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Title: Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe–S cluster assembly centers

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 formore » 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.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [2];  [2]; ORCiD logo [3]; ORCiD logo [4]
+ Show Author Affiliations
  1. Mayo Clinic, Rochester, MN (United States). Dept. of Pediatric & Adolescent Medicine; Mayo Clinic, Rochester, MN (United States). Dept of Biochemistry & Molecular Biology; Mayo Clinic, Rochester, MN (United States). Graduate School of Biomedical Sciences
  2. Mayo Clinic, Rochester, MN (United States). Dept. of Pediatric & Adolescent Medicine; Mayo Clinic, Rochester, MN (United States). Children's Research Center
  3. Mayo Clinic, Rochester, MN (United States). Dept of Biochemistry & Molecular Biology
  4. Mayo Clinic, Rochester, MN (United States). Dept. of Pediatric & Adolescent Medicine; Mayo Clinic, Rochester, MN (United States). Dept of Biochemistry & Molecular Biology; Mayo Clinic, Rochester, MN (United States). Children's Research Center
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health/National Institute on Aging
OSTI Identifier:
1624948
Grant/Contract Number:  
AC02-05CH11231; R01GM105404; AG15709
Resource Type:
Accepted Manuscript
Journal Name:
Metallomics
Additional Journal Information:
Journal Volume: 9; Journal Issue: 6; Journal ID: ISSN 1756-5901
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biochemistry & Molecular Biology

Citation Formats

Galeano, B. K., Ranatunga, W., Gakh, O., Smith, D. Y., Thompson, J. R., and Isaya, G. Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe–S cluster assembly centers. United States: N. p., 2017. Web. doi:10.1039/c7mt00089h.
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Galeano, B. K., Ranatunga, W., Gakh, O., Smith, D. Y., Thompson, J. R., & Isaya, G. Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe–S cluster assembly centers. United States. https://doi.org/10.1039/c7mt00089h
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Galeano, B. K., Ranatunga, W., Gakh, O., Smith, D. Y., Thompson, J. R., and Isaya, G. Fri . "Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe–S cluster assembly centers". United States. https://doi.org/10.1039/c7mt00089h. https://www.osti.gov/servlets/purl/1624948.
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@article{osti_1624948,
title = {Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe–S cluster assembly centers},
author = {Galeano, B. K. and Ranatunga, W. and Gakh, O. and Smith, D. Y. and Thompson, J. R. and Isaya, G.},
abstractNote = {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.},
doi = {10.1039/c7mt00089h},
journal = {Metallomics},
number = 6,
volume = 9,
place = {United States},
year = {Fri May 26 00:00:00 EDT 2017},
month = {Fri May 26 00:00:00 EDT 2017}
}
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  • Schwartz, C. J.; Djaman, O.; Imlay, J. A.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 16
  • DOI: 10.1073/pnas.160261497

ATSAS 2.1, a program package for small-angle scattering data analysis
journal, March 2006

  • Konarev, Petr V.; Petoukhov, Maxim V.; Volkov, Vladimir V.
  • Journal of Applied Crystallography, Vol. 39, Issue 2
  • DOI: 10.1107/S0021889806004699

The Asymmetric Trimeric Architecture of [2Fe–2S] IscU: Implications for Its Scaffolding during Iron–Sulfur Cluster Biosynthesis
journal, October 2008

  • Shimomura, Yoshimitsu; Wada, Kei; Fukuyama, Keiichi
  • Journal of Molecular Biology, Vol. 383, Issue 1
  • DOI: 10.1016/j.jmb.2008.08.015

Tissue sulfhydryl groups
journal, May 1959

The Yeast Scaffold Proteins Isu1p and Isu2p Are Required inside Mitochondria for Maturation of Cytosolic Fe/S Proteins
journal, May 2004

Rearrangement of Cruickshank's formulae for the diffraction-component precision index
journal, April 2002

(IscS-IscU)2Complex Structures Provide Insights into Fe2S2Biogenesis and Transfer
journal, April 2012

  • Marinoni, Elodie N.; de Oliveira, Jaim S.; Nicolet, Yvain
  • Angewandte Chemie, Vol. 124, Issue 22
  • DOI: 10.1002/ange.201201708

The Scaffold Protein IscU Retains a Structured Conformation in the FeS Cluster Assembly Complex
journal, July 2014

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Saccharomyces cerevisiae ISU1 and ISU2: members of a well-conserved gene family for iron-sulfur cluster assembly
journal, December 1999

  • Garland, Stacey A.; Hoff, Kevin; Vickery, Larry E.
  • Journal of Molecular Biology, Vol. 294, Issue 4
  • DOI: 10.1006/jmbi.1999.3294

Chances and pitfalls of chemical cross-linking with amine-reactive N-hydroxysuccinimide esters
journal, July 2008

A Dynamic Model of the Proteins that Form the Initial Iron-Sulfur Cluster Biogenesis Machinery in Yeast Mitochondria
journal, March 2013

Tissue sulfhydryl groups
journal, May 1959

Role of arginine in chemical cross-linking with N-hydroxysuccinimide esters
journal, March 2010

  • Mädler, Stefanie; Gschwind, Sabrina; Zenobi, Renato
  • Analytical Biochemistry, Vol. 398, Issue 1
  • DOI: 10.1016/j.ab.2009.11.020

Iron/sulfur proteins biogenesis in prokaryotes: Formation, regulation and diversity
journal, March 2013

  • Roche, Béatrice; Aussel, Laurent; Ezraty, Benjamin
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 3
  • DOI: 10.1016/j.bbabio.2012.12.010

Iron –sulfur cluster biogenesis in mammalian cells: New insights into the molecular mechanisms of cluster delivery
journal, June 2015

  • Maio, Nunziata; Rouault, Tracey A.
  • Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1853, Issue 6
  • DOI: 10.1016/j.bbamcr.2014.09.009

Anatomy of an iron-sulfur cluster scaffold protein: Understanding the determinants of [2Fe–2S] cluster stability on IscU
journal, June 2015

  • Adrover, Miquel; Howes, Barry D.; Iannuzzi, Clara
  • Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1853, Issue 6
  • DOI: 10.1016/j.bbamcr.2014.10.023

Iron Binding and Oxidation Kinetics in Frataxin CyaY of Escherichia coli
journal, August 2004

  • Bou-Abdallah, Fadi; Adinolfi, Salvatore; Pastore, Annalisa
  • Journal of Molecular Biology, Vol. 341, Issue 2
  • DOI: 10.1016/j.jmb.2004.05.072

Solution NMR Structure of the Iron–Sulfur Cluster Assembly Protein U (IscU) with Zinc Bound at the Active Site
journal, November 2004

  • Ramelot, Theresa A.; Cort, John R.; Goldsmith-Fischman, Sharon
  • Journal of Molecular Biology, Vol. 344, Issue 2
  • DOI: 10.1016/j.jmb.2004.08.038

Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007

The Asymmetric Trimeric Architecture of [2Fe–2S] IscU: Implications for Its Scaffolding during Iron–Sulfur Cluster Biosynthesis
journal, October 2008

  • Shimomura, Yoshimitsu; Wada, Kei; Fukuyama, Keiichi
  • Journal of Molecular Biology, Vol. 383, Issue 1
  • DOI: 10.1016/j.jmb.2008.08.015

Fourier shell correlation threshold criteria
journal, September 2005

EMAN2: An extensible image processing suite for electron microscopy
journal, January 2007

  • Tang, Guang; Peng, Liwei; Baldwin, Philip R.
  • Journal of Structural Biology, Vol. 157, Issue 1
  • DOI: 10.1016/j.jsb.2006.05.009

Structural characterization of proteins and complexes using small-angle X-ray solution scattering
journal, October 2010

Iron–sulfur cluster synthesis, iron homeostasis and oxidative stress in Friedreich ataxia
journal, July 2013

The Structures of Frataxin Oligomers Reveal the Mechanism for the Delivery and Detoxification of Iron
journal, October 2006

A new mitochondrial fluorescent zinc sensor
journal, September 2003

Characterization of an Iron−Sulfur Cluster Assembly Protein (ISU1) from Schizosaccharomyces pombe †
journal, April 2002

  • Wu, Gong; Mansy, Sheref S.; Wu, Shu-pao
  • Biochemistry, Vol. 41, Issue 15
  • DOI: 10.1021/bi016073s

Structure of Frataxin Iron Cores:  An X-ray Absorption Spectroscopic Study †
journal, May 2003

  • Nichol, Helen; Gakh, Oleksandr; O'Neill, Heather A.
  • Biochemistry, Vol. 42, Issue 20
  • DOI: 10.1021/bi027021l

Monomeric Yeast Frataxin Is an Iron-Binding Protein †
journal, June 2006

  • Cook, Jeremy D.; Bencze, Krisztina Z.; Jankovic, Ana D.
  • Biochemistry, Vol. 45, Issue 25
  • DOI: 10.1021/bi060424r

Human Frataxin Is an Allosteric Switch That Activates the Fe−S Cluster Biosynthetic Complex
journal, November 2010

  • Tsai, Chi-Lin; Barondeau, David P.
  • Biochemistry, Vol. 49, Issue 43
  • DOI: 10.1021/bi1013062

Human Frataxin Activates Fe–S Cluster Biosynthesis by Facilitating Sulfur Transfer Chemistry
journal, July 2014

  • Bridwell-Rabb, Jennifer; Fox, Nicholas G.; Tsai, Chi-Lin
  • Biochemistry, Vol. 53, Issue 30
  • DOI: 10.1021/bi500532e

The Human Iron–Sulfur Assembly Complex Catalyzes the Synthesis of [2Fe-2S] Clusters on ISCU2 That Can Be Transferred to Acceptor Molecules
journal, June 2015

  • Fox, Nicholas G.; Chakrabarti, Mrinmoy; McCormick, Sean P.
  • Biochemistry, Vol. 54, Issue 25
  • DOI: 10.1021/bi5014485

Structural Basis of the Iron Storage Function of Frataxin from Single-Particle Reconstruction of the Iron-Loaded Oligomer †
journal, April 2008

  • Schagerlöf, Ulrika; Elmlund, Hans; Gakh, Oleksandr
  • Biochemistry, Vol. 47, Issue 17
  • DOI: 10.1021/bi800052m

Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering
journal, May 2007

  • Bernadó, Pau; Mylonas, Efstratios; Petoukhov, Maxim V.
  • Journal of the American Chemical Society, Vol. 129, Issue 17
  • DOI: 10.1021/ja069124n

Accurate assessment of mass, models and resolution by small-angle scattering
journal, April 2013

Structural bases for the interaction of frataxin with the central components of iron–sulphur cluster assembly
journal, October 2010

  • Prischi, Filippo; Konarev, Petr V.; Iannuzzi, Clara
  • Nature Communications, Vol. 1, Issue 1
  • DOI: 10.1038/ncomms1097

Mammalian frataxin directly enhances sulfur transfer of NFS1 persulfide to both ISCU and free thiols
journal, January 2015

  • Parent, Aubérie; Elduque, Xavier; Cornu, David
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms6686

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
journal, July 2009

  • Hura, Greg L.; Menon, Angeli L.; Hammel, Michal
  • Nature Methods, Vol. 6, Issue 8
  • DOI: 10.1038/nmeth.1353

Protein structure prediction on the Web: a case study using the Phyre server
journal, February 2009

  • Kelley, Lawrence A.; Sternberg, Michael J. E.
  • Nature Protocols, Vol. 4, Issue 3
  • DOI: 10.1038/nprot.2009.2

Synchrotron-based small-angle X-ray scattering of proteins in solution
journal, June 2014

  • Skou, Soren; Gillilan, Richard E.; Ando, Nozomi
  • Nature Protocols, Vol. 9, Issue 7
  • DOI: 10.1038/nprot.2014.116

Bacterial frataxin CyaY is the gatekeeper of iron-sulfur cluster formation catalyzed by IscS
journal, March 2009

  • Adinolfi, Salvatore; Iannuzzi, Clara; Prischi, Filippo
  • Nature Structural & Molecular Biology, Vol. 16, Issue 4
  • DOI: 10.1038/nsmb.1579

Iron‐induced oligomerization of yeast frataxin homologue Yfh1 is dispensable in vivo
journal, November 2004

Acidic residues of yeast frataxin have an essential role in Fe–S cluster assembly
journal, December 2006

An interaction between frataxin and Isu1/Nfs1 that is crucial for Fe/S cluster synthesis on Isu1
journal, August 2003

In vitro characterization of a novel Isu homologue from Drosophila melanogaster for de novo FeS-cluster formation
journal, January 2017

  • Dzul, Stephen P.; Rocha, Agostinho G.; Rawat, Swati
  • Metallomics, Vol. 9, Issue 1
  • DOI: 10.1039/c6mt00163g

The gel-filtration behaviour of proteins related to their molecular weights over a wide range
journal, September 1965

Disordered form of the scaffold protein IscU is the substrate for iron-sulfur cluster assembly on cysteine desulfurase
journal, December 2011

  • Kim, J. H.; Tonelli, M.; Markley, J. L.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 2
  • DOI: 10.1073/pnas.1114372109

The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli
journal, July 2000

  • Schwartz, C. J.; Djaman, O.; Imlay, J. A.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 16
  • DOI: 10.1073/pnas.160261497

Mt-Hsp70 Homolog, Ssc2p, Required for Maturation of Yeast Frataxin and Mitochondrial Iron Homeostasis
journal, July 1998

  • Knight, Simon A. B.; Sepuri, Naresh Babu V.; Pain, Debkumar
  • Journal of Biological Chemistry, Vol. 273, Issue 29
  • DOI: 10.1074/jbc.273.29.18389

Yeast and Human Frataxin Are Processed to Mature Form in Two Sequential Steps by the Mitochondrial Processing Peptidase
journal, August 1999

  • Branda, Steven S.; Cavadini, Patrizia; Adamec, Jiri
  • Journal of Biological Chemistry, Vol. 274, Issue 32
  • DOI: 10.1074/jbc.274.32.22763

Normal and Friedreich ataxia cells express different isoforms of frataxin with complementary roles in iron-sulfur cluster assembly.
journal, March 2011

  • Gakh, Oleksandr; Bedekovics, Tibor; Duncan, Samantha F.
  • Journal of Biological Chemistry, Vol. 286, Issue 10
  • DOI: 10.1074/jbc.a110.145144

Missense Mutations Linked to Friedreich Ataxia Have Different but Synergistic Effects on Mitochondrial Frataxin Isoforms
journal, December 2012

  • Li, Hongqiao; Gakh, Oleksandr; Smith, Douglas Y.
  • Journal of Biological Chemistry, Vol. 288, Issue 6
  • DOI: 10.1074/jbc.m112.435263

The Molecular Basis of Iron-induced Oligomerization of Frataxin and the Role of the Ferroxidation Reaction in Oligomerization
journal, January 2013

  • Söderberg, Christopher A. G.; Rajan, Sreekanth; Shkumatov, Alexander V.
  • Journal of Biological Chemistry, Vol. 288, Issue 12
  • DOI: 10.1074/jbc.m112.442285

Binding of the Chaperone Jac1 Protein and Cysteine Desulfurase Nfs1 to the Iron-Sulfur Cluster Scaffold Isu Protein Is Mutually Exclusive
journal, August 2013

  • Majewska, Julia; Ciesielski, Szymon J.; Schilke, Brenda
  • Journal of Biological Chemistry, Vol. 288, Issue 40
  • DOI: 10.1074/jbc.m113.503524

Overlapping Binding Sites of the Frataxin Homologue Assembly Factor and the Heat Shock Protein 70 Transfer Factor on the Isu Iron-Sulfur Cluster Scaffold Protein
journal, September 2014

  • Manicki, Mateusz; Majewska, Julia; Ciesielski, Szymon
  • Journal of Biological Chemistry, Vol. 289, Issue 44
  • DOI: 10.1074/jbc.m114.596726

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery
journal, August 2016

  • Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y.
  • Journal of Biological Chemistry, Vol. 291, Issue 40
  • DOI: 10.1074/jbc.m116.738542

The Ferroxidase Activity of Yeast Frataxin
journal, July 2002

  • Park, Sungjo; Gakh, Oleksandr; Mooney, Steven M.
  • Journal of Biological Chemistry, Vol. 277, Issue 41
  • DOI: 10.1074/jbc.m206711200

Yeast Frataxin Sequentially Chaperones and Stores Iron by Coupling Protein Assembly with Iron Oxidation
journal, May 2003

  • Park, Sungjo; Gakh, Oleksandr; O'Neill, Heather A.
  • Journal of Biological Chemistry, Vol. 278, Issue 33
  • DOI: 10.1074/jbc.m303158200

Binding of Yeast Frataxin to the Scaffold for Fe-S Cluster Biogenesis, Isu
journal, March 2008

  • Wang, Tao; Craig, Elizabeth A.
  • Journal of Biological Chemistry, Vol. 283, Issue 18
  • DOI: 10.1074/jbc.m800399200

Assembly of the Iron-binding Protein Frataxin in Saccharomyces cerevisiae Responds to Dynamic Changes in Mitochondrial Iron Influx and Stress Level
journal, September 2008

  • Gakh, Oleksandr; Smith, Douglas Y.; Isaya, Grazia
  • Journal of Biological Chemistry, Vol. 283, Issue 46
  • DOI: 10.1074/jbc.m805415200

Components involved in assembly and dislocation of iron-sulfur clusters on the scaffold protein Isu1p
journal, September 2003

Mitochondrial formation of reactive oxygen species
journal, October 2003

Controlled Expression and Functional Analysis of Iron-Sulfur Cluster Biosynthetic Components within Azotobacter vinelandii
journal, August 2006

  • Johnson, Deborah C.; Unciuleac, Mihaela-Carmen; Dean, Dennis R.
  • Journal of Bacteriology, Vol. 188, Issue 21
  • DOI: 10.1128/jb.00596-06

Structural Basis for Fe–S Cluster Assembly and tRNA Thiolation Mediated by IscS Protein–Protein Interactions
journal, April 2010

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