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Olivieri P, Zupok A, Yildiz T, Oltmanns J, Lehmann A, Sokolowska E, Skirycz A, Schünemann V, Leimkühler S. TusA influences Fe-S cluster assembly and iron homeostasis in E. coli by reducing the translation efficiency of Fur. Microbiol Spectr 2024:e0055624. [PMID: 38916309 DOI: 10.1128/spectrum.00556-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/20/2024] [Indexed: 06/26/2024] Open
Abstract
All sulfur transfer pathways have generally a l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of numerous sulfur-containing biomolecules in the cell. In Escherichia coli, the housekeeping l-cysteine desulfurase IscS has several interaction partners, which bind at different sites of the protein. So far, the interaction sites of IscU, Fdx, CyaY, and IscX involved in iron-sulfur (Fe-S) cluster assembly have been mapped, in addition to TusA, which is required for molybdenum cofactor biosynthesis and mnm5s2U34 tRNA modifications, and ThiI, which is involved in thiamine biosynthesis and s4U8 tRNA modifications. Previous studies predicted that the sulfur acceptor proteins bind to IscS one at a time. E. coli TusA has, however, been suggested to be involved in Fe-S cluster assembly, as fewer Fe-S clusters were detected in a ∆tusA mutant. The basis for this reduction in Fe-S cluster content is unknown. In this work, we investigated the role of TusA in iron-sulfur cluster assembly and iron homeostasis. We show that the absence of TusA reduces the translation of fur, thereby leading to pleiotropic cellular effects, which we dissect in detail in this study.IMPORTANCEIron-sulfur clusters are evolutionarily ancient prosthetic groups. The ferric uptake regulator plays a major role in controlling the expression of iron homeostasis genes in bacteria. We show that a ∆tusA mutant is impaired in the assembly of Fe-S clusters and accumulates iron. TusA, therefore, reduces fur mRNA translation leading to pleiotropic cellular effects.
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Affiliation(s)
- Paolo Olivieri
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Arkadiuz Zupok
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Tugba Yildiz
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Jonathan Oltmanns
- Department of Physics, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Angelika Lehmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Ewelina Sokolowska
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Volker Schünemann
- Department of Physics, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
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2
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Oney-Hawthorne SD, Barondeau DP. Fe-S cluster biosynthesis and maturation: Mass spectrometry-based methods advancing the field. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119784. [PMID: 38908802 DOI: 10.1016/j.bbamcr.2024.119784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically been used to elucidate details of FeS cluster type, their assembly and transfer, and changes in redox and ligand binding properties. Structural probes of protein topology, complex formation, and conformational dynamics are also necessary to fully understand these FeS protein systems. Recent developments in mass spectrometry (MS) instrumentation and methods provide new tools to investigate FeS cluster and structural properties. With the unique advantage of sampling all species in a mixture, MS-based methods can be utilized as a powerful complementary approach to probe native dynamic heterogeneity, interrogate protein folding and unfolding equilibria, and provide extensive insight into protein binding partners within an entire proteome. Here, we highlight key advances in FeS protein studies made possible by MS methodology and contribute an outlook for its role in the field.
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Affiliation(s)
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA.
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3
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Wayment-Steele HK, Otten R, Pitsawong W, Ojoawo AM, Glaser A, Calderone LA, Kern D. The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597139. [PMID: 38895306 PMCID: PMC11185700 DOI: 10.1101/2024.06.03.597139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
How can a single protein domain encode a conformational landscape with multiple stably-folded states, and how do those states interconvert? Here, we use real-time and relaxation-dispersion NMR to characterize the conformational landscape of the circadian rhythm protein KaiB from Rhodobacter sphaeroides. Unique among known natural metamorphic proteins, this KaiB variant spontaneously interconverts between two monomeric states: the "Ground" and "Fold-switched" (FS) state. KaiB in its FS state interacts with multiple binding partners, including the central KaiC protein, to regulate circadian rhythms. We find that KaiB itself takes hours to interconvert between the Ground and FS state, underscoring the ability of a single sequence to encode the slow process needed for function. We reveal the rate-limiting step between the Ground and FS state is the cis-trans isomerization of three prolines in the fold-switching region by demonstrating interconversion acceleration by the prolyl isomerase CypA. The interconversion proceeds through a "partially disordered" (PD) state, where the C-terminal half becomes disordered while the N-terminal half remains stably folded. We discovered two additional properties of KaiB's landscape. Firstly, the Ground state experiences cold denaturation: at 4°C, the PD state becomes the majorly populated state. Secondly, the Ground state exchanges with a fourth state, the "Enigma" state, on the millisecond timescale. We combine AlphaFold2-based predictions and NMR chemical shift predictions to predict this "Enigma" state is a beta-strand register shift that eases buried charged residues, and support this structure experimentally. These results provide mechanistic insight in how evolution can design a single sequence that achieves specific timing needed for its function.
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Renee Otten
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Present address: Treeline Biosciences, Watertown, MA, USA
| | - Warintra Pitsawong
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Present address: Biomolecular Discovery, Relay Therapeutics, Cambridge, MA, USA
| | - Adedolapo M Ojoawo
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Andrew Glaser
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Logan A Calderone
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Dorothee Kern
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
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4
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Marszalek J, Craig EA, Pitek M, Dutkiewicz R. Chaperone function in Fe-S protein biogenesis: Three possible scenarios. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119717. [PMID: 38574821 DOI: 10.1016/j.bbamcr.2024.119717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/22/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Among the six known iron‑sulfur (FeS) cluster biogenesis machineries that function across all domains of life only one involves a molecular chaperone system. This machinery, called ISC for 'iron sulfur cluster', functions in bacteria and in mitochondria of eukaryotes including humans. The chaperone system - a dedicated J-domain protein co-chaperone termed Hsc20 and its Hsp70 partner - is essential for proper ISC machinery function, interacting with the scaffold protein IscU which serves as a platform for cluster assembly and subsequent transfer onto recipient apo-proteins. Despite many years of research, surprisingly little is known about the specific role(s) that the chaperones play in the ISC machinery. Here we review three non-exclusive scenarios that range from involvement of the chaperones in the cluster transfer to regulation of the cellular levels of IscU itself.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States of America.
| | - Marcin Pitek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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5
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Chitboonthavisuk C, Martin C, Huss P, Peters JM, Anantharaman K, Raman S. Systematic genome-wide discovery of host factors governing bacteriophage infectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.20.590424. [PMID: 38659955 PMCID: PMC11042327 DOI: 10.1101/2024.04.20.590424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bacterial host factors regulate the infection cycle of bacteriophages. Except for some well-studied host factors (e.g., receptors or restriction-modification systems), the contribution of the rest of the host genome on phage infection remains poorly understood. We developed PHAGEPACK, a pooled assay that systematically and comprehensively measures each host-gene impact on phage fitness. PHAGEPACK combines CRISPR interference with phage packaging to link host perturbation to phage fitness during active infection. Using PHAGEPACK, we constructed a genome-wide map of genes impacting T7 phage fitness in permissive E. coli, revealing pathways previously unknown to affect phage packaging. When applied to the non-permissive E. coli O121, PHAGEPACK identified pathways leading to host resistance; their removal increased phage susceptibility up to a billion-fold. Bioinformatic analysis indicates phage genomes carry homologs or truncations of key host factors, potentially for fitness advantage. In summary, PHAGEPACK offers valuable insights into phage-host interactions, phage evolution, and bacterial resistance.
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6
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Jelen M, Grochowina I, Grabinska-Rogala A, Ciesielski SJ, Dabrowska K, Tomiczek B, Nierzwicki L, Delewski W, Schilke B, Czub J, Dadlez M, Dutkiewicz R, Craig EA, Marszalek J. Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein. J Mol Biol 2023; 435:168283. [PMID: 37730084 DOI: 10.1016/j.jmb.2023.168283] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Hsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP interactions, this key step is not well understood. Here we leverage a well characterized Hsp70 system specialized for iron-sulfur cluster biogenesis, which like many systems, has a JDP that binds substrate on its own. Utilizing an ATPase-deficient Hsp70 variant, we isolated a Hsp70-JDP-substrate tripartite complex. Complex formation and stability depended on residues previously identified as essential for bipartite interactions: JDP-substrate, Hsp70-substrate and J-domain-Hsp70. Computational docking based on the established J-domain-Hsp70(ATP) interaction placed the substrate close to its predicted position in the peptide-binding cleft, with the JDP having the same architecture as when in a bipartite complex with substrate. Together, our results indicate that the structurally rigid JDP-substrate complex recruits Hsp70(ATP) via precise positioning of J-domain and substrate at their respective interaction sites - resulting in functionally high affinity (i.e., avidity). The exceptionally high avidity observed for this specialized system may be unusual because of the rigid architecture of its JDP and the additional JDP-Hsp70 interaction site uncovered in this study. However, functionally important avidity driven by JDP-substrate interactions is likely sufficient to explain synergistic ATPase stimulation and efficient substrate trapping in many Hsp70 systems.
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Affiliation(s)
- Marcin Jelen
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Igor Grochowina
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Aneta Grabinska-Rogala
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Szymon J Ciesielski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katarzyna Dabrowska
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bartlomiej Tomiczek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Lukasz Nierzwicki
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Brenda Schilke
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland; BioTechMed Center, Gdansk University of Technology, Gdansk, Poland
| | - Michal Dadlez
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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7
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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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8
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Lin CW, Oney-Hawthorne SD, Kuo ST, Barondeau DP, Russell DH. Mechanistic Insights into IscU Conformation Regulation for Fe-S Cluster Biogenesis Revealed by Variable Temperature Electrospray Ionization Native Ion Mobility Mass Spectrometry. Biochemistry 2022; 61:2733-2741. [PMID: 36351081 PMCID: PMC10009881 DOI: 10.1021/acs.biochem.2c00429] [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: 11/10/2022]
Abstract
Iron-sulfur (Fe-S) cluster (ISC) cofactors are required for the function of many critical cellular processes. In the ISC Fe-S cluster biosynthetic pathway, IscU assembles Fe-S cluster intermediates from iron, electrons, and inorganic sulfur, which is provided by the cysteine desulfurase enzyme IscS. IscU also binds to Zn, which mimics and competes for binding with the Fe-S cluster. Crystallographic and nuclear magnetic resonance spectroscopic studies reveal that IscU is a metamorphic protein that exists in multiple conformational states, which include at least a structured form and a disordered form. The structured form of IscU is favored by metal binding and is stable in a narrow temperature range, undergoing both cold and hot denaturation. Interestingly, the form of IscU that binds IscS and functions in Fe-S cluster assembly remains controversial. Here, results from variable temperature electrospray ionization (vT-ESI) native ion mobility mass spectrometry (nIM-MS) establish that IscU exists in structured, intermediate, and disordered forms that rearrange to more extended conformations at higher temperatures. A comparison of Zn-IscU and apo-IscU reveals that Zn(II) binding attenuates the cold/heat denaturation of IscU, promotes refolding of IscU, favors the structured and intermediate conformations, and inhibits the disordered high charge states. Overall, these findings provide a structural rationalization for the role of Zn(II) in stabilizing IscU conformations and IscS in altering the IscU active site to prepare for Zn(II) release and cluster synthesis. This work highlights how vT-ESI-nIM-MS can be applied as a powerful tool in mechanistic enzymology by providing details of relationships among temperature, protein conformations, and ligand/protein binding.
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Affiliation(s)
- Cheng-Wei Lin
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Shelby D Oney-Hawthorne
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Syuan-Ting Kuo
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David P Barondeau
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
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9
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Marszalek J, Craig EA. Interaction of client—the scaffold on which FeS clusters are build—with J-domain protein Hsc20 and its evolving Hsp70 partners. Front Mol Biosci 2022; 9:1034453. [PMID: 36310602 PMCID: PMC9596805 DOI: 10.3389/fmolb.2022.1034453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
In cells molecular chaperone systems consisting of Hsp70 and its obligatory J-domain protein (JDP) co-chaperones transiently interact with a myriad of client proteins—with JDPs typically recruiting their partner Hsp70 to interact with particular clients. The fundamentals of this cyclical interactions between JDP/Hsp70 systems and clients are well established. Much less is known about other aspects of JDP/Hsp70 system function, including how such systems evolved over time. Here we discuss the JDP/Hsp70 system involved in the biogenesis of iron-sulfur (FeS) clusters. Interaction between the client protein, the scaffold on which clusters are built, and its specialized JDP Hsc20 has stayed constant. However, the system’s Hsp70 has changed at least twice. In some species Hsc20’s Hsp70 partner interacts only with the scaffold, in others it has many JDP partners in addition to Hsc20 and interacts with many client proteins. Analysis of this switching of Hsp70 partners has provided insight into the insulation of JDP/Hsp70 systems from one another that can occur when more than one Hsp70 is present in a cellular compartment, as well as how competition among JDPs is balanced when an Hsp70 partner is shared amongst a number of JDPs. Of particularly broad relevance, even though the scaffold’s interactions with Hsc20 and Hsp70 are functionally critical for the biogenesis of FeS cluster-containing proteins, it is the modulation of the Hsc20-Hsp70 interaction per se that allows Hsc20 to function with such different Hsp70 partners.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
- *Correspondence: Jaroslaw Marszalek, ; Elizabeth A. Craig,
| | - Elizabeth A. Craig
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI, United States
- *Correspondence: Jaroslaw Marszalek, ; Elizabeth A. Craig,
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10
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Srour B, Gervason S, Hoock MH, Monfort B, Want K, Larkem D, Trabelsi N, Landrot G, Zitolo A, Fonda E, Etienne E, Gerbaud G, Müller CS, Oltmanns J, Gordon JB, Yadav V, Kleczewska M, Jelen M, Toledano MB, Dutkiewicz R, Goldberg DP, Schünemann V, Guigliarelli B, Burlat B, Sizun C, D'Autréaux B. Iron Insertion at the Assembly Site of the ISCU Scaffold Protein Is a Conserved Process Initiating Fe-S Cluster Biosynthesis. J Am Chem Soc 2022; 144:17496-17515. [PMID: 36121382 PMCID: PMC10163866 DOI: 10.1021/jacs.2c06338] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron-sulfur (Fe-S) clusters are prosthetic groups of proteins biosynthesized on scaffold proteins by highly conserved multi-protein machineries. Biosynthesis of Fe-S clusters into the ISCU scaffold protein is initiated by ferrous iron insertion, followed by sulfur acquisition, via a still elusive mechanism. Notably, whether iron initially binds to the ISCU cysteine-rich assembly site or to a cysteine-less auxiliary site via N/O ligands remains unclear. We show here by SEC, circular dichroism (CD), and Mössbauer spectroscopies that iron binds to the assembly site of the monomeric form of prokaryotic and eukaryotic ISCU proteins via either one or two cysteines, referred to the 1-Cys and 2-Cys forms, respectively. The latter predominated at pH 8.0 and correlated with the Fe-S cluster assembly activity, whereas the former increased at a more acidic pH, together with free iron, suggesting that it constitutes an intermediate of the iron insertion process. Iron not binding to the assembly site was non-specifically bound to the aggregated ISCU, ruling out the existence of a structurally defined auxiliary site in ISCU. Characterization of the 2-Cys form by site-directed mutagenesis, CD, NMR, X-ray absorption, Mössbauer, and electron paramagnetic resonance spectroscopies showed that the iron center is coordinated by four strictly conserved amino acids of the assembly site, Cys35, Asp37, Cys61, and His103, in a tetrahedral geometry. The sulfur receptor Cys104 was at a very close distance and apparently bound to the iron center when His103 was missing, which may enable iron-dependent sulfur acquisition. Altogether, these data provide the structural basis to elucidate the Fe-S cluster assembly process and establish that the initiation of Fe-S cluster biosynthesis by insertion of a ferrous iron in the assembly site of ISCU is a conserved mechanism.
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Affiliation(s)
- Batoul Srour
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sylvain Gervason
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maren Hellen Hoock
- Fachbereich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Beata Monfort
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Kristian Want
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Djabir Larkem
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nadine Trabelsi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Gautier Landrot
- Synchrotron SOLEIL, L'Orme des Merisiers, BP48 Saint Aubin 91192 Gif-Sur-Yvette, France
| | - Andrea Zitolo
- Synchrotron SOLEIL, L'Orme des Merisiers, BP48 Saint Aubin 91192 Gif-Sur-Yvette, France
| | - Emiliano Fonda
- Synchrotron SOLEIL, L'Orme des Merisiers, BP48 Saint Aubin 91192 Gif-Sur-Yvette, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Christina Sophia Müller
- Fachbereich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Jonathan Oltmanns
- Fachbereich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Jesse B Gordon
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Malgorzata Kleczewska
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Marcin Jelen
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Michel B Toledano
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Volker Schünemann
- Fachbereich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Bénédicte Burlat
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, Avenue de La Terrasse, 91190 Gif-sur-Yvette, France
| | - Benoit D'Autréaux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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11
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Dong Y, Zhang S, Zhao L. Unraveling the Structural Development of
Peptide‐Coordinated Iron‐Sulfur
Clusters: Prebiotic Evolution and Biosynthetic Strategies. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yijun Dong
- School of Life Sciences, Tsinghua University Beijing 100084 China
| | - Siqi Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
| | - Liang Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
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12
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Maio N, Rouault TA. Mammalian iron sulfur cluster biogenesis: From assembly to delivery to recipient proteins with a focus on novel targets of the chaperone and co‐chaperone proteins. IUBMB Life 2022; 74:684-704. [PMID: 35080107 PMCID: PMC10118776 DOI: 10.1002/iub.2593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/05/2021] [Accepted: 12/23/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development Bethesda Maryland USA
| | - Tracey A. Rouault
- Molecular Medicine Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development Bethesda Maryland USA
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13
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Spectroscopic and functional characterization of the [2Fe-2S] scaffold protein Nfu from Synechocystis PCC6803. Biochimie 2022; 192:51-62. [PMID: 34582998 PMCID: PMC8724361 DOI: 10.1016/j.biochi.2021.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023]
Abstract
Iron-sulfur clusters are ubiquitous cofactors required for various essential metabolic processes. Conservation of proteins required for their biosynthesis and trafficking allows for simple bacteria to be used as models to aid in exploring these complex pathways in higher organisms. Cyanobacteria are among the most investigated organisms for these processes, as they are unicellular and can survive under photoautotrophic and heterotrophic conditions. Herein, we report the potential role of Synechocystis PCC6803 NifU (now named SyNfu) as the principal scaffold protein required for iron-sulfur cluster biosynthesis in that organism. SyNfu is a well-folded protein with distinct secondary structural elements, as evidenced by circular dichroism and a well-dispersed pattern of 1H-15N HSQC NMR peaks, and readily reconstitutes as a [2Fe-2S] dimeric protein complex. Cluster exchange experiments show that glutathione can extract the cluster from holo-SyNfu, but the transfer is unidirectional. We also confirm the ability of SyNfu to transfer cluster to both human ferredoxin 1 and ferredoxin 2, while also demonstrating the capacity to deliver cluster to both monothiol glutaredoxin 3 and dithiol glutaredoxin 2. This evidence supports the hypothesis that SyNfu indeed serves as the main scaffold protein in Synechocystis, as it has been shown to be the only protein required for viability in the absence of photoautotrophic conditions. Similar to other NFU-type cluster donors and other scaffold and carrier proteins, such as ISCU, SyNfu is shown by DSC to be structurally less stable than regular protein donors, while retaining a relatively well-defined tertiary structure as represented by 1H-15N HSQC NMR experiments.
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14
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Arhar T, Shkedi A, Nadel CM, Gestwicki JE. The interactions of molecular chaperones with client proteins: why are they so weak? J Biol Chem 2021; 297:101282. [PMID: 34624315 PMCID: PMC8567204 DOI: 10.1016/j.jbc.2021.101282] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/30/2022] Open
Abstract
The major classes of molecular chaperones have highly variable sequences, sizes, and shapes, yet they all bind to unfolded proteins, limit their aggregation, and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, "client" proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK, and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone-client interactions are readily outcompeted by stronger, intra- and intermolecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.
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Affiliation(s)
- Taylor Arhar
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Arielle Shkedi
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA.
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15
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Petronek MS, Spitz DR, Allen BG. Iron-Sulfur Cluster Biogenesis as a Critical Target in Cancer. Antioxidants (Basel) 2021; 10:1458. [PMID: 34573089 PMCID: PMC8465902 DOI: 10.3390/antiox10091458] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Cancer cells preferentially accumulate iron (Fe) relative to non-malignant cells; however, the underlying rationale remains elusive. Iron-sulfur (Fe-S) clusters are critical cofactors that aid in a wide variety of cellular functions (e.g., DNA metabolism and electron transport). In this article, we theorize that a differential need for Fe-S biogenesis in tumor versus non-malignant cells underlies the Fe-dependent cell growth demand of cancer cells to promote cell division and survival by promoting genomic stability via Fe-S containing DNA metabolic enzymes. In this review, we outline the complex Fe-S biogenesis process and its potential upregulation in cancer. We also discuss three therapeutic strategies to target Fe-S biogenesis: (i) redox manipulation, (ii) Fe chelation, and (iii) Fe mimicry.
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Affiliation(s)
- Michael S. Petronek
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Douglas R. Spitz
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Bryan G. Allen
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
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16
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Madhurima K, Nandi B, Sekhar A. Metamorphic proteins: the Janus proteins of structural biology. Open Biol 2021; 11:210012. [PMID: 33878950 PMCID: PMC8059507 DOI: 10.1098/rsob.210012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The structural paradigm that the sequence of a protein encodes for a unique three-dimensional native fold does not acknowledge the intrinsic plasticity encapsulated in conformational free energy landscapes. Metamorphic proteins are a recently discovered class of biomolecules that illustrate this plasticity by folding into at least two distinct native state structures of comparable stability in the absence of ligands or cofactors to facilitate fold-switching. The expanding list of metamorphic proteins clearly shows that these proteins are not mere aberrations in protein evolution, but may have actually been a consequence of distinctive patterns in selection pressure such as those found in virus–host co-evolution. In this review, we describe the structure–function relationships observed in well-studied metamorphic protein systems, with specific focus on how functional residues are sequestered or exposed in the two folds of the protein. We also discuss the implications of metamorphosis for protein evolution and the efforts that are underway to predict metamorphic systems from sequence properties alone.
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Affiliation(s)
- Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Bodhisatwa Nandi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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17
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Jairajpuri DS, Malalla ZH, Sarray S, Mahmood N. Analysis of differential expression of hypoxia-inducible microRNA-210 gene targets in mild and severe preeclamptic patients. Noncoding RNA Res 2021; 6:51-57. [PMID: 33778218 PMCID: PMC7973385 DOI: 10.1016/j.ncrna.2021.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
Preeclampsia (PE) is a multi-system disorder that is specific to human pregnancy. Inadequate oxygenation of uterus and placenta is considered as one of the leading causes for the disease. MicroRNA-210(miR-210) is one of the prime molecules that has emerged in response to hypoxia. The objective of this study was to determine miR-210 expression patterns in plasma from severe PE and mild PE patients, and how that affects the expression of miR-210 target genes. The expression levels of miR-210 were validated using reverse transcription-quantitative PCR in plasma of severe PE (15) and mild PE (15) patients in comparison to controls subjects (15) with normal pregnancy. Then, the association between miR-210 and its downstream genes was validated by using human miR-210 targets RT2 profiler PCR Array. Both the categories (mild and severe) showed significantly high miR-210 expression levels. Also out of the 84 hypoxia miR-210 associated genes screened using mRNA, 18 genes were found to be differentially expressed in severe PE whereas 16 genes in mild PE cases with varying magnitude. All the genes in both the PE groups were found downregulated in comparison to controls. These downregulated genes expressed in both the cases were shown to be participating in immunosuppression, apoptosis, cell growth, signaling, angiogenesis, DNA repair. This study provides novel data on the genes that work downstream of miR-210 and how dysregulated expression of miR-210 can affect their expression and in turn functioning which can be associated with PE risk and severity. This study is the very first to determine the effect of miR-210 expression levels on associated genes in plasma samples.
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Affiliation(s)
- Deeba S. Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
- Corresponding author.,
| | - Zainab H. Malalla
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Sameh Sarray
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Naeema Mahmood
- Department of Obstetrics and Gynecology, Salmaniya Medical Complex, Manama, Bahrain
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18
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Sato S, Matsushima Y, Kanazawa M, Tanaka N, Fujishiro T, Kunichika K, Nakamura R, Tomioka H, Wada K, Takahashi Y. Evidence for dynamic in vivo interconversion of the conformational states of IscU during iron-sulfur cluster biosynthesis. Mol Microbiol 2020; 115:807-818. [PMID: 33202070 DOI: 10.1111/mmi.14646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/02/2020] [Accepted: 11/12/2020] [Indexed: 11/28/2022]
Abstract
IscU is a central component of the ISC machinery and serves as a scaffold for de novo assembly of Fe-S clusters. The dedicated chaperone system composed of the Hsp70-chaperone HscA and the J-protein cochaperone HscB synergistically interacts with IscU and facilitates cluster transfer from IscU to recipient apo-proteins. Here, we report that the otherwise essential roles of HscA and HscB can be bypassed in vivo by a number of single amino acid substitutions in IscU. CD spectroscopic studies of the variant IscU proteins capable of this bypass activity revealed dynamic interconversion between two conformations: the denatured (D) and the structured (S) state in the absence and presence of Zn2+ , respectively, which was far more prominent than interconversion observed in wild-type IscU. Furthermore, we found that neither the S-shifted (more structured) variants of IscU nor the perpetually denatured variants could perform their in vivo role regardless of whether the chaperone system was present or not. The present study thus provides for the first time evidence that an in vivo D-state of IscU exists and implies that conformational interconversion between the S- and D-states of the scaffolding protein is a fundamental requirement for the assembly and transfer of the Fe-S cluster.
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Affiliation(s)
- Sakiko Sato
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yumeka Matsushima
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Miaki Kanazawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Naoyuki Tanaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kouhei Kunichika
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Hiroaki Tomioka
- Department of Science Education, Graduate School of Education, Saitama University, Saitama, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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19
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Abstract
Iron–sulfur (Fe–S) clusters are protein cofactors of a multitude of enzymes performing essential biological functions. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe–S clusters are assembled and a cysteine desulfurase that provides sulfur in the form of a persulfide. The sulfide ions are produced by reductive cleavage of the persulfide, which involves specific reductase systems. Several other components are required for Fe–S biosynthesis, including frataxin, a key protein of controversial function and accessory components for insertion of Fe–S clusters in client proteins. Fe–S cluster biosynthesis is thought to rely on concerted and carefully orchestrated processes. However, the elucidation of the mechanisms of their assembly has remained a challenging task due to the biochemical versatility of iron and sulfur and the relative instability of Fe–S clusters. Nonetheless, significant progresses have been achieved in the past years, using biochemical, spectroscopic and structural approaches with reconstituted system in vitro. In this paper, we review the most recent advances on the mechanism of assembly for the founding member of the Fe–S cluster family, the [2Fe2S] cluster that is the building block of all other Fe–S clusters. The aim is to provide a survey of the mechanisms of iron and sulfur insertion in the scaffold proteins by examining how these processes are coordinated, how sulfide is produced and how the dinuclear [2Fe2S] cluster is formed, keeping in mind the question of the physiological relevance of the reconstituted systems. We also cover the latest outcomes on the functional role of the controversial frataxin protein in Fe–S cluster biosynthesis.
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20
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Alhajala HS, Markley JL, Kim JH, Al-Gizawiy MM, Schmainda KM, Kuo JS, Chitambar CR. The cytotoxicity of gallium maltolate in glioblastoma cells is enhanced by metformin through combined action on mitochondrial complex 1. Oncotarget 2020; 11:1531-1544. [PMID: 32391122 PMCID: PMC7197450 DOI: 10.18632/oncotarget.27567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/03/2020] [Indexed: 12/04/2022] Open
Abstract
New drugs are needed for glioblastoma, an aggressive brain tumor with a dismal prognosis. We recently reported that gallium maltolate (GaM) retards the growth of glioblastoma in a rat orthotopic brain tumor model by inhibiting mitochondrial function and iron-dependent ribonucleotide reductase (RR). However, GaM's mechanism of action at the mitochondrial level is not known. Given the interaction between gallium and iron metabolism, we hypothesized that gallium might target iron-sulfur (Fe-S) cluster-containing mitochondrial proteins. Using Extracellular Flux Analyzer technology, we confirmed that after a 24-h incubation, GaM 50 μmol/L inhibited glioblastoma cell growth by <10% but inhibited cellular oxygen consumption rate by 44% and abrogated mitochondrial reserve capacity. GaM blocked mitochondrial complex I activity and produced a 2.9-fold increase in cellular ROS. NMR spectroscopy revealed that gallium binds to IscU, the bacterial scaffold protein for Fe-S cluster assembly and stabilizes its folded state. Gallium inhibited the rate of in vitro cluster assembly catalyzed by bacterial cysteine desulfurase in a reaction mixture containing IscU, Fe (II), DTT, and L-cysteine. Metformin, a complex I inhibitor, enhanced GaM's inhibition of complex I, further increased cellular ROS levels, and synergistically enhanced GaM's cytotoxicity in glioblastoma cells in 2-D and 3-D cultures. Metformin did not affect GaM action on cellular iron uptake or transferrin receptor1 expression nor did it enhance the cytotoxicity of the RR inhibitor Didox. Our results show that GaM inhibits complex I by disrupting iron-sulfur cluster assembly and that its cytotoxicity can be synergistically enhanced by metformin through combined action on complex I.
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Affiliation(s)
- Hisham S. Alhajala
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - John L. Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jin Hae Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mona M. Al-Gizawiy
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - John S. Kuo
- Department of Neurosurgery and Mulva Clinic for the Neurosciences, Dell Medical School, Austin, Texas, USA
| | - Christopher R. Chitambar
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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21
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Baussier C, Fakroun S, Aubert C, Dubrac S, Mandin P, Py B, Barras F. Making iron-sulfur cluster: structure, regulation and evolution of the bacterial ISC system. Adv Microb Physiol 2020; 76:1-39. [PMID: 32408945 DOI: 10.1016/bs.ampbs.2020.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron sulfur (Fe-S) clusters rank among the most ancient and conserved prosthetic groups. Fe-S clusters containing proteins are present in most, if not all, organisms. Fe-S clusters containing proteins are involved in a wide range of cellular processes, from gene regulation to central metabolism, via gene expression, RNA modification or bioenergetics. Fe-S clusters are built by biogenesis machineries conserved throughout both prokaryotes and eukaryotes. We focus mostly on bacterial ISC machinery, but not exclusively, as we refer to eukaryotic ISC system when it brings significant complementary information. Besides covering the structural and regulatory aspects of Fe-S biogenesis, this review aims to highlight Fe-S biogenesis facets remaining matters of discussion, such as the role of frataxin, or the link between fatty acid metabolism and Fe-S homeostasis. Last, we discuss recent advances on strategies used by different species to make and use Fe-S clusters in changing redox environmental conditions.
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Affiliation(s)
- Corentin Baussier
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Soufyan Fakroun
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Corinne Aubert
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Sarah Dubrac
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France
| | - Pierre Mandin
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Frédéric Barras
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France
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22
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Lin CW, McCabe JW, Russell DH, Barondeau DP. Molecular Mechanism of ISC Iron-Sulfur Cluster Biogenesis Revealed by High-Resolution Native Mass Spectrometry. J Am Chem Soc 2020; 142:6018-6029. [PMID: 32131593 DOI: 10.1021/jacs.9b11454] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous protein cofactors that are required for many important biological processes including oxidative respiration, nitrogen fixation, and photosynthesis. Biosynthetic pathways assemble Fe-S clusters with different iron-to-sulfur stoichiometries and distribute these clusters to appropriate apoproteins. In the ISC pathway, the pyridoxal 5'-phosphate-dependent cysteine desulfurase enzyme IscS provides sulfur to the scaffold protein IscU, which templates the Fe-S cluster assembly. Despite their functional importance, mechanistic details for cluster synthesis have remained elusive. Recent advances in native mass spectrometry (MS) have allowed proteins to be preserved in native-like structures and support applications in the investigation of protein structure, dynamics, ligand interactions, and the identification of protein-associated intermediates. Here, we prepared samples under anaerobic conditions and then applied native MS to investigate the molecular mechanism for Fe-S cluster synthesis. This approach was validated by the high agreement between native MS and traditional visible circular dichroism spectroscopic assays. Time-dependent native MS experiments revealed potential iron- and sulfur-based intermediates that decay as the [2Fe-2S] cluster signal developed. Additional experiments establish that (i) Zn(II) binding stabilizes IscU and protects the cysteine residues from oxidation, weakens the interactions between IscU and IscS, and inhibits Fe-S cluster biosynthesis; and (ii) Fe(II) ions bind to the IscU active site cysteine residues and another lower affinity binding site and promote the intermolecular sulfur transfer reaction from IscS to IscU. Overall, these results support an iron-first model for Fe-S cluster synthesis and highlight the power of native MS in defining protein-associated intermediates and elucidating mechanistic details of enzymatic processes.
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Affiliation(s)
- Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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23
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Bellanda M, Maso L, Doni D, Bortolus M, De Rosa E, Lunardi F, Alfonsi A, Noguera ME, Herrera MG, Santos J, Carbonera D, Costantini P. Exploring iron-binding to human frataxin and to selected Friedreich ataxia mutants by means of NMR and EPR spectroscopies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2019; 1867:140254. [PMID: 31344531 DOI: 10.1016/j.bbapap.2019.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/12/2019] [Accepted: 07/18/2019] [Indexed: 11/23/2022]
Abstract
The neurodegenerative disease Friedreich ataxia results from a deficiency of frataxin, a mitochondrial protein. Most patients have a GAA expansion in the first intron of both alleles of frataxin gene, whereas a minority of them are heterozygous for the expansion and contain a mutation in the other allele. Frataxin has been claimed to participate in iron homeostasis and biosynthesis of FeS clusters, however its role in both pathways is not unequivocally defined. In this work we combined different advanced spectroscopic analyses to explore the iron-binding properties of human frataxin, as isolated and at the FeS clusters assembly machinery. For the first time we used EPR spectroscopy to address this key issue providing clear evidence of the formation of a complex with a low symmetry coordination of the metal ion. By 2D NMR, we confirmed that iron can be bound in both oxidation states, a controversial issue, and, in addition, we were able to point out a transient interaction of frataxin with a N-terminal 6his-tagged variant of ISCU, the scaffold protein of the FeS clusters assembly machinery. To obtain insights on structure/function relationships relevant to understand the disease molecular mechanism(s), we extended our studies to four clinical frataxin mutants. All variants showed a moderate to strong impairment in their ability to activate the FeS cluster assembly machinery in vitro, while keeping the same iron-binding features of the wild type protein. This supports the multifunctional nature of frataxin and the complex biochemical consequences of its mutations.
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Affiliation(s)
- Massimo Bellanda
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Lorenzo Maso
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Edith De Rosa
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Federica Lunardi
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Arianna Alfonsi
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160 - Ciudad Universitaria, 1428EGA C.A.B.A., Argentina; Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD C.A.B.A., Argentina
| | - Maria Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160 - Ciudad Universitaria, 1428EGA C.A.B.A., Argentina; Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD C.A.B.A., Argentina
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160 - Ciudad Universitaria, 1428EGA C.A.B.A., Argentina; Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD C.A.B.A., Argentina
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
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24
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Tanaka N, Yuda E, Fujishiro T, Hirabayashi K, Wada K, Takahashi Y. Identification of IscU residues critical for de novo iron-sulfur cluster assembly. Mol Microbiol 2019; 112:1769-1783. [PMID: 31532036 DOI: 10.1111/mmi.14392] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2019] [Indexed: 01/16/2023]
Abstract
IscU is a central component of the ISC machinery and serves as a scaffold for the de novo assembly of iron-sulfur (Fe-S) clusters prior to their delivery to target apo-Fe-S proteins. However, the molecular mechanism is not yet fully understood. In this study, we have conducted mutational analysis of E. coli IscU using the recently developed genetic complementation system of a mutant that can survive without Fe-S clusters. The Fe-S cluster ligands (C37, C63, H105, C106) and the proximal D39 and K103 residues are essential for in vivo function of IscU and could not be substituted with any other amino acids. Furthermore, we found that substitution of Y3, a strictly conserved residue among IscU homologs, abolished in vivo functions. Surprisingly, a second-site suppressor mutation in IscS (A349V) reverted the defect caused by IscU Y3 substitutions. Biochemical analysis revealed that IscU Y3 was crucial for functional interaction with IscS and sulfur transfer between the two proteins. Our findings suggest that the critical role of IscU Y3 is linked to the conformational dynamics of the flexible loop of IscS, which is required for the ingenious sulfur transfer to IscU.
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Affiliation(s)
- Naoyuki Tanaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Eiki Yuda
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Kei Hirabayashi
- Department of Medical Sciences, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
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25
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Pastore A, Martin SR, Temussi PA. Generalized View of Protein Folding: In Medio Stat Virtus. J Am Chem Soc 2019; 141:2194-2200. [PMID: 30566837 DOI: 10.1021/jacs.8b10779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteins are often described in textbooks as being only "marginally stable" but many proteins, specifically those with a high free energy of unfolding are, in fact, so stable that they exist only in the fully folded state except under harsh denaturing conditions. Proteins that are truly only marginally stable, those with a low free energy of unfolding, exist as an equilibrium mixture of folded and unfolded forms under "normal" conditions. To some extent such proteins have some features in common with "intrinsically disordered" proteins. We analyzed the relationship between these marginally stable proteins and intrinsically disordered proteins in order to fully understand the twilight zone that distinguishes the two ensembles in the hope of clarifying the fuzzy borders of the current classification that divides the protein world into folded and intrinsically disordered ones. Our analysis suggests that the division may be too drastic and misleading, because it puts within the same category proteins with very different behaviors. We propose a restricted, albeit operational, definition of "marginally stable proteins", referring by this term only to proteins whose free energy difference between the folded and unfolded states falls in the interval 0-3 kcal/mol. These proteins have special features because they normally exist as equilibrium mixtures of folded and unfolded species or as molten globule states. This coexistence makes marginally stable proteins ideal tools to study even small environmental changes to which they may behave as natural sensors.
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Affiliation(s)
- Annalisa Pastore
- The Wohl Institute, King's College London , 5 Cutcombe Road , London SE59RT , United Kingdom.,Department of Molecular Medicine , University of Pavia , Pavia 27100 , Italy
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute , 1 Midland Road , London NW1 1AT , United Kingdom
| | - Piero Andrea Temussi
- The Wohl Institute, King's College London , 5 Cutcombe Road , London SE59RT , United Kingdom.,Dipartimento di Scienze Chimiche , Universita' di Napoli Federico II , Napoli 80126 , Italy
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26
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Fox NG, Martelli A, Nabhan JF, Janz J, Borkowska O, Bulawa C, Yue WW. Zinc(II) binding on human wild-type ISCU and Met140 variants modulates NFS1 desulfurase activity. Biochimie 2018; 152:211-218. [PMID: 30031876 PMCID: PMC6098246 DOI: 10.1016/j.biochi.2018.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/18/2018] [Indexed: 12/01/2022]
Abstract
Human de novo iron-sulfur (Fe-S) assembly complex consists of cysteine desulfurase NFS1, accessory protein ISD11, acyl carrier protein ACP, scaffold protein ISCU, and allosteric activator frataxin (FXN). FXN binds the NFS1-ISD11-ACP-ISCU complex (SDAU), to activate the desulfurase activity and Fe-S cluster biosynthesis. In the absence of FXN, the NFS1-ISD11-ACP (SDA) complex was reportedly inhibited by binding of recombinant ISCU. Recent studies also reported a substitution at position Met141 on the yeast ISCU orthologue Isu, to Ile, Leu, Val, or Cys, could bypass the requirement of FXN for Fe-S cluster biosynthesis and cell viability. Here, we show that recombinant human ISCU binds zinc(II) ion, as previously demonstrated with the E. coli orthologue IscU. Surprisingly, the relative proportion between zinc-bound and zinc-depleted forms varies among purification batches. Importantly the presence of zinc in ISCU impacts SDAU desulfurase activity. Indeed, removal of zinc(II) ion from ISCU causes a moderate but significant increase in activity compared to SDA alone, and FXN can activate both zinc-depleted and zinc-bound forms of ISCU complexed to SDA. Taking into consideration the inhibition of desulfurase activity by zinc-bound ISCU, we characterized wild type ISCU and the M140I, M140L, and M140V variants under both zinc-bound and zinc-depleted conditions, and did not observe significant differences in the biochemical and biophysical properties between wild-type and variants. Importantly, in the absence of FXN, ISCU variants behaved like wild-type and did not stimulate the desulfurase activity of the SDA complex. This study therefore identifies an important regulatory role for zinc-bound ISCU in modulation of the human Fe-S assembly system in vitro and reports no 'FXN bypass' effect on mutations at position Met140 in human ISCU. Furthermore, this study also calls for caution in interpreting studies involving recombinant ISCU by taking into consideration the influence of the bound zinc(II) ion on SDAU complex activity.
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Affiliation(s)
- Nicholas G Fox
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Alain Martelli
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States
| | - Joseph F Nabhan
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States
| | - Jay Janz
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States
| | - Oktawia Borkowska
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Christine Bulawa
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States.
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK.
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27
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NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis. Molecules 2018; 23:molecules23092213. [PMID: 30200358 PMCID: PMC6205161 DOI: 10.3390/molecules23092213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/03/2018] [Accepted: 08/20/2018] [Indexed: 12/15/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters, the ubiquitous protein cofactors found in all kingdoms of life, perform a myriad of functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. The biogenesis of Fe-S clusters is a multi-step process that involves the participation of many protein partners. Recent biophysical studies, involving X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and small angle X-ray scattering (SAXS), have greatly improved our understanding of these steps. In this review, after describing the biological importance of iron sulfur proteins, we focus on the contributions of NMR spectroscopy has made to our understanding of the structures, dynamics, and interactions of proteins involved in the biosynthesis of Fe-S cluster proteins.
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28
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Cai K, Frederick RO, Tonelli M, Markley JL. Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly. J Inorg Biochem 2018; 183:107-116. [PMID: 29576242 PMCID: PMC5951399 DOI: 10.1016/j.jinorgbio.2018.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/15/2022]
Abstract
Frataxin (FXN) is involved in mitochondrial iron‑sulfur (Fe-S) cluster biogenesis and serves to accelerate Fe-S cluster formation. FXN deficiency is associated with Friedreich ataxia, a neurodegenerative disease. We have used a combination of isothermal titration calorimetry and multinuclear NMR spectroscopy to investigate interactions among the components of the biological machine that carries out the assembly of iron‑sulfur clusters in human mitochondria. Our results show that FXN tightly binds a single Fe2+ but not Fe3+. While FXN (with or without bound Fe2+) does not bind the scaffold protein ISCU directly, the two proteins interact mutually when each is bound to the cysteine desulfurase complex ([NFS1]2:[ISD11]2:[Acp]2), abbreviated as (NIA)2, where "N" represents the cysteine desulfurase (NFS1), "I" represents the accessory protein (ISD11), and "A" represents acyl carrier protein (Acp). FXN binds (NIA)2 weakly in the absence of ISCU but more strongly in its presence. Fe2+-FXN binds to the (NIA)2-ISCU2 complex without release of iron. However, upon the addition of both l-cysteine and a reductant (either reduced FDX2 or DTT), Fe2+ is released from FXN as consistent with Fe2+-FXN being the proximal source of iron for Fe-S cluster assembly.
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Affiliation(s)
- Kai Cai
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - Ronnie O Frederick
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - John L Markley
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States.
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29
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Roy P, Bauman MA, Almutairi HH, Jayawardhana WG, Johnson NM, Torelli AT. Comparison of the Response of Bacterial IscU and SufU to Zn 2+ and Select Transition-Metal Ions. ACS Chem Biol 2018; 13:591-599. [PMID: 29210568 DOI: 10.1021/acschembio.7b00442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
IscU, the central scaffold protein in the bacterial ISC iron-sulfur (Fe-S) cluster biosynthesis system, has long been recognized to bind a Zn2+ ion at its active site. While initially regarded as an artifact, Zn2+ binding has been shown to induce stabilization of the IscU structure that may mimic a state biologically relevant to IscU's role in Fe-S cluster biosynthesis. More recent studies have revealed that SufU, a homologous protein involved in Fe-S cluster biosynthesis in Gram-positive bacteria, also binds a Zn2+ ion with structural implications. Given the widespread occurrence of the "IscU-like" protein fold, particularly among Fe-S cluster biosynthesis systems, an interesting question arises as to whether Zn2+ ion binding and the resulting structural alterations are common properties in IscU-like proteins. Interactions between IscU and specific metal ions are investigated and compared side-by-side with those of SufU from a representative Gram-positive bacterium in the phylum Firmicutes. These studies were extended with additional transition metal ions chosen to investigate the influence of coordination geometry on selectivity for binding at the active sites of IscU and SufU. Monitoring and comparing the conformational behavior and stabilization afforded by different transition metal ions upon IscU and SufU revealed similarities between the two proteins and suggest that metal-dependent conformational transitions may be characteristic of U-type proteins involved in Fe-S cluster biosynthesis.
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Affiliation(s)
- Poorna Roy
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Mariia A. Bauman
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Hayfa Habes Almutairi
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Walimuni Geethamala Jayawardhana
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Nathan M. Johnson
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Andrew T. Torelli
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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30
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Wachnowsky C, Liu Y, Yoon T, Cowan JA. Regulation of human Nfu activity in Fe-S cluster delivery-characterization of the interaction between Nfu and the HSPA9/Hsc20 chaperone complex. FEBS J 2017; 285:391-410. [PMID: 29211945 DOI: 10.1111/febs.14353] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/24/2017] [Accepted: 12/01/2017] [Indexed: 12/11/2022]
Abstract
Iron-sulfur cluster biogenesis is a complex, but highly regulated process that involves de novo cluster formation from iron and sulfide ions on a scaffold protein, and subsequent delivery to final targets via a series of Fe-S cluster-binding carrier proteins. The process of cluster release from the scaffold/carrier for transfer to the target proteins may be mediated by a dedicated Fe-S cluster chaperone system. In human cells, the chaperones include heat shock protein HSPA9 and the J-type chaperone Hsc20. While the role of chaperones has been somewhat clarified in yeast and bacterial systems, many questions remain over their functional roles in cluster delivery and interactions with a variety of human Fe-S cluster proteins. One such protein, Nfu, has recently been recognized as a potential interaction partner of the chaperone complex. Herein, we examined the ability of human Nfu to function as a carrier by interacting with the human chaperone complex. Human Nfu is shown to bind to both chaperone proteins with binding affinities similar to those observed for IscU binding to the homologous HSPA9 and Hsc20, while Nfu can also stimulate the ATPase activity of HSPA9. Additionally, the chaperone complex was able to promote Nfu function by enhancing the second-order rate constants for Fe-S cluster transfer to target proteins and providing directionality in cluster transfer from Nfu by eliminating promiscuous transfer reactions. Together, these data support a hypothesis in which Nfu can serve as an alternative carrier protein for chaperone-mediated cluster release and delivery in Fe-S cluster biogenesis and trafficking.
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Affiliation(s)
- Christine Wachnowsky
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.,The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Yushi Liu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.,The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Taejin Yoon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - J A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.,The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
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31
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Maio N, Rouault TA. Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20. Metallomics 2017; 8:1032-1046. [PMID: 27714045 DOI: 10.1039/c6mt00167j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery.
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Affiliation(s)
- N Maio
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
| | - T A Rouault
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
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32
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Fidai I, Wachnowsky C, Cowan JA. Mapping cellular Fe-S cluster uptake and exchange reactions - divergent pathways for iron-sulfur cluster delivery to human ferredoxins. Metallomics 2017; 8:1283-1293. [PMID: 27878189 DOI: 10.1039/c6mt00193a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ferredoxins are protein mediators of biological electron-transfer reactions and typically contain either [2Fe-2S] or [4Fe-4S] clusters. Two ferredoxin homologues have been identified in the human genome, Fdx1 and Fdx2, that share 43% identity and 69% similarity in protein sequence and both bind [2Fe-2S] clusters. Despite the high similarity, the two ferredoxins play very specific roles in distinct physiological pathways and cannot replace each other in function. Both eukaryotic and prokaryotic ferredoxins and homologues have been reported to receive their Fe-S cluster from scaffold/delivery proteins such as IscU, Isa, glutaredoxins, and Nfu. However, the preferred and physiologically relevant pathway for receiving the [2Fe-2S] cluster by ferredoxins is subject to speculation and is not clearly identified. In this work, we report on in vitro UV-visible (UV-vis) circular dichroism studies of [2Fe-2S] cluster transfer to the ferredoxins from a variety of partners. The results reveal rapid and quantitative transfer to both ferredoxins from several donor proteins (IscU, Isa1, Grx2, and Grx3). Transfer from Isa1 to Fdx2 was also observed to be faster than that of IscU to Fdx2, suggesting that Fdx2 could receive its cluster from Isa1 instead of IscU. Several other transfer combinations were also investigated and the results suggest a complex, but kinetically detailed map for cellular cluster trafficking. This is the first step toward building a network map for all of the possible iron-sulfur cluster transfer pathways in the mitochondria and cytosol, providing insights on the most likely cellular pathways and possible redundancies in these pathways.
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Affiliation(s)
- Insiya Fidai
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA. and The Biophysics Graduate Program, The Ohio State University, USA
| | - Christine Wachnowsky
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA. and The Ohio State Biochemistry Program, The Ohio State University, USA
| | - J A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA. and The Biophysics Graduate Program, The Ohio State University, USA and The Ohio State Biochemistry Program, The Ohio State University, USA
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33
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Galeano BK, Ranatunga W, Gakh O, Smith DY, Thompson JR, Isaya G. Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers. Metallomics 2017; 9:773-801. [PMID: 28548666 PMCID: PMC5552075 DOI: 10.1039/c7mt00089h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/02/2017] [Indexed: 02/06/2023]
Abstract
Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.
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Affiliation(s)
- B. K. Galeano
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Graduate School of Biomedical Sciences , Rochester , Minnesota , USA
| | - W. Ranatunga
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - O. Gakh
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - D. Y. Smith
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - J. R. Thompson
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
| | - G. Isaya
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
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34
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Cai K, Frederick RO, Tonelli M, Markley JL. Mitochondrial Cysteine Desulfurase and ISD11 Coexpressed in Escherichia coli Yield Complex Containing Acyl Carrier Protein. ACS Chem Biol 2017; 12:918-921. [PMID: 28233492 PMCID: PMC5404276 DOI: 10.1021/acschembio.6b01005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Mitochondrial
cysteine desulfurase is an essential component of
the machinery for iron–sulfur cluster biosynthesis. It has
been known that human cysteine desulfurase that is catalytically active in vitro can be prepared by overexpressing in Escherichia
coli cells two protein components of this system, the cysteine
desulfurase protein NFS1 and the auxiliary protein ISD11. We report
here that this active preparation contains, in addition, the holo-form
of E. coli acyl carrier protein (Acp). We have determined
the stoichiometry of the complex to be [Acp]2:[ISD11]2:[NFS1]2. Acyl carrier protein recently has been
found to be an essential component of the iron–sulfur protein
biosynthesis machinery in mitochondria; thus, because of the activity
of [Acp]2:[ISD11]2:[NFS1]2 in supporting
iron–sulfur cluster assembly in vitro, it
appears that E. coli Acp can substitute for its human
homologue.
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Affiliation(s)
- Kai Cai
- Biochemistry Department, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Ronnie O. Frederick
- Biochemistry Department, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Marco Tonelli
- Biochemistry Department, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - John L. Markley
- Biochemistry Department, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
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35
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Structural/Functional Properties of Human NFU1, an Intermediate [4Fe-4S] Carrier in Human Mitochondrial Iron-Sulfur Cluster Biogenesis. Structure 2016; 24:2080-2091. [PMID: 27818104 DOI: 10.1016/j.str.2016.08.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/03/2016] [Accepted: 10/05/2016] [Indexed: 01/26/2023]
Abstract
Human mitochondrial NFU1 functions in the maturation of iron-sulfur proteins, and NFU1 deficiency is associated with a fatal mitochondrial disease. We determined three-dimensional structures of the N- and C-terminal domains of human NFU1 by nuclear magnetic resonance spectroscopy and used these structures along with small-angle X-ray scattering (SAXS) data to derive structural models for full-length monomeric apo-NFU1, dimeric apo-NFU1 (an artifact of intermolecular disulfide bond formation), and holo-NFUI (the [4Fe-4S] cluster-containing form of the protein). Apo-NFU1 contains two cysteine residues in its C-terminal domain, and two apo-NFU1 subunits coordinate one [4Fe-4S] cluster to form a cluster-linked dimer. Holo-NFU1 consists of a complex of three of these dimers as shown by molecular weight estimates from SAXS and size-exclusion chromatography. The SAXS-derived structural model indicates that one N-terminal region from each of the three dimers forms a tripartite interface. The activity of the holo-NFU1 preparation was verified by demonstrating its ability to activate apo-aconitase.
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36
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Bothe JR, Tonelli M, Ali IK, Dai Z, Frederick RO, Westler WM, Markley JL. The Complex Energy Landscape of the Protein IscU. Biophys J 2016; 109:1019-25. [PMID: 26331259 PMCID: PMC4564936 DOI: 10.1016/j.bpj.2015.07.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/20/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
IscU, the scaffold protein for iron-sulfur (Fe-S) cluster biosynthesis in Escherichia coli, traverses a complex energy landscape during Fe-S cluster synthesis and transfer. Our previous studies showed that IscU populates two interconverting conformational states: one structured (S) and one largely disordered (D). Both states appear to be functionally important because proteins involved in the assembly or transfer of Fe-S clusters have been shown to interact preferentially with either the S or D state of IscU. To characterize the complex structure-energy landscape of IscU, we employed NMR spectroscopy, small-angle x-ray scattering (SAXS), and differential scanning calorimetry. Results obtained for IscU at pH 8.0 show that its S state is maximally populated at 25°C and that heating or cooling converts the protein toward the D state. Results from NMR and DSC indicate that both the heat- and cold-induced S→D transitions are cooperative and two-state. Low-resolution structural information from NMR and SAXS suggests that the structures of the cold-induced and heat-induced D states are similar. Both states exhibit similar 1H-15N HSQC spectra and the same pattern of peptidyl-prolyl peptide bond configurations by NMR, and both appear to be similarly expanded compared with the S state based on analysis of SAXS data. Whereas in other proteins the cold-denatured states have been found to be slightly more compact than the heat-denatured states, these two states occupy similar volumes in IscU.
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Affiliation(s)
- Jameson R Bothe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ibrahim K Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ziqi Dai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ronnie O Frederick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - William M Westler
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin.
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37
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Nielsen JT, Mulder FAA. There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order". Front Mol Biosci 2016; 3:4. [PMID: 26904549 PMCID: PMC4749933 DOI: 10.3389/fmolb.2016.00004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
The protein universe consists of a continuum of structures ranging from full order to complete disorder. As the structured part of the proteome has been intensively studied, stably folded proteins are increasingly well documented and understood. However, proteins that are fully, or in large part, disordered are much less well characterized. Here we collected NMR chemical shifts in a small database for 117 protein sequences that are known to contain disorder. We demonstrate that NMR chemical shift data can be brought to bear as an exquisite judge of protein disorder at the residue level, and help in validation. With the help of secondary chemical shift analysis we demonstrate that the proteins in the database span the full spectrum of disorder, but still, largely segregate into two classes; disordered with small segments of order scattered along the sequence, and structured with small segments of disorder inserted between the different structured regions. A detailed analysis reveals that the distribution of order/disorder along the sequence shows a complex and asymmetric distribution, that is highly protein-dependent. Access to ratified training data further suggests an avenue to improving prediction of disorder from sequence.
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Affiliation(s)
- Jakob T Nielsen
- Department of Chemistry and Interdisciplinary Nanoscience Center, University of Aarhus Aarhus, Denmark
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center, University of Aarhus Aarhus, Denmark
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38
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Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL. Probabilistic validation of protein NMR chemical shift assignments. JOURNAL OF BIOMOLECULAR NMR 2016; 64:17-25. [PMID: 26724815 PMCID: PMC4744101 DOI: 10.1007/s10858-015-0007-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/20/2015] [Indexed: 05/05/2023]
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/.
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Affiliation(s)
- Hesam Dashti
- Graduate Program in Biophysics, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Tonelli
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Woonghee Lee
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - William M Westler
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Gabriel Cornilescu
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Eldon L Ulrich
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - John L Markley
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA.
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA.
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39
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Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates. Sci Rep 2015; 5:13794. [PMID: 26387727 PMCID: PMC4585668 DOI: 10.1038/srep13794] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 08/05/2015] [Indexed: 12/15/2022] Open
Abstract
Organohalide respiration is an environmentally important but poorly characterized type of anaerobic respiration. We compared the global proteome of the versatile organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans grown with different electron acceptors (fumarate, nitrate, or tetrachloroethene [PCE]). The most significant differences in protein abundance were found for gene products of the organohalide respiration region. This genomic region encodes the corrinoid and FeS cluster containing PCE reductive dehalogenase PceA and other proteins putatively involved in PCE metabolism such as those involved in corrinoid biosynthesis. The latter gene products as well as PceA and a putative quinol dehydrogenase were almost exclusively detected in cells grown with PCE. This finding suggests an electron flow from the electron donor such as formate or pyruvate via the quinone pool and a quinol dehydrogenase to PceA and the terminal electron acceptor PCE. Two putative accessory proteins, an IscU-like protein and a peroxidase-like protein, were detected with PCE only and might be involved in PceA maturation. The proteome of cells grown with pyruvate instead of formate as electron donor indicates a route of electrons from reduced ferredoxin via an Epsilonproteobacterial complex I and the quinone pool to PCE.
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40
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Iametti S, Barbiroli A, Bonomi F. Functional implications of the interaction between HscB and IscU in the biosynthesis of FeS clusters. J Biol Inorg Chem 2015; 20:1039-48. [PMID: 26246371 DOI: 10.1007/s00775-015-1285-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/20/2015] [Indexed: 11/25/2022]
Abstract
In bacteria, HscB is the cochaperone of HscA in modulating the transfer of 2Fe2S clusters from a cluster-loaded form of the scaffold protein IscU to acceptor apoproteins. HscB binding to the IscU apoform (apoIscU) reportedly impairs the structural flexibility of apoIscU, but the effects of HscB on cluster formation on IscU have never been assessed. We report that presence of HscB impaired the rate-but not the equilibrium-of the appearance of the distinctive circular dichroism signals associated with formation of a stable 2Fe-2S cluster on IscU in reconstitution experiments. This impairment: (1) was independent of the source of cluster sulfide; (2) was not observed for HscB mutants unable to bind IscU; (3) implied formation of a 1/1 HscB/IscU complex; (4) was not observed for a D39A mutant of IscU, with a much more rigid structure than wt IscU. The cluster species assembled on IscU in the presence of HscB were transferred to apoferredoxin at a slower rate than those formed in the absence of HscB, unless ATP and HscA were also present. At contrast, HscB was found to improve the "catalytic" function of IscU with respect to cluster assembly in the presence of a large apoferredoxin excess. Thus, the HscB/IscU interaction may modulate formation and transfer of FeS clusters by accelerating cluster biosynthesis when appropriate target apoproteins are abundant or by slowing it down when the rate of apoprotein synthesis is slow, and cluster-loaded IscU is more likely to play a role as a "FeS storage" protein.
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Affiliation(s)
- Stefania Iametti
- Section of Chemical and Biomolecular Sciences, DeFENS, University of Milan, Via Celoria 2, 20133, Milan, Italy
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41
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Fox NG, Das D, Chakrabarti M, Lindahl PA, Barondeau DP. Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe-S Assembly Complex. Biochemistry 2015; 54:3880-9. [PMID: 26016518 PMCID: PMC4675465 DOI: 10.1021/bi5014497] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Iron-sulfur (Fe-S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe-S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe-S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe-S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe-S assembly complex. Here the kinetics of Fe-S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe-S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe-S assembly complex.
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Affiliation(s)
- Nicholas G. Fox
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Deepika Das
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Mrinmoy Chakrabarti
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Paul A. Lindahl
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States
| | - David P. Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
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42
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Yoon H, Knight SAB, Pandey A, Pain J, Turkarslan S, Pain D, Dancis A. Turning Saccharomyces cerevisiae into a Frataxin-Independent Organism. PLoS Genet 2015; 11:e1005135. [PMID: 25996596 PMCID: PMC4440810 DOI: 10.1371/journal.pgen.1005135] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/10/2015] [Indexed: 01/08/2023] Open
Abstract
Frataxin (Yfh1 in yeast) is a conserved protein and deficiency leads to the neurodegenerative disease Friedreich's ataxia. Frataxin is a critical protein for Fe-S cluster assembly in mitochondria, interacting with other components of the Fe-S cluster machinery, including cysteine desulfurase Nfs1, Isd11 and the Isu1 scaffold protein. Yeast Isu1 with the methionine to isoleucine substitution (M141I), in which the E. coli amino acid is inserted at this position, corrected most of the phenotypes that result from lack of Yfh1 in yeast. This suppressor Isu1 behaved as a genetic dominant. Furthermore frataxin-bypass activity required a completely functional Nfs1 and correlated with the presence of efficient scaffold function. A screen of random Isu1 mutations for frataxin-bypass activity identified only M141 substitutions, including Ile, Cys, Leu, or Val. In each case, mitochondrial Nfs1 persulfide formation was enhanced, and mitochondrial Fe-S cluster assembly was improved in the absence of frataxin. Direct targeting of the entire E. coli IscU to ∆yfh1 mitochondria also ameliorated the mutant phenotypes. In contrast, expression of IscU with the reverse substitution i.e. IscU with Ile to Met change led to worsening of the ∆yfh1 phenotypes, including severely compromised growth, increased sensitivity to oxygen, deficiency in Fe-S clusters and heme, and impaired iron homeostasis. A bioinformatic survey of eukaryotic Isu1/prokaryotic IscU database entries sorted on the amino acid utilized at the M141 position identified unique groupings, with virtually all of the eukaryotic scaffolds using Met, and the preponderance of prokaryotic scaffolds using other amino acids. The frataxin-bypassing amino acids Cys, Ile, Leu, or Val, were found predominantly in prokaryotes. This amino acid position 141 is unique in Isu1, and the frataxin-bypass effect likely mimics a conserved and ancient feature of the prokaryotic Fe-S cluster assembly machinery.
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Affiliation(s)
- Heeyong Yoon
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Simon A. B. Knight
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alok Pandey
- Department of Pharmacology and Physiology, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Jayashree Pain
- Department of Pharmacology and Physiology, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Serdar Turkarslan
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Debkumar Pain
- Department of Pharmacology and Physiology, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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43
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Kim JH, Bothe JR, Alderson TR, Markley JL. Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1416-28. [PMID: 25450980 DOI: 10.1016/j.bbamcr.2014.11.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/18/2014] [Accepted: 11/13/2014] [Indexed: 12/26/2022]
Abstract
Proteins containing iron-sulfur (Fe-S) clusters arose early in evolution and are essential to life. Organisms have evolved machinery consisting of specialized proteins that operate together to assemble Fe-S clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. To date, the best studied system is the iron-sulfur cluster (isc) operon of Escherichia coli, and the eight ISC proteins it encodes. Our investigations over the past five years have identified two functional conformational states for the scaffold protein (IscU) and have shown that the other ISC proteins that interact with IscU prefer to bind one conformational state or the other. From analyses of the NMR spectroscopy-derived network of interactions of ISC proteins, small-angle X-ray scattering (SAXS) data, chemical crosslinking experiments, and functional assays, we have constructed working models for Fe-S cluster assembly and delivery. Future work is needed to validate and refine what has been learned about the E. coli system and to extend these findings to the homologous Fe-S cluster biosynthetic machinery of yeast and human mitochondria. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Jin Hae Kim
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jameson R Bothe
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - T Reid Alderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
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44
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Kim JH, Alderson TR, Frederick RO, Markley JL. Nucleotide-dependent interactions within a specialized Hsp70/Hsp40 complex involved in Fe-S cluster biogenesis. J Am Chem Soc 2014; 136:11586-9. [PMID: 25080945 PMCID: PMC4140450 DOI: 10.1021/ja5055252] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
structural mechanism by which Hsp70-type chaperones interact
with Hsp40-type co-chaperones has been of great interest, yet still
remains a matter of debate. Here, we used solution NMR spectroscopy
to investigate the ATP-/ADP-dependent interactions between Escherichia coli HscA and HscB, the specialized Hsp70/Hsp40
molecular chaperones that mediate iron–sulfur cluster transfer.
We observed that NMR signals assigned to amino acid residues in the
J-domain and its “HPD” motif of HscB broadened severely
upon the addition of ATP-bound HscA, but these signals were not similarly
broadened by ADP-bound HscA or the isolated nucleotide binding domain
of HscA complexed with either ATP or ADP. An HscB variant with an
altered HPD motif, HscB(H32A,P33A,D34A), failed to manifest WT-like
NMR signal perturbations and also abolished WT-like stimulation of
ATP hydrolysis by HscA. In addition, residues 153–171 in the
C-terminal region of HscB exhibited NMR signal perturbations upon
interaction with HscA, alone or complexed with ADP or ATP. These results
demonstrate that the HPD motif in the J-domain of HscB directly interacts
with ATP-bound HscA and suggest that a second, less nucleotide-dependent
binding site for HscA resides in the C-terminal region of HscB.
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Affiliation(s)
- Jin Hae Kim
- Mitochondrial Protein Partnership, Center for Eukaryotic Structural Genomics, and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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45
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Bridwell-Rabb J, Fox N, Tsai CL, Winn AM, Barondeau DP. Human frataxin activates Fe-S cluster biosynthesis by facilitating sulfur transfer chemistry. Biochemistry 2014; 53:4904-13. [PMID: 24971490 PMCID: PMC4215901 DOI: 10.1021/bi500532e] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 06/26/2014] [Indexed: 01/11/2023]
Abstract
Iron-sulfur clusters are ubiquitous protein cofactors with critical cellular functions. The mitochondrial Fe-S assembly complex, which consists of the cysteine desulfurase NFS1 and its accessory protein (ISD11), the Fe-S assembly protein (ISCU2), and frataxin (FXN), converts substrates l-cysteine, ferrous iron, and electrons into Fe-S clusters. The physiological function of FXN has received a tremendous amount of attention since the discovery that its loss is directly linked to the neurodegenerative disease Friedreich's ataxia. Previous in vitro results revealed a role for human FXN in activating the cysteine desulfurase and Fe-S cluster biosynthesis activities of the Fe-S assembly complex. Here we present radiolabeling experiments that indicate FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe-S clusters. Additional mutagenesis, enzyme kinetic, UV-visible, and circular dichroism spectroscopic studies suggest conserved ISCU2 residue C104 is critical for FXN activation, whereas C35, C61, and C104 are all essential for Fe-S cluster formation on the assembly complex. These results cannot be fully explained by the hypothesis that FXN functions as an iron donor for Fe-S cluster biosynthesis, and further support an allosteric regulator role for FXN. Together, these results lead to an activation model in which FXN accelerates persulfide formation on NFS1 and favors a helix-to-coil interconversion on ISCU2 that facilitates the transfer of sulfur from NFS1 to ISCU2 as an initial step in Fe-S cluster biosynthesis.
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Affiliation(s)
- Jennifer Bridwell-Rabb
- Department of Chemistry, Texas A&M
University, College Station, Texas 77842, United States
| | - Nicholas
G. Fox
- Department of Chemistry, Texas A&M
University, College Station, Texas 77842, United States
| | - Chi-Lin Tsai
- Department of Chemistry, Texas A&M
University, College Station, Texas 77842, United States
| | - Andrew M. Winn
- Department of Chemistry, Texas A&M
University, College Station, Texas 77842, United States
| | - David P. Barondeau
- Department of Chemistry, Texas A&M
University, College Station, Texas 77842, United States
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46
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Dai Z, Kim JH, Tonelli M, Ali IK, Markley JL. pH-induced conformational change of IscU at low pH correlates with protonation/deprotonation of two conserved histidine residues. Biochemistry 2014; 53:5290-7. [PMID: 25055301 PMCID: PMC4139155 DOI: 10.1021/bi500313t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
IscU, the scaffold protein for the
major iron–sulfur cluster
biosynthesis pathway in microorganisms and mitochondria (ISC pathway),
plays important roles in the formation of [2Fe–2S] and [4Fe–4S]
clusters and their delivery to acceptor apo-proteins. Our laboratory
has shown that IscU populates two distinct, functionally relevant
conformational states, a more structured state (S) and a more dynamic
state (D), that differ by cis/trans isomerizations about two peptidyl-prolyl peptide bonds [Kim, J.
H., Tonelli, M., and Markley, J. L. (2012) Proc. Natl. Acad.
Sci. U.S.A., 109, 454–459. Dai Z.,
Tonelli, M., and Markley, J. L. (2012) Biochemistry, 51, 9595–9602. Cai, K., Frederick, R. O.,
Kim, J. H., Reinen, N. M., Tonelli, M., and Markley, J. L. (2013) J. Biol. Chem., 288, 28755–28770].
Here, we report our findings on the pH dependence of the D ⇄
S equilibrium for Escherichia coli IscU
in which the D-state is stabilized at low and high pH values. We show
that the lower limb of the pH dependence curve results from differences
in the pKa values of two conserved histidine
residues (His10 and His105) in the two states. The net proton affinity
of His10 is about 50 times higher and that of His105 is 13 times higher
in the D-state than in the S-state. The origin of the high limb of
the D ⇄ S pH dependence remains to be determined. These results
show that changes in proton inventory need to be taken into account
in the steps in iron–sulfur cluster assembly and transfer that
involve transitions of IscU between its S- and D-states.
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Affiliation(s)
- Ziqi Dai
- Biophysics Graduate Program, ‡Biochemistry Department, and §National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison , Madison, Wisconsin 53715, United States
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47
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Cammack R, Balk J. Iron-sulfur Clusters. BINDING, TRANSPORT AND STORAGE OF METAL IONS IN BIOLOGICAL CELLS 2014. [DOI: 10.1039/9781849739979-00333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Iron-sulfur clusters are universally distributed groups occurring in iron-sulfur proteins. They have a wide range of cellular functions which reflect the chemistry of the clusters. Some clusters are involved in electron transport and energy transduction in photosynthesis and respiration. Others can bind substrates and participate in enzyme catalysis. Regulatory functions have also been documented for clusters that respond to oxygen partial pressure and iron availability. Finally, there are some for which no function has been defined; they may act as stabilizing structures, for example, in enzymes involved in nucleic acid metabolism. The clusters are constructed intracellularly and inserted into proteins, which can then be transported to intracellular targets, in some cases, across membranes. Three different types of iron-sulfur cluster assembly machinery have evolved in prokaryotes: NIF, ISC and SUF. Each system involves a scaffold protein on which the cluster is constructed (encoded by genes nifU, iscU, sufU or sufB) and a cysteine desulfurase (encoded by nifS, iscS or sufS) which provides the sulfide sulfur. In eukaryotic cells, clusters are formed in the mitochondria for the many iron-sulfur proteins in this organelle. The mitochondrial biosynthesis pathway is linked to the cytoplasmic iron-sulfur assembly system (CIA) for the maturation of cytoplasmic and nuclear iron-sulfur proteins. In plant cells, a SUF-type system is used for cluster assembly in the plastids. Many accessory proteins are involved in cluster transfer before insertion into the appropriate sites in Fe-S proteins.
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Affiliation(s)
- Richard Cammack
- King's College London, Department of Biochemistry, 150 Stamford Street London SE1 9NH UK
| | - Janneke Balk
- John Innes Centre and University of East Anglia Norwich Research Park, Colney Lane Norwich NR4 7UH UK
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Yan R, Kelly G, Pastore A. The Scaffold Protein IscU Retains a Structured Conformation in the FeS Cluster Assembly Complex. Chembiochem 2014; 15:1682-6. [DOI: 10.1002/cbic.201402211] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 11/12/2022]
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Kim JH, Bothe JR, Frederick R, Holder JC, Markley JL. Role of IscX in iron-sulfur cluster biogenesis in Escherichia coli. J Am Chem Soc 2014; 136:7933-42. [PMID: 24810328 PMCID: PMC4063190 DOI: 10.1021/ja501260h] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 01/09/2023]
Abstract
The Escherichia coli isc operon encodes key proteins involved in the biosynthesis of iron-sulfur (Fe-S) clusters. Whereas extensive studies of most ISC proteins have revealed their functional properties, the role of IscX (also dubbed YfhJ), a small acidic protein encoded by the last gene in the operon, has remained in question. Previous studies showed that IscX binds iron ions and interacts with the cysteine desulfurase (IscS) and the scaffold protein for cluster assembly (IscU), and it has been proposed that IscX functions either as an iron supplier or a regulator of Fe-S cluster biogenesis. We have used a combination of NMR spectroscopy, small-angle X-ray scattering (SAXS), chemical cross-linking, and enzymatic assays to enlarge our understanding of the interactions of IscX with iron ions, IscU, and IscS. We used chemical shift perturbation to identify the binding interfaces of IscX and IscU in their complex. NMR studies showed that Fe(2+) from added ferrous ammonium sulfate binds IscX much more avidly than does Fe(3+) from added ferric ammonium citrate and that Fe(2+) strengthens the interaction between IscX and IscU. We found that the addition of IscX to the IscU-IscS binary complex led to the formation of a ternary complex with reduced cysteine desulfurase activity, and we determined a low-resolution model for that complex from a combination of NMR and SAXS data. We postulate that the inhibition of cysteine desulfurase activity by IscX serves to reduce unproductive conversion of cysteine to alanine. By incorporating these new findings with results from prior studies, we propose a detailed mechanism for Fe-S cluster assembly in which IscX serves both as a donor of Fe(2+) and as a regulator of cysteine desulfurase activity.
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Affiliation(s)
- Jin Hae Kim
- Mitochondrial
Protein Partnership, Center for Eukaryotic Structural
Genomics and Department of Biochemistry, University
of Wisconsin, 433 Babcock
Drive, Madison, Wisconsin 53706, United States
| | - Jameson R. Bothe
- Mitochondrial
Protein Partnership, Center for Eukaryotic Structural
Genomics and Department of Biochemistry, University
of Wisconsin, 433 Babcock
Drive, Madison, Wisconsin 53706, United States
| | - Ronnie
O. Frederick
- Mitochondrial
Protein Partnership, Center for Eukaryotic Structural
Genomics and Department of Biochemistry, University
of Wisconsin, 433 Babcock
Drive, Madison, Wisconsin 53706, United States
| | - Johneisa C. Holder
- Mitochondrial
Protein Partnership, Center for Eukaryotic Structural
Genomics and Department of Biochemistry, University
of Wisconsin, 433 Babcock
Drive, Madison, Wisconsin 53706, United States
| | - John L. Markley
- Mitochondrial
Protein Partnership, Center for Eukaryotic Structural
Genomics and Department of Biochemistry, University
of Wisconsin, 433 Babcock
Drive, Madison, Wisconsin 53706, United States
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Global identification of genes affecting iron-sulfur cluster biogenesis and iron homeostasis. J Bacteriol 2014; 196:1238-49. [PMID: 24415728 DOI: 10.1128/jb.01160-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors that are crucial for many physiological processes in all organisms. In Escherichia coli, assembly of Fe-S clusters depends on the activity of the iron-sulfur cluster (ISC) assembly and sulfur mobilization (SUF) apparatus. However, the underlying molecular mechanisms and the mechanisms that control Fe-S cluster biogenesis and iron homeostasis are still poorly defined. In this study, we performed a global screen to identify the factors affecting Fe-S cluster biogenesis and iron homeostasis using the Keio collection, which is a library of 3,815 single-gene E. coli knockout mutants. The approach was based on radiolabeling of the cells with [2-(14)C]dihydrouracil, which entirely depends on the activity of an Fe-S enzyme, dihydropyrimidine dehydrogenase. We identified 49 genes affecting Fe-S cluster biogenesis and/or iron homeostasis, including 23 genes important only under microaerobic/anaerobic conditions. This study defines key proteins associated with Fe-S cluster biogenesis and iron homeostasis, which will aid further understanding of the cellular mechanisms that coordinate the processes. In addition, we applied the [2-(14)C]dihydrouracil-labeling method to analyze the role of amino acid residues of an Fe-S cluster assembly scaffold (IscU) as a model of the Fe-S cluster assembly apparatus. The analysis showed that Cys37, Cys63, His105, and Cys106 are essential for the function of IscU in vivo, demonstrating the potential of the method to investigate in vivo function of proteins involved in Fe-S cluster assembly.
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