METALS IN CELLS

EIBC BooksEncyclopedia ofInorganic andBioinorganicChemistry

Application of Physical Methods to Inorganic and Bioinorganic ChemistryEdited by Robert A. Scott and Charles M. LukehartISBN 978-0-470-03217-6

Nanomaterials: Inorganic and Bioinorganic PerspectivesEdited by Charles M. Lukehart and Robert A. ScottISBN 978-0-470-51644-7

Computational Inorganic and Bioinorganic ChemistryEdited by Edward I. Solomon, R. Bruce King and Robert A. ScottISBN 978-0-470-69997-3

Radionuclides in the EnvironmentEdited by David A. AtwoodISBN 978-0-470-71434-8

Energy Production and Storage: Inorganic Chemical Strategies for a Warming WorldEdited by Robert H. CrabtreeISBN 978-0-470-74986-9

The Rare Earth Elements: Fundamentals and ApplicationsEdited by David A. AtwoodISBN 978-1-119-95097-4

Metals in CellsEdited by Valeria Culotta and Robert A. ScottISBN 978-1-119-95323-4

Forthcoming

Metal-Organic Framework MaterialsEdited by Leonard R. MacGillivray and Charles M. LukehartISBN 978-1-119-95289-3

The Lightest MetalsEdited by Timothy P. HanusaISBN 978-1-11870328-1

Sustainable Inorganic ChemistryEdited by David A. AtwoodISBN 978-1-11870342-7

Encyclopedia of Inorganic and Bioinorganic Chemistry

The Encyclopedia of Inorganic and Bioinorganic Chemistry (EIBC) was created as an online reference in 2012 by merging theEncyclopedia of Inorganic Chemistry and the Handbook of Metalloproteins. The resulting combination proves to be the definingreference work in the field of inorganic and bioinorganic chemistry. The online edition is regularly updated and expanded. Forinformation see:

www.wileyonlinelibrary.com/ref/eibc

METALS IN CELLS

Editors

Valeria CulottaJohns Hopkins University, Baltimore, MD, USA

Robert A. ScottUniversity of Georgia, Athens, GA, USA

This edition first published 2013© 2013 John Wiley & Sons Ltd

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Library of Congress Cataloging-in-Publication Data

Metals in cells / editors, Valeria Culotta, Robert A. Scott.p. ; cm.

Includes bibliographical references and index.ISBN 978-1-119-95323-4 (cloth)

I. Culotta, Valeria. II. Scott, Robert A., 1953-[DNLM: 1. Cell Physiological Phenomena. 2. Chemistry, Inorganic.

3. Metals. QU 375]QP532612’.01524--dc23

2013013974

A catalogue record for this book is available from the British Library.

ISBN-13: 978-1-119-95323-4

Set in 91/2/111/2 pt TimesNewRomanPS by Laserwords (Private) Limited, Chennai, IndiaPrinted and bound in Singapore by Markono Print Media Pte Ltd.

Encyclopedia of Inorganic and Bioinorganic Chemistry

Editorial Board

Editor-in-Chief

Robert A. ScottUniversity of Georgia, Athens, GA, USA

Section Editors

David A. AtwoodUniversity of Kentucky, Lexington, KY, USA

Timothy P. HanusaVanderbilt University, Nashville, TN, USA

Charles M. LukehartVanderbilt University, Nashville, TN, USA

Albrecht MesserschmidtMax-Planck-Institute fur Biochemie, Martinsried, Germany

Robert A. ScottUniversity of Georgia, Athens, GA, USA

Editors-in-Chief Emeritus & Senior Advisors

Robert H. CrabtreeYale University, New Haven, CT, USA

R. Bruce KingUniversity of Georgia, Athens, GA, USA

International Advisory Board

Michael BruceAdelaide, Australia

Tristram ChiversCalgary, Canada

Valeria CulottaMD, USA

Mirek CyglerSaskatchewan, Canada

Marcetta DarensbourgTX, USA

Michel EphritikhineGif-sur-Yvette, France

Robert HuberMartinsried, Germany

Susumu KitagawaKyoto, Japan

Leonard R. MacGillivrayIA, USA

Thomas PoulosCA, USA

David SchubertCO, USA

Edward I. SolomonCA, USA

Katherine ThompsonVancouver, Canada

T. Don TilleyCA, USA

Karl E. WieghardtMulheim an der Ruhr, Germany

Vivian YamHong Kong

Contents

Contributors xi

Series Preface xix

Volume Preface xxi

PART 1: INTRODUCTION 1

Mechanisms Controlling the Cellular Metal Economy 3Benjamin A. Gilston and Thomas V. O’Halloran

PART 2: PROBING METALS AND CROSS TALK IN THE METALLOME 15

The Metallome 17Vadim N. Gladyshev and Yan Zhang

Cyanobacterial Models that Address Cross-Talk in Metal Homeostasis 39Carl J. Patterson, Rafael Pernil, Andrew W. Foster and Nigel J. Robinson

Sparing and Salvaging Metals in Chloroplasts 51Crysten E. Blaby-Haas and Sabeeha S. Merchant

Fluorescent Probes for Monovalent Copper 65M. Thomas Morgan, Pritha Bagchi and Christoph J. Fahrni

Fluorescent Zinc Sensors 85Amy E. Palmer, Jose G. Miranda and Kyle P. Carter

X-Ray Fluorescence Microscopy 99James E. Penner-Hahn

PART 3: MOVING METALS IN CELLS 111

Iron and Heme Transport and Trafficking 113Yvette Y. Yien and Barry H. Paw

Iron in Plants 131Jessica B. Weng and Mary Lou Guerinot

VIII CONTENTS

Transport of Nickel and Cobalt in Prokaryotes 145Thomas Eitinger

Transport Mechanism and Cellular Functions of Bacterial Cu(I)-ATPases 155Jose M. Arguello, Teresita Padilla-Benavides and Jessica M. Collins

Copper Transport in Fungi 163Simon Labbe, Jude Beaudoin and Raphael Ioannoni

Structural Biology of Copper Transport 175Adrian G. Flores, Christopher R. Pope and Vinzenz M. Unger

Zinc Transporters and Trafficking in Yeast 183Yi-Hsuan Wu and David J. Eide

Cadmium Transport in Eukaryotes 195Nathan Smith, Wenzhong Wei and Jaekwon Lee

PART 4: METALS IN REGULATION 207

Metal Specificity of Metallosensors 209Khadine A. Higgins and David P. Giedroc

Metal Homeostasis and Oxidative Stress in Bacillus subtilis 225Zhen Ma and John D. Helmann

Regulation of Manganese and Iron Homeostasis in the Rhizobia and Related α-Proteobacteria 237Mark R. O’Brian

The Iron Starvation Response in Saccharomyces cerevisiae 249Caroline C. Philpott and Pamela M. Smith

Hepcidin Regulation of Iron Homeostasis 265Clara Camaschella and Laura Silvestri

NikR: Mechanism and Function in Nickel Homeostasis 277Michael D. Jones, Andrew M. Sydor and Deborah B. Zamble

Regulation of Copper Homeostasis in Plants 289Marinus Pilon and Wiebke Tapken

Regulation of Zinc Transport 301Taiho Kambe

CONTENTS IX

Selenoproteins—Regulation 311Lucia A. Seale and Marla J. Berry

PART 5: METALS IN CELLULAR DAMAGE AND DISEASE 321

Metals in Bacterial Pathogenicity and Immunity 323Jennifer S. Cavet

Manganese in Neurodegeneration 335Daiana Silva Avila, Robson Luiz Puntel, Felix Antunes Soares, Joao Batista Teixeira da Rocha and Michael Aschner

Iron Sequestration in Immunity 349Colin Correnti and Roland K. Strong

Molecular Basis of Hemochromatosis 361Paul J. Schmidt

Copper in Brain and Neurodegeneration 373Jeffrey R. Liddell, Ashley I. Bush and Anthony R. White

Copper Transporting ATPases in Mammalian Cells 395Nan Yang and Svetlana Lutsenko

Copper in Immune Cells 409Karrera Y. Djoko, Maud E.S. Achard and Alastair G. McEwan

Selenoenzymes and Selenium Trafficking: An Emerging Target for Therapeutics 421William Self and Sarah Rosario

Resistance Pathways for Metalloids and Toxic Metals 429Zijuan Liu, Christopher Rensing and Barry P. Rosen

PART 6: COFACTOR ASSEMBLY 443

Fe–S Cluster Biogenesis in Archaea and Bacteria 445Harsimranjit K. Chahal, Jeff M. Boyd and F. Wayne Outten

Mitochondrial Iron Metabolism and the Synthesis of Iron–Sulfur Clusters 473Andrew Dancis and Paul A. Lindahl

[FeFe]-Hydrogenase Cofactor Assembly 491Eric M. Shepard, Amanda S. Byer, Eric S. Boyd, Kevin D. Swanson, John W. Peters and Joan B. Broderick

[NiFe]-Hydrogenase Cofactor Assembly 507Basem Soboh and R. Gary Sawers

X CONTENTS

Copper in Mitochondria 517Katherine E. Vest and Paul A. Cobine

Mo Cofactor Biosynthesis and Crosstalk with FeS 529Florian Bittner and Ralf R. Mendel

Nitrogenase Cofactor Assembly 543Jared A. Wiig, Chi Chung Lee, Markus W. Ribbe and Yilin Hu

Index 555

Contributors

Maud E.S. Achard University of Queensland, St. Lucia, QLD, Australia• Copper in Immune Cells

Jose M. Arguello Worcester Polytechnic Institute, Worcester, MA, USA• Transport Mechanism and Cellular Functions of

Bacterial Cu(I)-ATPases

Michael Aschner The Kennedy Center for Research on Human Development and the Molecular ToxicologyCenter, Nashville, TN, USA• Manganese in Neurodegeneration

Daiana Silva Avila Universidade Federal do Pampa, Uruguaiana, RS, Brazil• Manganese in Neurodegeneration

Pritha Bagchi Georgia Institute of Technology, Atlanta, GA, USA• Fluorescent Probes for Monovalent Copper

Jude Beaudoin Universite de Sherbrooke, Sherbrooke, QC, Canada• Copper Transport in Fungi

Marla J. Berry University of Hawaii at Manoa, Honolulu, HI, USA• Selenoproteins—Regulation

Florian Bittner Braunschweig University of Technology, Braunschweig, Germany• Mo Cofactor Biosynthesis and Crosstalk with FeS

Crysten E. Blaby-Haas University of California, Los Angeles, CA, USA• Sparing and Salvaging Metals in Chloroplasts

Eric S. Boyd Montana State University, Bozeman, MT, USA• [FeFe]-Hydrogenase Cofactor Assembly

Jeff M. Boyd Rutgers University, New Brunswick, NJ, USA• Fe–S Cluster Biogenesis in Archaea and Bacteria

Joan B. Broderick Montana State University, Bozeman, MT, USA• [FeFe]-Hydrogenase Cofactor Assembly

Ashley I. Bush University of Melbourne, Parkville, VIC, Australia• Copper in Brain and Neurodegeneration

XII CONTRIBUTORS

Amanda S. Byer Montana State University, Bozeman, MT, USA• [FeFe]-Hydrogenase Cofactor Assembly

Clara Camaschella Vita-Salute University and San Raffaele Scientific Institute, Milano, Italy• Hepcidin Regulation of Iron Homeostasis

Kyle P. Carter University of Colorado, Boulder, CO, USA• Fluorescent Zinc Sensors

Jennifer S. Cavet University of Manchester, Manchester, UK• Metals in Bacterial Pathogenicity and Immunity

Harsimranjit K. Chahal Rutgers University, New Brunswick, NJ, USA• Fe–S Cluster Biogenesis in Archaea and Bacteria

Paul A. Cobine Auburn University, Auburn, AL, USA• Copper in Mitochondria

Jessica M. Collins Worcester Polytechnic Institute, Worcester, MA, USA• Transport Mechanism and Cellular Functions of

Bacterial Cu(I)-ATPases

Colin Correnti Fred Hutchinson Cancer Research Center, Seattle, WA, USA• Iron Sequestration in Immunity

Joao Batista Teixeira da Rocha Universidade Federal de Santa Maria, Santa Maria,RS, Brazil• Manganese in Neurodegeneration

Andrew Dancis University of Pennsylvania, Philadelphia, PA, USA• Mitochondrial Iron Metabolism and the Synthesis of Iron–Sulfur Clusters

Karrera Y. Djoko University of Queensland, St. Lucia, QLD, Australia• Copper in Immune Cells

David J. Eide University of Wisconsin-Madison, Madison, WI, USA• Zinc Transporters and Trafficking in Yeast

Thomas Eitinger Humboldt-Universitat zu Berlin, Berlin, Germany• Transport of Nickel and Cobalt in Prokaryotes

Christoph J. Fahrni Georgia Institute of Technology, Atlanta, GA, USA• Fluorescent Probes for Monovalent Copper

Adrian G. Flores Northwestern University, Evanston, IL, USA• Structural Biology of Copper Transport

Andrew W. Foster University of Durham, Durham, UK• Cyanobacterial Models that Address Cross-Talk in Metal Homeostasis

CONTRIBUTORS XIII

David P. Giedroc Indiana University, Bloomington, IN, USA• Metal Specificity of Metallosensors

Benjamin A. Gilston Northwestern University, Evanston, IL, USA• Mechanisms Controlling the Cellular Metal Economy

Vadim N. Gladyshev Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA• The Metallome

Mary Lou Guerinot Dartmouth College, Hanover, NH, USA• Iron in Plants

John D. Helmann Cornell University, Ithaca, NY, USA• Metal Homeostasis and Oxidative Stress in Bacillus subtilis

Khadine A. Higgins Indiana University, Bloomington, IN, USA• Metal Specificity of Metallosensors

Yilin Hu University of California, Irvine, CA, USA• Nitrogenase Cofactor Assembly

Raphael Ioannoni Universite de Sherbrooke, Sherbrooke, QC, Canada• Copper Transport in Fungi

Michael D. Jones University of Toronto, Toronto, ON, Canada• NikR: Mechanism and Function in Nickel Homeostasis

Taiho Kambe Kyoto University, Kyoto, Japan• Regulation of Zinc Transport

Simon Labbe Universite de Sherbrooke, Sherbrooke, QC, Canada• Copper Transport in Fungi

Chi Chung Lee University of California, Irvine, CA, USA• Nitrogenase Cofactor Assembly

Jaekwon Lee University of Nebraska-Lincoln, Lincoln, NE, USA• Cadmium Transport in Eukaryotes

Jeffrey R. Liddell University of Melbourne, Parkville, VIC, Australia• Copper in Brain and Neurodegeneration

Paul A. Lindahl Texas A&M University, College Station, TX, USA• Mitochondrial Iron Metabolism and the Synthesis of Iron–Sulfur Clusters

Zijuan Liu Oakland University, Rochester, MI, USA• Resistance Pathways for Metalloids and Toxic Metals

Svetlana Lutsenko Johns Hopkins University, Baltimore, MD, USA• Copper Transporting ATPases in Mammalian Cells

XIV CONTRIBUTORS

Zhen Ma Cornell University, Ithaca, NY, USA• Metal Homeostasis and Oxidative Stress in Bacillus subtilis

Alastair G. McEwan University of Queensland, St. Lucia, QLD, Australia• Copper in Immune Cells

Ralf R. Mendel Braunschweig University of Technology, Braunschweig, Germany• Mo Cofactor Biosynthesis and Crosstalk with FeS

Sabeeha S. Merchant University of California, Los Angeles, CA, USA• Sparing and Salvaging Metals in Chloroplasts

Jose G. Miranda University of Colorado, Boulder, CO, USA• Fluorescent Zinc Sensors

M. Thomas Morgan Georgia Institute of Technology, Atlanta, GA, USA• Fluorescent Probes for Monovalent Copper

Mark R. O’Brian State University of New York at Buffalo, Buffalo, NY, USA• Regulation of Manganese and Iron Homeostasis in the Rhizobia and Related

α-Proteobacteria

Thomas V. O’Halloran Northwestern University, Evanston, IL, USA• Mechanisms Controlling the Cellular Metal Economy

F. Wayne Outten University of South Carolina, Columbia, SC, USA• Fe–S Cluster Biogenesis in Archaea and Bacteria

Teresita Padilla-Benavides Worcester Polytechnic Institute, Worcester, MA, USA• Transport Mechanism and Cellular Functions of Bacterial Cu(I)-ATPases

Amy E. Palmer University of Colorado, Boulder, CO, USA• Fluorescent Zinc Sensors

Carl J. Patterson University of Durham, Durham, UK• Cyanobacterial Models that Address Cross-Talk in Metal Homeostasis

Barry H. Paw Brigham and Women’s Hospital and Boston Children’s Hospital and Dana-Farber CancerInstitute, Harvard Medical School, Boston, MA, USA• Iron and Heme Transport and Trafficking

James E. Penner-Hahn University of Michigan, Ann Arbor, MI, USA• X-Ray Fluorescence Microscopy

Rafael Pernil University of Durham, Durham, UK• Cyanobacterial Models that Address Cross-Talk in Metal Homeostasis

John W. Peters Montana State University, Bozeman, MT, USA• [FeFe]-Hydrogenase Cofactor Assembly

CONTRIBUTORS XV

Caroline C. Philpott National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes ofHealth, Bethesda, MD, USA• The Iron Starvation Response in Saccharomyces

cerevisiae

Marinus Pilon Colorado State University, Fort Collins, CO, USA• Regulation of Copper Homeostasis in Plants

Christopher R. Pope Northwestern University, Evanston, IL, USA• Structural Biology of Copper Transport

Robson Luiz Puntel Universidade Federal do Pampa, Uruguaiana, RS, Brazil• Manganese in Neurodegeneration

Christopher Rensing University of Copenhagen, Frederiksberg, Denmark• Resistance Pathways for Metalloids and Toxic Metals

Markus W. Ribbe University of California, Irvine, CA, USA• Nitrogenase Cofactor Assembly

Nigel J. Robinson University of Durham, Durham, UK• Cyanobacterial Models that Address Cross-Talk in Metal Homeostasis

Sarah Rosario University of Central Florida, Orlando, FL, USA• Selenoenzymes and Selenium Trafficking: An Emerging Target for Therapeutics

Barry P. Rosen Florida International University, Miami, FL, USA• Resistance Pathways for Metalloids and Toxic Metals

R. Gary Sawers Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany• [NiFe]-Hydrogenase Cofactor Assembly

Paul J. Schmidt Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA• Molecular Basis of Hemochromatosis

Lucia A. Seale University of Hawaii at Manoa, Honolulu, HI, USA• Selenoproteins—Regulation

William Self University of Central Florida, Orlando, FL, USA• Selenoenzymes and Selenium Trafficking: An Emerging Target for Therapeutics

Eric M. Shepard Montana State University, Bozeman, MT, USA• [FeFe]-Hydrogenase Cofactor Assembly

Laura Silvestri Vita-Salute University and San Raffaele Scientific Institute, Milano, Italy• Hepcidin Regulation of Iron Homeostasis

Nathan Smith University of Nebraska-Lincoln, Lincoln, NE, USA• Cadmium Transport in Eukaryotes

XVI CONTRIBUTORS

Pamela M. Smith National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes ofHealth, Bethesda, MD, USA• The Iron Starvation Response in Saccharomyces cerevisiae

Felix Antunes Soares Universidade Federal de Santa Maria, Santa Maria, RS, Brazil• Manganese in Neurodegeneration

Basem Soboh Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany• [NiFe]-Hydrogenase Cofactor Assembly

Roland K. Strong Fred Hutchinson Cancer Research Center, Seattle, WA, USA• Iron Sequestration in Immunity

Kevin D. Swanson Montana State University, Bozeman, MT, USA• [FeFe]-Hydrogenase Cofactor Assembly

Andrew M. Sydor University of Toronto, Toronto, ON, Canada• NikR: Mechanism and Function in Nickel Homeostasis

Wiebke Tapken Colorado State University, Fort Collins, CO, USA• Regulation of Copper Homeostasis in Plants

Vinzenz M. Unger Northwestern University, Evanston, IL, USA• Structural Biology of Copper Transport

Katherine E. Vest Auburn University, Auburn, AL, USA• Copper in Mitochondria

Wenzhong Wei University of Nebraska-Lincoln, Lincoln, NE, USA• Cadmium Transport in Eukaryotes

Jessica B. Weng Dartmouth College, Hanover, NH, USA• Iron in Plants

Anthony R. White University of Melbourne, Parkville, VIC, Australia• Copper in Brain and Neurodegeneration

Jared A. Wiig University of California, Irvine, CA, USA• Nitrogenase Cofactor Assembly

Yi-Hsuan Wu University of Wisconsin-Madison, Madison, WI, USA• Zinc Transporters and Trafficking in Yeast

Nan Yang Johns Hopkins University, Baltimore, MD, USA• Copper Transporting ATPases in Mammalian Cells

Yvette Y. Yien Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA• Iron and Heme Transport and Trafficking

CONTRIBUTORS XVII

Deborah B. Zamble University of Toronto, Toronto, ON, Canada• NikR: Mechanism and Function in Nickel Homeostasis

Yan Zhang Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai,People’s Republic of China• The Metallome

Series Preface

The success of the Encyclopedia of Inorganic Chem-istry (EIC), pioneered by Bruce King, the founding editor-in-chief, led to the 2012 integration of articles from the Handbookof Metalloproteins to create the newly launched Encyclopediaof Inorganic and Bioinorganic Chemistry (EIBC). This hasbeen accompanied by a significant expansion of our Edito-rial Advisory Board with international representation in allareas of inorganic chemistry. It was under Bruce’s successor,Bob Crabtree, that it was recognized that not everyone wouldnecessarily need access to the full extent of EIBC. All EIBCarticles are online and are searchable, but we still recognizedvalue in more concise thematic volumes targeted to a specificarea of interest. This idea encouraged us to produce a series ofEIC (now EIBC) books, focusing on topics of current interest.These will continue to appear on an approximately annualbasis and will feature the leading scholars in their fields, oftenbeing guest coedited by one of these leaders. Like the Encyclo-pedia, we hope that EIBC books continue to provide both thestarting research student and the confirmed research workera critical distillation of the leading concepts and provide astructured entry into the fields covered.

The EIBC books are referred to as ‘‘spin-on’’ books,recognizing that all the articles in these thematic volumesare destined to become part of the online content of EIBC,usually forming a new category of articles in the EIBC topicalstructure. We find that this provides multiple routes to find thelatest summaries of current research.

I fully recognize that this latest transformation ofEIBC is built upon the efforts of my predecessors, Bruce Kingand Bob Crabtree, my fellow editors, as well as the Wileypersonnel, and, most particularly, the numerous authors ofEIBC articles. It is the dedication and commitment of all thesepeople that is responsible for the creation and production ofthis series and the ‘‘parent’’ EIBC.

Robert A. ScottUniversity of Georgia

September 2013

Volume Preface

Our understanding of metals and other trace elementsin cells has witnessed an explosion over recent years. This hasbeen prompted by a combination of new methods to probeintracellular metal locations and the dynamics of metal move-ment in cells, high-resolution detection of metal–biomoleculeinteractions, and the revolution of genomic, proteomic,metabolic, and even ‘‘metallomic’’ approaches to the study ofinorganic physiology. Environmental metals and metalloids,including iron, copper, zinc, cobalt, molybdenum, selenium,and manganese, are all accumulated by cells and organisms inthe micro- to millimolar range. Yet despite this abundant seaof diverse metals, only the correct metal cofactor is matchedwith a partner metalloprotein—mistakes in metal ion biologyrarely occur. At the same time, free metal ions can be detri-mental to cellular components and processes, so systems haveevolved to control carefully the trace element concentrationsand locations (homeostasis). The mechanisms underlying this‘‘perfect’’ handling of metals are the goal of studies of thecell biology of metals.

Metals in Cells covers topics describing recentadvances made by top researchers in the field including:regulated metal ion uptake and trafficking, sensing of metalswithin cells and across tissues, and identification of the vastarray of cellular factors designed to orchestrate assembly ofmetal cofactor sites while minimizing toxic side reactionsof metals. In addition, it features the aspects of metals indisease, including the role of metals in neurodegeneration,liver disease, and inflammation, as a way to highlight thedetrimental effects of mishandling of metal trafficking andresponse to ‘‘foreign’’ metals.

While it is not possible to provide a comprehensivetreatment of transport, homeostasis, sensing, and regulation of

the entire ‘‘biological periodic table,’’ what Metals in Cellsdoes, is give a broad sampling of the current knowledge andresearch frontiers in these areas. The reader will get a sense ofsome of the general principles of biological response to traceelements, but will also marvel at the disparate evolutionaryresponses of different organisms to a variable and changinginorganic environment. One of the ultimate goals in this areais to find the principles of inorganic chemistry in the biologicalresponses.

Metals in Cells also gives an up-to-date descriptionof many of the current tools being used to study inorganic cellbiology. Genetics and biochemistry are combining with morerecent genomic, proteomic, and metallomic approaches. In-creasingly sophisticated microscopy and imaging technologiesprovide information about dynamic distribution of inorganicelements in cells and subcellular compartments. There isyet more room for improvement by collaborative approachesamong physicists, chemists, and biologists.

With the breadth of our recently acquired under-standing of inorganic cell biology, we believe that Metals inCells, featuring key aspects of cellular handling of inorganicelements, is both timely and important. At this point in ourprogress, it is worthwhile to step back and take an expan-sive view of how far our understanding has come, while alsohighlighting how much we still do not know.

Valeria Culotta Robert A. ScottJohns Hopkins University University of GeorgiaBaltimore, MD, USA Athens, GA, USA

September 2013

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PART 1Introduction

Mechanisms Controlling the Cellular Metal EconomyBenjamin A. Gilston and Thomas V. O’Halloran

Northwestern University, Evanston, IL, USA

1 Introduction 32 Understanding the Cellular Metallome 43 Moving Metals Across Cellular Membranes 54 Insights into Iron, Copper, and Zinc

Homeostases 65 Role of Transition Metals in Differentiation and

Development 106 High Metal Quotas in Specialized Cells: Pathogens that

Stand Out 107 Concluding Remarks 108 Acknowledgments 119 Abbreviations and Acronyms 11

10 References 11

1 INTRODUCTION

This book introduces an authoritative and extensiveset of articles on the chemistry of transition metals in cells. Thereader will find several in-depth overviews of progress at theconfluence of several fields. In this brief introductory article,we discuss some emerging concepts and controversial ideas,which are addressed in more detail elsewhere. Biomedicalresearch as an enterprise is undergoing a major shift inunderstanding the roles of transition metals in biology. Ourunderstanding of the cellular roles of transition metals is not aswell developed as, for instance, lipid biology, for a number ofhistorical reasons, the first of which is evident in the etymologyof the word bioinorganic chemistry. The term inorganic ofcourse originates in an archaic grouping of elements; thosefound in living things were classified as organic and thosethat were not were classified as inorganic. Analytical methodsapplied at the cellular level are now revealing a host ofinorganic elements once invisible to science. The legacy ofartificial divisions is clear in other misnomers within thefield. The term ‘‘biological trace elements’’ is commonlyassociated with transition metals, and this usage unfortunatelyobscures the true portrait of how cellular processes are carriedout. As students of biology consider the roles of metals incellular processes, one hurdle they must overcome involvesthe seemingly small number of metal ions that ‘‘trace’’ elementimplies. After all, if something is trace, there is hardly anything

Metals in Cells. Edited by Valeria Culotta and Robert A. Scott. © 2013 John Wiley & Sons, Ltd. ISBN 978-1-119-95323-4

there, and if there is hardly anything there, how important canit be? From the cellular perspective, transition metals areanything but trace elements (Figure 1): intracellular metalssuch as zinc and iron are not present at low levels butare routinely maintained in most cells at surprisingly highlevels (i.e., 0.5 mM) even when cells are grown in a mediumthat has metal concentrations stripped down to nanomolarlevels. In fact, the minimal required metal quotas for zincand iron are so high that they guide major cellular decisionsincluding growth, spore formation, differentiation, or death.Furthermore, a growing body of evidence links disordersin transition metal physiology to neurological disorders andmetabolic and infectious diseases. Such findings underscorethe imperative to establish and test a set of fundamentalprinciples that relate the chemistry and cellular functions oftransition metal ions.

Over the past 20 years, there have been a seriesof breakthroughs describing the structure, properties, mech-anisms, and physiology of metal-trafficking and -sensingmachinery. These studies have helped the biological commu-nity to realize that the subgroup of metallic elements knownas transition metals are much more complex than their distantcousins in the periodic table, namely the essential alkali andalkaline earth metal ions (K, Ca, and Mg). For instance, manywell-trained biomedical researchers would find it difficult todescribe the difference in bonding and reaction chemistry ofthe alkaline earth metal such as magnesium on the one hand

4 METALS IN CELLS

Mg12

[Met

al] to

tal (

mol

L−1

)

1.0

10−1

10−2

Cells grown in MMMM

10−3

10−4

10−5

10−6

10−7

10−8

10−9

K19 Ca20 V23 Cr24 Mn25 Fe26 Co27 Ni28 Cu29 Zn30 Se34 Mo42

Figure 1 Depicted in this graph is the E. coli metallome, that is, the total metal content of the cell. The y-axis corresponds to the moles percellular volume for cells grown in minimal medium and compared with the total metal concentrations in the relevant growth medium. Thesegraphs highlight the high concentrations of transition metal ions with which E. coli cells retain metals from the media they are grown in. Thesemeasurements were obtained using ICP-MS (inductively coupled plasma–mass spectrometry). The unfilled columns represent detection limitsfor low-abundance elements under these experimental conditions. (Reproduced with permission from Ref. 1. © AAAS, 2001.)

and the transition metal manganese on the other. Their reac-tion chemistry is as different as night and day: the former hasone available oxidation state and forms bonds that are strictlyionic in character, that is, nondirectional, whereas the latterhas several accessible oxidation states and forms coordinationbonds that have significant covalent character. This affordsthe transition metal the ability to form complex ions witha wide variety of biopolymer side chains using a variety ofspecific geometries. The case is becoming clear that transitionmetals are employed in regulatory and metabolic circuitriesofthe cell; their functional roles go well beyond catalyticwidgets or a type of ionic glue that helps hold together variousbiopolymers.

A number of discoveries have led the biomedicalresearch community to examine more deeply the chemicalbiology of transition metals. Evidence of the pressure tounderstand the mechanisms of metal homeostasis at themolecular level can be seen in three collective advancesin the field. First is the realization that approximately 30%of the known protein-encoding genes in human and microbialgenomes correspond to transition-metal-dependent proteins.2,3

Second, the number of studies showing disruptions of metalmetabolism associated with human diseases is significantand growing.4–9 Finally, as previously mentioned, it is clearthat intracellular concentrations of metals, such as zinc andiron, are not negligible but in fact are routinely maintainedat much higher levels.1 In order to accomplish this task,a host of cellular machinery is needed to sort out andallocate these reactive species to the appropriate addressin the cell. These insights, as well as the linkage of metalphysiology to toxicology,10,11 neurological disorders,12–16

and metabolic4,6,7 and infectious diseases,17–20 underscore theimperative to establish the fundamental principles governingcellular transition metal ion regulation. Finally, a significantnumber of other connections between human health and

fundamental aspects of metalloregulation have emerged inthe past few years.21–40

In this article, we highlight a few of the emergingthemes in the field of inorganic physiology and as such ouraccount is neither comprehensive nor complete. As an in-troduction to the field, we selected a few key unansweredquestions: how do cells control the overall metal economy fora given growth condition, differentiation state, or variousstages in host–pathogen conflict? What are the common prin-ciples involved in cellular metal sensing, allocation, uptake,storage, and processing? How do the normal metal-trafficking,-sensing, and management processes differ between a baselineand an activated state of any given cell? In order to tacklethese challenging questions, researchers use interrogation ofthe physiochemical mechanisms of the metalloregulatory pro-teins, metallochaperones, from a diverse array of speciesincluding Escherichia coli, Saccharomyces cerevisiae, Musmusculus, and Homo sapiens.

2 UNDERSTANDING THE CELLULARMETALLOME

The total intracellular concentration of essential metalions is referred to as the metallome, a term coined twicein 2001: once to describe the profile of transition metalconcentrations in E. coli grown under metal replete anddepleted conditions,1 and independently by R.J.P. Williams41

in an impressive commentary on the future of metallobiology.When the number of metal ions was considered on a cellvolume basis for E. coli grown under a variety of growthconditions, it became clear that cells maintain tight regulationof the numbers of intracellular metal ions in terms of totalmetal concentration.3,42 The idea that other cell types might

MECHANISMS CONTROLLING THE CELLULAR METAL ECONOMY 5

Periplasm

Chromosome

Zur ZntR+Zn

+Zn Znu genes Znt genes

A+Zn

AC BX

X

YiiP/Fie

ZnuA

ZnuB

ZnuC

Zn(II)

Zn(II)

Zn enzymes andtranscription factors

ZntA

Zn(II)

Figure 2 Here, we show a simplified version of an E. coli cell which uses both transport proteins (ZnuABC and ZntA) and metalloregulatoryproteins (Zur and ZntR) to maintain a steady-state concentration of Zn (II) ions in the cell.46 Metalloregulatory proteins Zur and ZntR functionto repress zinc importer genes (znu genes) and activate zinc exporter genes (znt genes), respectively based on the changing environment ofthe cell.47 Both ZnuA and YiiP were crystallized bound to zinc.48,49 While the YiiP protein has been shown use a proton antiport mechanismto shuttle iron and zinc into the periplasmic space, its regulatory mechanism is unknown.50 (Image prepared in part by Caryn E. Outten,unpublished.)

also maintain similarly high intracellular metal concentrationsis being examined in fungal and mammalian systems aswell.43–45 The question then arises: how does the cellmaintain such tight control over the metal economy andkeep metal quotas constant in the face of metal shortagesand excesses within the growth environment? Some of thefactors that regulate the cellular zinc economy in E. coli areshown in Figure 2; however, overall regulation is perhapsbest understood as a convergence of regulatory networks,structurally specific and energetically tuned metal-traffickingmechanisms, soluble metal receptors, and integral membranetransport systems. Physical characterization of gene regulatoryswitches has led to some general principles and mechanismsthat control metal ion homeostasis in normal and diseasestates.

3 MOVING METALS ACROSS CELLULARMEMBRANES

Recent structural characterization of metal transporterproteins has shed light on the movement of transition

metals across cellular membranes for both prokaryotes andeukaryotes.51 First characterized in 1995, eukaryotic zinctransporters shuttle Zn(II) ions across cell membranes andare classified into two families. ZIP (zinc IRT-like protein)and CDF (cation diffusion facilitator) work in opposition toone another, bringing zinc into and out of the cytoplasm,respectively. To date, 14 members of the ZIP family(Zip 1–14) and 10 members of the CDF family (ZnT1–10) have been identified.52 Interestingly, malfunctionsin the transporters may play a role in diseases such asAlzheimer’s disease,14 type 2 diabetes,53 and zinc deficiencyin breast milk.54 Owing to the importance of these proteins,researchers have set out to characterize structurally thesetransmembrane proteins and understand their mechanismof movement. In 2007, the first CDF member YiiP wasstructurally characterized from E. coli as a homodimer in aY-shaped structure.55 This protein utilized a highly conservednetwork of salt bridges at the dimer interface to position thetransmembrane α-helices for stable movement of Zn(II) ionsacross the membrane.56 Surprisingly, the crystal structurerevealed that the portion of this large protein located inthe cytoplasm contains a metallochaperone-like fold, whichis conserved among many CDF family proteins. Previous