engl 2007; 46:6688-91. [PMID: 17582808 PMCID: PMC5242183 DOI: 10.1002/anie.200701729] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Olga Iranzo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | | | | |
Collapse
|