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Burger N, Mittenbühler MJ, Xiao H, Shin S, Bozi LHM, Wei S, Sprenger HG, Sun Y, Zhu Y, Darabedian N, Petrocelli JJ, Muro PL, Che J, Chouchani ET. A comprehensive landscape of the zinc-regulated human proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574225. [PMID: 38260676 PMCID: PMC10802333 DOI: 10.1101/2024.01.04.574225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Zinc is an essential micronutrient that regulates a wide range of physiological processes, principally through Zn 2+ binding to protein cysteine residues. Despite being critical for modulation of protein function, for the vast majority of the human proteome the cysteine sites subject to regulation by Zn 2+ binding remain undefined. Here we develop ZnCPT, a comprehensive and quantitative mapping of the zinc-regulated cysteine proteome. We define 4807 zinc-regulated protein cysteines, uncovering protein families across major domains of biology that are subject to either constitutive or inducible modification by zinc. ZnCPT enables systematic discovery of zinc-regulated structural, enzymatic, and allosteric functional domains. On this basis, we identify 52 cancer genetic dependencies subject to zinc regulation, and nominate malignancies sensitive to zinc-induced cytotoxicity. In doing so, we discover a mechanism of zinc regulation over Glutathione Reductase (GSR) that drives cell death in GSR-dependent lung cancers. We provide ZnCPT as a resource for understanding mechanisms of zinc regulation over protein function.
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Bennett SP, Crack JC, Puglisi R, Pastore A, Le Brun NE. Native mass spectrometric studies of IscSU reveal a concerted, sulfur-initiated mechanism of iron-sulfur cluster assembly. Chem Sci 2022; 14:78-95. [PMID: 36605734 PMCID: PMC9769115 DOI: 10.1039/d2sc04169c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are cofactors essential for life. Though the proteins that function in the assembly of Fe-S clusters are well known, details of the molecular mechanism are less well established. The Isc (iron-sulfur cluster) biogenesis apparatus is widespread in bacteria and is the closest homologue to the human system. Mutations in certain components of the human system lead to disease, and so further studies of this system could be important for developing strategies for medical treatments. We have studied two core components of the Isc biogenesis system: IscS, a cysteine desulfurase; and IscU, a scaffold protein on which clusters are built before subsequent transfer onto recipient apo-proteins. Fe2+-binding, sulfur transfer, and formation of a [2Fe-2S] was followed by a range of techniques, including time-resolved mass spectrometry, and intermediate and product species were unambiguously identified through isotopic substitution experiments using 57Fe and 34S. Under cluster synthesis conditions, sulfur adducts and the [2Fe-2S] cluster product readily accumulated on IscU, but iron adducts (other than the cluster itself) were not observed at physiologically relevant Fe2+ concentrations. Our data indicate that either Fe2+ or sulfur transfer can occur first, but that the transfer of sulfane sulfur (S0) to IscU must occur first if Zn2+ is bound to IscU, suggesting that it is the key step that initiates cluster assembly. Following this, [2Fe-2S] cluster formation is a largely concerted reaction once Fe2+ is introduced.
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Affiliation(s)
- Sophie P. Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Jason C. Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Rita Puglisi
- The Wohl Institute, King's College London, Denmark Hill CampusLondon SE5 8AFUK
| | - Annalisa Pastore
- The Wohl Institute, King's College London, Denmark Hill CampusLondon SE5 8AFUK
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
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Steunou AS, Bourbon M, Babot M, Durand A, Liotenberg S, Yamaichi Y, Ouchane S. Increasing the copper sensitivity of microorganisms by restricting iron supply, a strategy for bio-management practices. Microb Biotechnol 2020; 13:1530-1545. [PMID: 32558275 PMCID: PMC7415376 DOI: 10.1111/1751-7915.13590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/28/2022] Open
Abstract
Pollution by copper (Cu2+ ) extensively used as antimicrobial in agriculture and farming represents a threat to the environment and human health. Finding ways to make microorganisms sensitive to lower metal concentrations could help decreasing the use of Cu2 + in agriculture. In this respect, we showed that limiting iron (Fe) uptake makes bacteria much more susceptible to Cu2 + or Cd2+ poisoning. Using efflux mutants of the purple bacterium Rubrivivax gelatinosus, we showed that Cu+ and Cd2+ resistance relies on the expression of the Fur-regulated FbpABC and Ftr iron transporters. To support this conclusion, inactivation of these Fe-importers in the Cu+ or Cd2+ -ATPase efflux mutants gave rise to hypersensitivity towards these ions. Moreover, in metal overloaded cells the expression of FbpA, the periplasmic iron-binding component of the ferric ion transport FbpABC system was induced, suggesting that cells perceived an 'iron-starvation' situation and responded to it by inducing Fe-importers. In this context, the Fe-Sod activity increased in response to Fe homoeostasis dysregulation. Similar results were obtained for Vibrio cholerae and Escherichia coli, suggesting that perturbation of Fe-homoeostasis by metal excess appeared as an adaptive response commonly used by a variety of bacteria. The presented data support a model in which metal excess induces Fe-uptake to support [4Fe-4S] synthesis and thereby induce ROS detoxification system.
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Affiliation(s)
- Anne Soisig Steunou
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Marie‐Line Bourbon
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Marion Babot
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Anne Durand
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Sylviane Liotenberg
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Yoshiharu Yamaichi
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Soufian Ouchane
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
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Steunou AS, Babot M, Bourbon M, Tambosi R, Durand A, Liotenberg S, Krieger‐Liszkay A, Yamaichi Y, Ouchane S. Additive effects of metal excess and superoxide, a highly toxic mixture in bacteria. Microb Biotechnol 2020; 13:1515-1529. [PMID: 32558268 PMCID: PMC7415354 DOI: 10.1111/1751-7915.13589] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Heavy metal contamination is a serious environmental problem. Understanding the toxicity mechanisms may allow to lower concentration of metals in the metal-based antimicrobial treatments of crops, and reduce metal content in soil and groundwater. Here, we investigate the interplay between metal efflux systems and the superoxide dismutase (SOD) in the purple bacterium Rubrivivax gelatinosus and other bacteria through analysis of the impact of metal accumulation. Exposure of the Cd2+ -efflux mutant ΔcadA to Cd2+ caused an increase in the amount and activity of the cytosolic Fe-Sod SodB, thereby suggesting a role of SodB in the protection against Cd2+ . In support of this conclusion, inactivation of sodB gene in the ΔcadA cells alleviated detoxification of superoxide and enhanced Cd2+ toxicity. Similar findings were described in the Cu+ -efflux mutant with Cu+ . Induction of the Mn-Sod or Fe-Sod in response to metals in other bacteria, including Escherichia coli, Pseudomonas aeruginosa, Pseudomonas putida, Vibrio cholera and Bacillus subtilis, was also shown. Both excess Cd2+ or Cu+ and superoxide can damage [4Fe-4S] clusters. The additive effect of metal and superoxide on the [4Fe-4S] could therefore explain the hypersensitive phenotype in mutants lacking SOD and the efflux ATPase. These findings underscore that ROS defence system becomes decisive for bacterial survival under metal excess.
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Affiliation(s)
- Anne Soisig Steunou
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Marion Babot
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Marie‐Line Bourbon
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Reem Tambosi
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Anne Durand
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Sylviane Liotenberg
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Anja Krieger‐Liszkay
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Yoshiharu Yamaichi
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Soufian Ouchane
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
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Steunou AS, Durand A, Bourbon ML, Babot M, Tambosi R, Liotenberg S, Ouchane S. Cadmium and Copper Cross-Tolerance. Cu + Alleviates Cd 2 + Toxicity, and Both Cations Target Heme and Chlorophyll Biosynthesis Pathway in Rubrivivax gelatinosus. Front Microbiol 2020; 11:893. [PMID: 32582041 PMCID: PMC7283390 DOI: 10.3389/fmicb.2020.00893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/16/2020] [Indexed: 11/17/2022] Open
Abstract
Cadmium, although not redox active is highly toxic. Yet, the underlying mechanisms driving toxicity are still to be characterized. In this study, we took advantage of the purple bacterium Rubrivivax gelatinosus strain with defective Cd2 +-efflux system to identify targets of this metal. Exposure of the ΔcadA strain to Cd2 + causes a decrease in the photosystem amount and in the activity of respiratory complexes. As in case of Cu+ toxicity, the data indicated that Cd2 + targets the porphyrin biosynthesis pathway at the level of HemN, a S-adenosylmethionine and CxxxCxxC coordinated [4Fe-4S] containing enzyme. Cd2 + exposure therefore results in a deficiency in heme and chlorophyll dependent proteins and metabolic pathways. Given the importance of porphyrin biosynthesis, HemN represents a key metal target to account for toxicity. In the environment, microorganisms are exposed to mixture of metals. Nevertheless, the biological effects of such mixtures, and the toxicity mechanisms remain poorly addressed. To highlight a potential cross-talk between Cd2 + and Cu+ -efflux systems, we show (i) that Cd2 + induces the expression of the Cd2 +-efflux pump CadA and the Cu+ detoxification system CopA and CopI; and (ii) that Cu+ ions improve tolerance towards Cd2 +, demonstrating thus that metal mixtures could also represent a selective advantage in the environment.
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Affiliation(s)
- Anne Soisig Steunou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Anne Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Marie-Line Bourbon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Marion Babot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Reem Tambosi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sylviane Liotenberg
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Soufian Ouchane
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Lewis BE, Mason Z, Rodrigues AV, Nuth M, Dizin E, Cowan JA, Stemmler TL. Unique roles of iron and zinc binding to the yeast Fe-S cluster scaffold assembly protein "Isu1". Metallomics 2019; 11:1820-1835. [PMID: 31532427 DOI: 10.1039/c9mt00172g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mitochondrial Fe-S cluster biosynthesis is accomplished within yeast utilizing the biophysical attributes of the "Isu1" scaffold assembly protein. As a member of a highly homologous protein family, Isu1 has sequence conservation between orthologs and a conserved ability to assemble [2Fe-2S] clusters. Regardless of species, scaffold orthologs have been shown to exist in both "disordered" and "structured" conformations, a structural architecture that is directly related to conformations utilized during Fe-S cluster assembly. During assembly, the scaffold helps direct the delivery and utilization of Fe(ii) and persulfide substrates to produce [2Fe-2S] clusters, however Zn(ii) binding alters the activity of the scaffold while at the same time stabilizes the protein in its structured state. Additional studies confirm Zn binds to the scaffold's Cys rich active site, and has an impact on the protein's ability to make Fe-S clusters. Understanding the interplay between Fe(ii) and Zn(ii) binding to Isu1 in vitro may help clarify metal loading events that occur during Fe-S cluster assembly in vivo. Here we determine the metal : protein stoichiometry for Isu1 Zn and Fe binding to be 1 : 1 and 2 : 1, respectively. As expected, while Zn binding shifts the Isu1 to its structured state, folding is not influenced by Fe(ii) binding. X-ray absorption spectroscopy (XAS) confirms Zn(ii) binds to the scaffold's cysteine rich active site but Fe(ii) binds at a location distinct from the active site. XAS results show Isu1 binding initially of either Fe(ii) or Zn(ii) does not significantly perturb the metal site structure of alternate metal. XAS confirmed that four scaffold orthologs bind iron as high-spin Fe(ii) at a site composed of ca. 6 oxygen and nitrogen nearest neighbor ligands. Finally, in our report Zn binding dramatically reduces the Fe-S cluster assembly activity of Isu1 even in the presence of frataxin. Given the Fe-binding activity we report for Isu1 and its orthologs here, a possible mechanism involving Fe(ii) transport to the scaffold's active site during cluster assembly has been considered.
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Affiliation(s)
- Brianne E Lewis
- Department of Pharmaceutical Science, Wayne State University, Detroit, MI 48201, USA.
| | - Zachary Mason
- Department of Pharmaceutical Science, Wayne State University, Detroit, MI 48201, USA.
| | - Andria V Rodrigues
- Department of Pharmaceutical Science, Wayne State University, Detroit, MI 48201, USA.
| | - Manunya Nuth
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Dizin
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - J A Cowan
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Science, Wayne State University, Detroit, MI 48201, USA.
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