101
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Wu ZX, Gan NQ, Huang Q, Song LR. Response of microcystis to copper stress: do phenotypes of microcystis make a difference in stress tolerance? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2007; 147:324-30. [PMID: 16828944 DOI: 10.1016/j.envpol.2006.05.022] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 05/24/2006] [Indexed: 05/10/2023]
Abstract
To elucidate the role of phenotype in stress-tolerant bloom-forming cyanobacterium Microcystis, two phenotypes of M. aeruginosa - unicellular and colonial strains were selected to investigate how they responded to copper stress. Flow cytometry (FCM) examination indicated that the percents of viable cells in unicellular and colonial Microcystis were 1.92-2.83% and 72.3-97.51%, respectively, under 0.25 mgl(-1) copper sulfate treatment for 24h. Upon exposure to 0.25 mgl(-1) copper sulfate, the activities of antioxidative enzyme, such as superoxide dismutase (SOD) and catalase (CAT), were significantly increased in colonial Microcystis compared to unicellular Microcystis. Meanwhile, the values of the photosynthetic parameters (F(v)/F(m), ETR(max), and oxygen evolution rate) decreased more rapidly in unicellular Microcystis than in colonial Microcystis. The results indicate that colonial Microcystis has a higher endurance to copper than unicellular Microcystis. This suggests that the efficient treatment concentration of copper sulfate as algaecides will be dependent on the phenotypes of Microcystis.
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Affiliation(s)
- Zhong-Xing Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, PR China
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102
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Dwyer DJ, Kohanski MA, Hayete B, Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol 2007; 3:91. [PMID: 17353933 PMCID: PMC1847949 DOI: 10.1038/msb4100135] [Citation(s) in RCA: 340] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 01/26/2007] [Indexed: 01/08/2023] Open
Abstract
Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase-catalyzed strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic gyrase inhibitors, which trap the gyrase molecule at the DNA cleavage stage. Owing to this interaction, double-stranded DNA breaks are introduced and replication machinery is arrested at blocked replication forks. This immediately results in bacteriostasis and ultimately induces cell death. Here we demonstrate, through a series of phenotypic and gene expression analyses, that superoxide and hydroxyl radical oxidative species are generated following gyrase poisoning and play an important role in cell killing by gyrase inhibitors. We show that superoxide-mediated oxidation of iron–sulfur clusters promotes a breakdown of iron regulatory dynamics; in turn, iron misregulation drives the generation of highly destructive hydroxyl radicals via the Fenton reaction. Importantly, our data reveal that blockage of hydroxyl radical formation increases the survival of gyrase-poisoned cells. Together, this series of biochemical reactions appears to compose a maladaptive response, that serves to amplify the primary effect of gyrase inhibition by oxidatively damaging DNA, proteins and lipids.
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Affiliation(s)
- Daniel J Dwyer
- Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA, USA
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA, USA
| | - Michael A Kohanski
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Boris Hayete
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - James J Collins
- Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA, USA
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Center for BioDynamics and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA. Tel.: +617 353 0390; Fax: +617 353 5462;
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103
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Leão PN, Vasconcelos MTSD, Vasconcelos VM. Role of marine cyanobacteria in trace metal bioavailability in seawater. MICROBIAL ECOLOGY 2007; 53:104-9. [PMID: 17186147 DOI: 10.1007/s00248-006-9153-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 07/26/2006] [Indexed: 05/13/2023]
Abstract
In seawater, several trace metals with biological significance are highly complexed with organic matter. Marine cyanobacteria are an important phytoplanktonic group, with the ability to release trace metal-binding compounds to the seawater medium, which in turn modulates their bioavailability and influences their biogeochemical cycles. Such interactions may allow cyanobacteria to more easily access less available trace metals essential for their metabolic processes, or, conversely, keep the toxic forms of the trace metals from reaching intolerable levels. In this minireview, Cu and Fe interactions with cyanobacteria received special attention, although other trace metals (Co, Pb, Zn, and Cd) are also covered. Recent research has shed light on many aspects of trace metal-cyanobacteria ecology in seawater; nevertheless, the biochemical processes behind this dynamics and the structure of the vast majority of the metal binding compounds remain unclear.
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Affiliation(s)
- Pedro N Leão
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas 289, 4050-123, Porto, Portugal.
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104
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Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS. An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol 2006; 2:47. [PMID: 16969339 PMCID: PMC1681521 DOI: 10.1038/msb4100091] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 07/25/2006] [Indexed: 11/09/2022] Open
Abstract
Cellular response to stress entails complex mRNA and protein abundance changes, which translate into physiological adjustments to maintain homeostasis as well as to repair and minimize damage to cellular components. We have characterized the response of the halophilic archaeon Halobacterium salinarum NRC-1 to (60)Co ionizing gamma radiation in an effort to understand the correlation between genetic information processing and physiological change. The physiological response model we have constructed is based on integrated analysis of temporal changes in global mRNA and protein abundance along with protein-DNA interactions and evolutionarily conserved functional associations. This systems view reveals cooperation among several cellular processes including DNA repair, increased protein turnover, apparent shifts in metabolism to favor nucleotide biosynthesis and an overall effort to repair oxidative damage. Further, we demonstrate the importance of time dimension while correlating mRNA and protein levels and suggest that steady-state comparisons may be misleading while assessing dynamics of genetic information processing across transcription and translation.
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Affiliation(s)
| | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA
- Baliga Lab, Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA. Tel.: +1 206 732 1266; Fax: +1 206 374 3050; E-mail:
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105
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Ettema TJG, Brinkman AB, Lamers PP, Kornet NG, de Vos WM, van der Oost J. Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2. Microbiology (Reading) 2006; 152:1969-1979. [PMID: 16804172 DOI: 10.1099/mic.0.28724-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using a comparative genomics approach, a copper resistance gene cluster has been identified in multiple archaeal genomes. The cop cluster is predicted to encode a metallochaperone (CopM), a P-type copper-exporting ATPase (CopA) and a novel, archaea-specific transcriptional regulator (CopT) which might control the expression of the cop genes. Sequence analysis revealed that CopT has an N-terminal DNA-binding helix–turn–helix domain and a C-terminal TRASH domain; TRASH is a novel domain which has recently been proposed to be uniquely involved in metal-binding in sensors, transporters and trafficking proteins in prokaryotes. The present study describes the molecular characterization of the cop gene cluster in the thermoacidophilic crenarchaeon Sulfolobus solfataricus. The polycistronic copMA transcript was found to accumulate in response to growth-inhibiting copper concentrations, whereas copT transcript abundance appeared to be constitutive. DNA-binding assays revealed that CopT binds to the copMA promoter at multiple sites, both upstream and downstream of the predicted TATA-BRE site. Copper was found to specifically modulate the affinity of DNA binding by CopT. This study describes a copper-responsive operon in archaea, a new family of archaeal DNA-binding proteins, and supports the idea that this domain plays a prominent role in the archaeal copper response. A model is proposed for copper-responsive transcriptional regulation of the copMA gene cluster.
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Affiliation(s)
- Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - Arie B Brinkman
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - Packo P Lamers
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - Noor G Kornet
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
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106
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Yang J, Panek HR, O'Brian MR. Oxidative stress promotes degradation of the Irr protein to regulate haem biosynthesis in Bradyrhizobium japonicum. Mol Microbiol 2006; 60:209-18. [PMID: 16556232 DOI: 10.1111/j.1365-2958.2006.05087.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The haem proteins catalase and peroxidase are stress response proteins that detoxify reactive oxygen species. In the bacterium Bradyrhizobium japonicum, expression of the gene encoding the haem biosynthesis enzyme delta-aminolevulinic acid dehydratase (ALAD) is normally repressed by the Irr protein in iron-limited cells. Irr degrades in the presence of iron, which requires haem binding to the protein. Here, we found that ALAD levels were elevated in iron-limited cells of a catalase-deficient mutant, which corresponded with aberrantly low levels of Irr. Irr was undetectable in wild-type cells within 90 min after exposure to exogenous H2O2, but not in a haem-deficient mutant strain. In addition, Irr did not degrade in response to iron in the absence of O2. The findings indicate that reactive oxygen species promote Irr turnover mediated by haem, and are involved in iron-dependent degradation. We demonstrated Irr oxidation in vitro, which required haem, O2 and a reductant. A truncated Irr mutant unable to bind ferrous haem does not degrade in vivo, and was not oxidized in vitro. We suggest that Irr oxidation is a signal for its degradation, and that cells sense and respond to oxidative stress through Irr to regulate haem biosynthesis.
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Affiliation(s)
- Jianhua Yang
- Department of Biochemistry and Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York at Buffalo, Buffalo, NY 14214, USA
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107
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Arnesano F, Banci L, Bertini I, Capozzi F, Ciofi-Baffoni S, Ciurli S, Luchinat C, Mangani S, Rosato A, Turano P, Viezzoli MS. An Italian contribution to structural genomics: Understanding metalloproteins. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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108
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Banci L, Bertini I, Ciofi-Baffoni S, Kandias NG, Robinson NJ, Spyroulias GA, Su XC, Tottey S, Vanarotti M. The delivery of copper for thylakoid import observed by NMR. Proc Natl Acad Sci U S A 2006; 103:8320-5. [PMID: 16707580 PMCID: PMC1482492 DOI: 10.1073/pnas.0600142103] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The thylakoid compartments of plant chloroplasts are a vital destination for copper. Copper is needed to form holo-plastocyanin, which must shuttle electrons between photosystems to convert light into biologically useful chemical energy. Copper can bind tightly to proteins, so it has been hypothesized that copper partitions onto ligand-exchange pathways to reach intracellular locations without inflicting damage en route. The copper metallochaperone Atx1 of chloroplast-related cyanobacteria (ScAtx1) engages in bacterial two-hybrid interactions with N-terminal domains of copper-transporting ATPases CtaA (cell import) and PacS (thylakoid import). Here we visualize copper delivery. The N-terminal domain PacS(N) has a ferredoxin-like fold that forms copper-dependent heterodimers with ScAtx1. Removal of copper, by the addition of the cuprous-ion chelator bathocuproine disulfonate, disrupts this heterodimer, as shown from a reduction of the overall tumbling rate of the protein mixture. The NMR spectral changes of the heterodimer versus the separate proteins reveal that loops 1, 3, and 5 (the carboxyl tail) of the ScAtx1 Cu(I) site switch to an apo-like configuration in the heterodimer. NMR data ((2)J(NH) couplings in the imidazole ring of (15)N ScAtx1 His-61) also show that His-61, bound to copper(I) in [Cu(I)ScAtx1](2), is not coordinated to copper in the heterodimer. A model for the PacS(N)/Cu(I)/ScAtx1 complex is presented. Contact with PacS(N) induces change to the ScAtx1 copper-coordination sphere that drives copper release for thylakoid import. These data also elaborate on the mechanism to keep copper(I) out of the ZiaA(N) ATPase zinc sites.
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Affiliation(s)
- Lucia Banci
- *Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Ivano Bertini
- *Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- To whom correspondence should be addressed. E-mail:
| | - Simone Ciofi-Baffoni
- *Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Nikolaos G. Kandias
- *Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Nigel J. Robinson
- Department of Cell and Molecular Bioscience, Medical School, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom; and
| | - Georgios A. Spyroulias
- *Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26500 Rion, Patras, Greece
| | - Xun-Cheng Su
- *Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Stephen Tottey
- Department of Cell and Molecular Bioscience, Medical School, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom; and
| | - Murugendra Vanarotti
- *Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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109
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Kung CCS, Huang WN, Huang YC, Yeh KC. Proteomic survey of copper-binding proteins inArabidopsis roots by immobilized metal affinity chromatography and mass spectrometry. Proteomics 2006; 6:2746-58. [PMID: 16526091 DOI: 10.1002/pmic.200500108] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To plants, copper is vitally essential at low concentrations but extremely toxic at elevated concentrations. Plants have evolved a suite of mechanisms that modulate the uptake, distribution, and utilization of copper ions. These mechanisms require copper-interacting proteins for transporting, chelating, and sequestrating copper ions. In this study, we have systematically screened for copper-interacting proteins in Arabidopsis roots via copper-immobilized metal affinity chromatography (Cu-IMAC). We also compared Arabidopsis root metalloproteomes with affinity to Cu-IMAC and Zn-IMAC. From the identities of 38 protein spots with affinity to Cu-IMAC, 35 unique proteins were identified. Functional classification of these proteins includes redox/hydrolytic reactions, amino acid metabolism, glutathione metabolism, phosphorylation, translation machinery, membrane-associated proteins, and vegetative storage proteins. Potential copper-interacting motifs were predicted and scored. Six candidate motifs, H-(X)5 -H, H-(X)7 -H, H-(X)12 -H, H-(X)6 -M, M-(X)7 -H, and H-(X)3 -C, are present in Cu-IMAC-isolated proteins with higher frequency than in the whole Arabidopsis proteome.
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Affiliation(s)
- Cheng-Che S Kung
- Institute of BioAgricultural Sciences, Academia Sinica, Taipei, Taiwan, Republic of China
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110
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Kassab DM, Roane TM. Differential responses of a mine tailings Pseudomonas isolate to cadmium and lead exposures. Biodegradation 2006; 17:379-87. [PMID: 16477362 DOI: 10.1007/s10532-005-9010-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Accepted: 08/04/2005] [Indexed: 10/25/2022]
Abstract
We examined cadmium and lead resistance in Pseudomonas sp. S8A, an isolate obtained from mine tailings-contaminated soil. Resistant to soluble metal concentrations up to 200 mg l(-1) cadmium and 300 mg l(-1) lead, S8A produced both exopolymer and biosurfactant. Upon growth, this pseudomonad diverged into two morphologically distinct colony subtypes; small and round or large and flat. In the presence of lead and in the no metal control the large morphotype appeared only in late stationary phase. With cadmium the large morphotype appeared immediately following exposure. Results show that the large morphotype produced greater amounts of surfactant than the small morphotype, suggesting a unique subpopulation response to cadmium toxicity. Results also indicate that an unidentified 28 kDa protein was expressed following exposure to >10 mg l(-1) cadmium. This study demonstrates new links between surfactant production, differential subpopulation response and metal exposure.
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Affiliation(s)
- Duried M Kassab
- Department of Biology, University of Colorado at Denver, Denver, USA
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111
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Baker-Austin C, Dopson M, Wexler M, Sawers RG, Bond PL. Molecular insight into extreme copper resistance in the extremophilic archaeon 'Ferroplasma acidarmanus' Fer1. MICROBIOLOGY-SGM 2005; 151:2637-2646. [PMID: 16079342 DOI: 10.1099/mic.0.28076-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
'Ferroplasma acidarmanus' strain Fer1 is an extremely acidophilic archaeon involved in the genesis of acid mine drainage, and was isolated from copper-contaminated mine solutions at Iron Mountain, CA, USA. Here, the initial proteomic and molecular investigation of Cu(2+) resistance in this archaeon is presented. Analysis of Cu(2+) toxicity via batch growth experiments and inhibition of oxygen uptake in the presence of ferrous iron demonstrated that Fer1 can grow and respire in the presence of 20 g Cu(2+) l(-1). The Fer1 copper resistance (cop) loci [originally detected by Ettema, T. J. G., Huynen, M. A., de Vos, W. M. & van der Oost, J. Trends Biochem Sci 28, 170-173 (2003)] include genes encoding a putative transcriptional regulator (copY), a putative metal-binding chaperone (copZ) and a putative copper-transporting P-type ATPase (copB). Transcription analyses demonstrated that copZ and copB are co-transcribed, and transcript levels were increased significantly in response to exposure to high levels of Cu(2+), suggesting that the transport system is operating for copper efflux. Proteomic analysis of Fer1 cells exposed to Cu(2+) revealed the induction of stress proteins associated with protein folding and DNA repair (including RadA, thermosome and DnaK homologues), suggesting that 'Ferroplasma acidarmanus' Fer1 uses multiple mechanisms for resistance to high levels of copper.
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Affiliation(s)
- Craig Baker-Austin
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Mark Dopson
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Margaret Wexler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - R Gary Sawers
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
| | - Philip L Bond
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich NR4 7TJ, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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112
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Tottey S, Harvie DR, Robinson NJ. Understanding how cells allocate metals using metal sensors and metallochaperones. Acc Chem Res 2005; 38:775-83. [PMID: 16231873 DOI: 10.1021/ar0300118] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Each metalloprotein must somehow acquire the correct metal. We review the insights into metal specificity in cells provided by studies of ArsR-SmtB DNA binding, metal-responsive transcriptional repressors, and a bacterial copper chaperone. Cyanobacteria are the one bacterial group that have known enzymatic demand for cytoplasmic copper import. The copper chaperone and ATPases that supply cyanobacterial plastocyanin and cytochrome oxidase are reviewed, along with related ATPases for cobalt and zinc. These studies highlight the contributions of protein-protein interactions to metal speciation. Metal sensors and metallochaperones, along with metal transporters and metal-storage proteins, act in concert not only to supply the correct metals but also to withhold the wrong ones.
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Affiliation(s)
- Stephen Tottey
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle, NE2 4HH, United Kingdom
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113
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Silver S, Phung LT. A bacterial view of the periodic table: genes and proteins for toxic inorganic ions. J Ind Microbiol Biotechnol 2005; 32:587-605. [PMID: 16133099 DOI: 10.1007/s10295-005-0019-6] [Citation(s) in RCA: 253] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Accepted: 07/11/2005] [Indexed: 10/25/2022]
Abstract
Essentially all bacteria have genes for toxic metal ion resistances and these include those for Ag+, AsO2-, AsO4(3-), Cd2+ Co2+, CrO4(2-), Cu2+, Hg2+, Ni2+, Pb2+, TeO3(2-), Tl+ and Zn2+. The largest group of resistance systems functions by energy-dependent efflux of toxic ions. Fewer involve enzymatic transformations (oxidation, reduction, methylation, and demethylation) or metal-binding proteins (for example, metallothionein SmtA, chaperone CopZ and periplasmic silver binding protein SilE). Some of the efflux resistance systems are ATPases and others are chemiosmotic ion/proton exchangers. For example, Cd2+-efflux pumps of bacteria are either inner membrane P-type ATPases or three polypeptide RND chemiosmotic complexes consisting of an inner membrane pump, a periplasmic-bridging protein and an outer membrane channel. In addition to the best studied three-polypeptide chemiosmotic system, Czc (Cd2+, Zn2+, and Co2), others are known that efflux Ag+, Cu+, Ni2+, and Zn2+. Resistance to inorganic mercury, Hg2+ (and to organomercurials, such as CH3Hg+ and phenylmercury) involve a series of metal-binding and membrane transport proteins as well as the enzymes mercuric reductase and organomercurial lyase, which overall convert more toxic to less toxic forms. Arsenic resistance and metabolizing systems occur in three patterns, the widely-found ars operon that is present in most bacterial genomes and many plasmids, the more recently recognized arr genes for the periplasmic arsenate reductase that functions in anaerobic respiration as a terminal electron acceptor, and the aso genes for the periplasmic arsenite oxidase that functions as an initial electron donor in aerobic resistance to arsenite.
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Affiliation(s)
- Simon Silver
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL 60612, USA.
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114
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Banci L, Bertini I, Ciofi-Baffoni S, Katsari E, Katsaros N, Kubicek K, Mangani S. A copper(I) protein possibly involved in the assembly of CuA center of bacterial cytochrome c oxidase. Proc Natl Acad Sci U S A 2005; 102:3994-9. [PMID: 15753304 PMCID: PMC554794 DOI: 10.1073/pnas.0406150102] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Indexed: 11/18/2022] Open
Abstract
Sco1 and Cox17 are accessory proteins required for the correct assembly of eukaryotic cytochrome c oxidase. At variance with Sco1, Cox17 orthologs are found only in eukaryotes. We browsed bacterial genomes to search proteins functionally equivalent to Cox17, and we identified a class of proteins of unknown function displaying a conserved gene neighborhood to bacterial Sco1 genes, all sharing a potential metal binding motif H(M)X10MX21HXM. Two members of this group, DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus, were expressed, and their interaction with copper was investigated. The solution structure and extended x-ray absorption fine structure data on the former protein reveal that the protein binds copper(I) through a histidine and three Mets in a cupredoxin-like fold. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria. On the basis of our results, a possible pathway for copper delivery to the Cu(A) center in bacteria is proposed.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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115
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Functions and homeostasis of zinc, copper, and nickel in plants. TOPICS IN CURRENT GENETICS 2005. [DOI: 10.1007/4735_96] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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116
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Zhang JW, Butland G, Greenblatt JF, Emili A, Zamble DB. A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway. J Biol Chem 2004; 280:4360-6. [PMID: 15569666 DOI: 10.1074/jbc.m411799200] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The [NiFe] centers at the active sites of the Escherichia coli hydrogenase enzymes are assembled by a team of accessory proteins that includes the products of the hyp genes. To determine whether any other proteins are involved in this process, the sequential peptide affinity system was used. The analysis of the proteins in a complex with HypB revealed the peptidyl-prolyl cis/trans-isomerase SlyD, a metal-binding protein that has not been previously linked to the hydrogenase biosynthetic pathway. The association between HypB and SlyD was confirmed by chemical cross-linking of purified proteins. Deletion of the slyD gene resulted in a marked reduction of the hydrogenase activity in cell extracts prepared from anaerobic cultures, and an in-gel assay was used to demonstrate diminished activities of both hydrogenase 1 and 2. Western analysis revealed a decrease in the final proteolytic processing of the hydrogenase 3 HycE protein, indicating that the metal center was not assembled properly. These deficiencies were all rescued by growth in medium containing excess nickel, but zinc did not have any phenotypic effect. Experiments with radioactive nickel demonstrated that less nickel accumulated in DeltaslyD cells compared with wild type, and overexpression of SlyD from an inducible promoter doubled the level of cellular nickel. These experiments demonstrate that SlyD has a role in the nickel insertion step of the hydrogenase maturation pathway, and the possible functions of SlyD are discussed.
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Affiliation(s)
- Jie Wei Zhang
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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117
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Berducci G, Mazzetti AP, Rotilio G, Battistoni A. Periplasmic competition for zinc uptake between the metallochaperone ZnuA and Cu,Zn superoxide dismutase. FEBS Lett 2004; 569:289-92. [PMID: 15225650 DOI: 10.1016/j.febslet.2004.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Revised: 06/02/2004] [Accepted: 06/02/2004] [Indexed: 10/26/2022]
Abstract
We have investigated the availability of zinc in the periplasmic space of Escherichia coli using a mutant Cu,Zn superoxide dismutase whose dimerization is triggered by zinc binding. This mutant enzyme accumulates in the monomeric form when wild type cells are grown in minimal medium, but assembles in the dimeric form when it is produced in the same medium by a mutant strain lacking the periplasmic zinc metallochaperone ZnuA. These results indicate that periplasmic zinc-containing proteins compete for metal binding when bacteria grow in environments where this element is present in traces. The effective ZnuA ability to sequester the available zinc ions from the periplasm suggests that zinc-containing cytoplasmic proteins are more important for bacterial viability than the periplasmic ones.
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Affiliation(s)
- Giovanni Berducci
- Dipartimento di Biologia, Università di Roma Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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118
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Balatri E, Banci L, Bertini I, Cantini F, Ciofi-Baffoni S. Solution structure of Sco1: a thioredoxin-like protein Involved in cytochrome c oxidase assembly. Structure 2004; 11:1431-43. [PMID: 14604533 DOI: 10.1016/j.str.2003.10.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sco1, a protein required for the proper assembly of cytochrome c oxidase, has a soluble domain anchored to the cytoplasmic membrane through a single transmembrane segment. The solution structure of the soluble part of apoSco1 from Bacillus subtilis has been solved by NMR and the internal mobility characterized. Its fold places Sco1 in a distinct subgroup of the functionally unrelated thioredoxin proteins. In vitro Sco1 binds copper(I) through a CXXXCP motif and possibly His 135 and copper(II) in two different species, thus suggesting that copper(II) is adventitious more than physiological. The Sco1 structure represents the first structure of this class of proteins, present in a variety of eukaryotic and bacterial organisms, and elucidates a link between copper trafficking proteins and thioredoxins. The availability of the structure has allowed us to model the homologs Sco1 and Sco2 from S. cerevisiae and to discuss the physiological role of the Sco family.
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Affiliation(s)
- Erica Balatri
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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119
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Kretschmer XC, Meitzner G, Gardea-Torresdey JL, Webb R. Determination of Cu environments in the cyanobacterium Anabaena flos-aquae by X-ray absorption spectroscopy. Appl Environ Microbiol 2004; 70:771-80. [PMID: 14766554 PMCID: PMC348884 DOI: 10.1128/aem.70.2.771-780.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole cells and peptidoglycan isolated from cell walls of the cyanobacterium Anabaena flos-aquae were lyophilized and used at pH 2 and pH 5 in Cu(II) binding studies. X-ray absorption spectra measured at the Cu K-edge were used to determine the oxidation states and chemical environments of Cu species in the whole-cell and peptidoglycan samples. In the whole-cell samples, most of the Cu retained at both pH values was coordinated by phosphate ligands. The whole-cell fractions contained significant concentrations of Cu(I) as well as Cu(II). An X-ray absorption near-edge spectrum analysis suggested that Cu(I) was coordinated by amine and thiol ligands. An analysis of the peptidoglycan fractions found that more Cu was adsorbed by the peptidoglycan fraction prepared at pH 5, due to increased chelation by amine and carboxyl ligands. The peptidoglycan fractions, also referred to as the cell wall fractions, contained little or no Cu(I). The Cu loading level was 30 times higher in the cell wall sample prepared at pH 5 than in the sample prepared at pH 2. Amine and bidentate carboxyl ligands had similar relative levels of importance in cell wall peptidoglycan samples prepared at both pH values, but phosphate coordination was insignificant.
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Affiliation(s)
- X C Kretschmer
- Department of Environmental Science and Engineering, The University of Texas at El Paso, El Paso, Texas 79968, USA.
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120
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Banci L, Bertini I, Ciofi-Baffoni S, Su XC, Borrelly GPM, Robinson NJ. Solution Structures of a Cyanobacterial Metallochaperone. J Biol Chem 2004; 279:27502-10. [PMID: 15075318 DOI: 10.1074/jbc.m402005200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Atx1 copper metallochaperone from Synechocystis PCC 6803, ScAtx1, interacts with two P(1)-type copper ATPases to supply copper proteins within intracellular compartments, avoiding ATPases for other metals en route. Here we report NMR-derived solution structures for ScAtx1. The monomeric apo form has a betaalphabetabetaalpha fold with backbone motions largely restricted to loop 1 containing Cys-12 and Cys-15. The tumbling rate of Cu(I)ScAtx1 (0.1-0.8 mm) implies dimers. Experimental restraints are satisfied by symmetrical dimers with Cys-12 or His-61, but not Cys-15, invading the copper site of the opposing subunit. A full sequence of copper ligands from the cell surface to thylakoid compartments is proposed, considering in vitro homodimer liganding to mimic in vivo liganding in ScAtx1-ATPase heterodimers. A monomeric high resolution structure for Cu(I)ScAtx1, with Cys-12, Cys-15, and His-61 as ligands, is calculated without violations despite the rotational correlation time. (2)J(NH) couplings in the imidazole ring of His-61 establish coordination of N(epsilon2) to copper. His-61 is analogous to Lys-65 in eukaryotic metallochaperones, stabilizing Cu(I)S(2) complexes but by binding Cu(I) rather than compensating charge. Cys-Cys-His ligand sets are an emergent theme in some copper metallochaperones, although not in related Atx1, CopZ, or Hah1. Surface charge (Glu-13) close to the metal-binding site of ScAtx1 is likely to support interaction with complementary surfaces of copper-transporting ATPases (PacS-Arg-11 and CtaA-Lys-14) but to discourage interaction with zinc ATPase ZiaA and so inhibit aberrant formation of copper-ZiaA complexes.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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121
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Arnesano F, Banci L, Bertini I, Ciofi‐Baffoni S. Perspectives in Inorganic Structural Genomics: A Trafficking Route for Copper. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200300841] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Fabio Arnesano
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy, Fax: (internat.) + 39‐055‐4574271
| | - Lucia Banci
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy, Fax: (internat.) + 39‐055‐4574271
| | - Ivano Bertini
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy, Fax: (internat.) + 39‐055‐4574271
| | - Simone Ciofi‐Baffoni
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy, Fax: (internat.) + 39‐055‐4574271
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122
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Arnesano F, Banci L, Bertini I, Bonvin AMJJ. A Docking Approach to the Study of Copper Trafficking Proteins. Structure 2004; 12:669-76. [PMID: 15062089 DOI: 10.1016/j.str.2004.03.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Revised: 01/15/2004] [Accepted: 01/20/2004] [Indexed: 10/26/2022]
Abstract
A structural model of the transient complex between the yeast copper chaperone Atx1 and the first soluble domain of the copper transporting ATPase Ccc2 was obtained with HADDOCK, combining NMR chemical shift mapping information with in silico docking. These two proteins are involved in copper trafficking in yeast cells. Calculations were performed starting with the copper ion either bound to Atx1 or to Ccc2 and using the experimental structures of the copper-loaded and apo forms of each protein. The copper binding motifs of the two proteins are found in close proximity. Copper tends to move from Atx1 to Ccc2, consistent with the physiological direction of transfer, with concomitant structural rearrangements, in agreement with experimental observations. The interaction is mainly of an electrostatic nature with hydrogen bonds stabilizing the complex. The structural data are relevant for a number of proteins homologous to Atx1 and Ccc2 and conserved from bacteria to humans.
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Affiliation(s)
- Fabio Arnesano
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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123
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Banci L, Bertini I, Del Conte R. Solution Structure of Apo CopZ from Bacillus subtilis: Further Analysis of the Changes Associated with the Presence of Copper. Biochemistry 2003; 42:13422-8. [PMID: 14621987 DOI: 10.1021/bi0353326] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solution structure of apo CopZ from Bacillus subtilis has been determined with the aim of investigating the changes in the hydrophobic interactions around the M-X-C-X-X-C copper(I) binding motif upon metal binding. The methionine of this motif (Met 11 in CopZ) points toward the solvent in apo CopZ, whereas its sulfur atom is close to the metal ion in the metal-loaded protein, though probably not at binding distance. This change is associated with the weakening of the interaction between Leu 37 and Cys 16, present in the apo form, and the formation of an interaction between Met 11 and Tyr 65. Loops 1, 3, and 5 are affected by metal binding. Comparison with the structure of other homologous proteins confirms that often metal binding affects a hydrophobic patch around the metal site, possibly for optimizing and tuning the hydrophobic interactions with the partners. It is also shown that copper(I) exchanges among apo CopZ molecules in slow exchange on the NMR time scale, whereas it is known that such exchange between partner molecules (i.e., metallochaperones and metal pumps) is fast.
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Affiliation(s)
- Lucia Banci
- Department of Chemistry and Centro di Risonanze Magnetiche, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
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124
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Abstract
It is difficult to over-state the importance of Zn(II) in biology. It is a ubiquitous essential metal ion and plays a role in catalysis, protein structure and perhaps as a signal molecule, in organisms from all three kingdoms. Of necessity, organisms have evolved to optimise the intracellular availability of Zn(II) despite the extracellular milieu. To this end, prokaryotes contain a range of Zn(II) import, Zn(II) export and/or binding proteins, some of which utilise either ATP or the chemiosmotic potential to drive the movement of Zn(II) across the cytosolic membrane, together with proteins that facilitate the diffusion of this ion across either the outer or inner membranes of prokaryotes. This review seeks to give an overview of the systems currently classified as altering Zn(II) availability in prokaryotes.
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Affiliation(s)
- Dayle K Blencowe
- Cardiff School of Biosciences (2), Cardiff University, Museum Avenue, P.O. Box 911, Cardiff CF10 3US, Wales, UK
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125
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Abstract
What makes a heavy metal resistant bacterium heavy metal resistant? The mechanisms of action, physiological functions, and distribution of metal-exporting proteins are outlined, namely: CBA efflux pumps driven by proteins of the resistance-nodulation-cell division superfamily, P-type ATPases, cation diffusion facilitator and chromate proteins, NreB- and CnrT-like resistance factors. The complement of efflux systems of 63 sequenced prokaryotes was compared with that of the heavy metal resistant bacterium Ralstonia metallidurans. This comparison shows that heavy metal resistance is the result of multiple layers of resistance systems with overlapping substrate specificities, but unique functions. Some of these systems are widespread and serve in the basic defense of the cell against superfluous heavy metals, but some are highly specialized and occur only in a few bacteria. Possession of the latter systems makes a bacterium heavy metal resistant.
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Affiliation(s)
- Dietrich H Nies
- Institute of Microbiology, Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06099 Halle/Saale, Germany.
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126
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127
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Silver S. Bacterial silver resistance: molecular biology and uses and misuses of silver compounds. FEMS Microbiol Rev 2003; 27:341-53. [PMID: 12829274 DOI: 10.1016/s0168-6445(03)00047-0] [Citation(s) in RCA: 736] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Resistance to silver compounds as determined by bacterial plasmids and genes has been defined by molecular genetics. Silver resistance conferred by the Salmonella plasmid pMGH100 involves nine genes in three transcription units. A sensor/responder (SilRS) two-component transcriptional regulatory system governs synthesis of a periplasmic Ag(I)-binding protein (SilE) and two efflux pumps (a P-type ATPase (SilP) plus a three-protein chemiosmotic RND Ag(I)/H+ exchange system (SilCBA)). The same genes were identified on five of 19 additional IncH incompatibility class plasmids but thus far not on other plasmids. Of 70 random enteric isolates from a local hospital, isolates from catheters and other Ag-exposed sites, and total genomes of enteric bacteria, 10 have recognizable sil genes. The centrally located six genes are found and functional in the chromosome of Escherichia coli K-12, and also occur on the genome of E. coli O157:H7. The use of molecular epidemiological tools will establish the range and diversity of such resistance systems in clinical and non-clinical sources. Silver compounds are used widely as effective antimicrobial agents to combat pathogens (bacteria, viruses and eukaryotic microorganisms) in the clinic and for public health hygiene. Silver cations (Ag+) are microcidal at low concentrations and used to treat burns, wounds and ulcers. Ag is used to coat catheters to retard microbial biofilm development. Ag is used in hygiene products including face creams, "alternative medicine" health supplements, supermarket products for washing vegetables, and water filtration cartridges. Ag is generally without adverse effects for humans, and argyria (irreversible discoloration of the skin resulting from subepithelial silver deposits) is rare and mostly of cosmetic concern.
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Affiliation(s)
- Simon Silver
- Department of Microbiology and Immunology, M/C 790, University of Illinois, 835 South Wolcott Avenue, Chicago, IL 60612-7344, USA.
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