Metallomics and the Cell

Dedication to Ivano Bertini......Page 6
Metal Ions in Life Sciences.......Page 8
Metallomics and the Cell......Page 10
Contents......Page 12
Contributors to Volume 12......Page 18
Titles of Volumes 1-44 in the Metal Ions in Biological Systems Series......Page 22
Contents of Volumes in the Metal Ions in Life Sciences Series......Page 24
Chapter 1: Metallomics and the Cell: Some Definitions and General Comments......Page 38
1 Introduction......Page 39
2 The “Omics” Perspective......Page 40
3 The “Cellular” Perspective......Page 43
4 Towards Systems Biology......Page 44
Abbreviations......Page 46
References......Page 47
Chapter 2: Technologies for Detecting Metals in Single Cells......Page 51
1 Introduction and Scope......Page 52
1.2 Importance of Single Cell and Spatially Resolved Measurement......Page 53
2 Mass Spectrometry......Page 54
2.1 Secondary Ion Mass Spectrometry......Page 55
2.2 Laser Ablation Mass Spectrometry......Page 57
2.4 Examples......Page 58
3.1 Design Considerations for Metal-Specific Fluorophores......Page 60
3.1.1 Metal-Binding Equilibria......Page 61
3.1.2 Other Considerations......Page 62
3.1.4 Endogenous Fluorophores......Page 63
3.3 Examples......Page 64
4 Intrinsic X-Ray Fluorescence......Page 65
4.1 Particle Excitation......Page 66
4.2 X-ray Excitation......Page 67
4.3 Examples......Page 68
4.3.1 Metal Speciation......Page 71
5 Concluding Remarks and Future Directions......Page 73
References......Page 74
Chapter 3: Sodium/Potassium Homeostasis in the Cell......Page 77
1 Introduction......Page 78
2.1 Ionic Properties......Page 79
2.2 Sodium- and Potassium-Dependent Enzymes......Page 81
3 The Membrane Potential......Page 83
3.1 The Action Potential......Page 84
4.1 Uptake of Amino Acids, Sugars, and Transmitters......Page 86
4.2.1 Cell Volume......Page 88
4.2.3 Re-uptake of Inorganic Solutes......Page 89
5.1 The Subunits of the Na +,K + -ATPase......Page 91
5.2 The Structure of the Na +,K + -ATPase......Page 92
5.3 The Mechanism of the Na +,K + -ATPase......Page 93
5.4.1 Posttranslational Modifications......Page 94
5.4.2 Cellular Interactions......Page 95
5.5.1 Cardiotonic Glycosides......Page 96
5.5.2 Palytoxin......Page 97
6 Pathophysiology of Na +,K + -ATPase Disturbance......Page 98
Abbreviations......Page 99
References......Page 100
Chapter 4: Magnesium Homeostasis in Mammalian Cells......Page 104
1 Introduction......Page 105
2 Cellular Mg 2+ Distribution......Page 106
3 Mg 2+ Transport Mechanisms......Page 107
3.1 Channels......Page 108
3.1.1.1 TRPM7:......Page 109
3.1.1.2 TRPM6:......Page 112
3.1.2 Claudins......Page 115
3.1.3 MagT1......Page 116
3.1.5 MMgTs......Page 117
3.2.1 Na + -Dependent Exchanger (Na + /Mg 2+ Exchanger)......Page 118
3.2.3 Mg 2+ /H + Exchange......Page 120
3.3.1 SLC41 (Solute Carrier Family 41)......Page 121
3.3.3 NIPA......Page 123
3.4 Mg 2+ Transport in Purified Plasma Membrane Vesicles......Page 124
4 Regulation of Mg 2+ Transport and Homeostasis......Page 127
4.1.1 Cyclic AMP-Dependent Mg 2+ Extrusion......Page 128
4.1.2 Cyclic AMP-Independent Mg 2+ Extrusion......Page 130
4.1.4 Mg 2+ Homeostasis and ATP......Page 131
4.2.1 Role of Protein Kinase C......Page 133
5 Serum Mg 2+ Level and Mg 2+ -Sensing Mechanism......Page 135
6 Physiological Role of Intracellular Mg 2+......Page 138
6.1 Ca 2+ and K + Channels......Page 139
6.2 Mitochondrial Dehydrogenases......Page 140
6.4 Cell pH and Volume......Page 142
7 Conclusions......Page 143
Abbreviations......Page 144
References......Page 146
Chapter 5: Intracellular Calcium Homeostasis and Signaling......Page 154
1 Introduction......Page 155
2 Distinctive Properties of the Ca 2+ Signal......Page 158
3 The Ambivalent Nature of the Ca 2+ Signal......Page 160
4 Regulation of the Ca 2+ Signal by Ca 2+ Buffering and Ca 2+ Sensor Proteins......Page 162
5.1.1 The Voltage-Gated Channels......Page 168
5.1.2 The Receptor-Operated Channels......Page 171
5.1.3 The Store-Operated Ca 2+ Entry channels......Page 172
5.1.4 Transient Receptor Potential Channels......Page 173
5.1.5 The Intracellular Ca 2+ Channels......Page 174
5.2 Ca 2+ Pumps......Page 175
5.3 The Plasma Membrane Na + /Ca 2+ Exchanger......Page 181
6.1 Mitochondria......Page 184
6.2 The Acidic Compartments......Page 188
6.3 Ca 2+ Regulation in the Nucleus: An Open Problem......Page 189
7 Physiology of the Ca 2+ Signal: A Selection of Cellular Processes Controlled by Ca 2+......Page 190
Abbreviations......Page 195
References......Page 197
Chapter 6: Manganese Homeostasis and Transport......Page 204
1 Introduction......Page 205
2 Manganese Transport......Page 206
2.1 Divalent Metal Transporter 1......Page 207
2.2 ZIP-Dependent Uptake of Manganese......Page 212
2.3 Calcium(II) Channel-Dependent Transport of Manganese......Page 213
2.4 Manganese Efflux......Page 214
3.1 Mitochondria, Dopamine, and Manganese-Induced Neurotoxicity......Page 215
3.3 Manganese and Apoptosis......Page 218
3.4 Effects of Manganese on DNA......Page 219
3.6 Manganese Nanoparticles......Page 220
3.7 Manganese and Cytoplasmic Inclusions......Page 221
3.8 Manganese and Dopaminergic Circuitry......Page 222
3.9 Manganese and Microglia......Page 223
4 Manganese and Genetics......Page 224
5 Concluding Remarks......Page 227
ABBREVIATIONS AND DEFINITIONS......Page 228
References......Page 229
Chapter 7: Control of Iron Metabolism in Bacteria......Page 237
1 Introduction......Page 238
2 Life Is Wedded to Iron – For Better or for Worse......Page 239
3.1.1 Introduction......Page 240
3.1.2 Siderophore Receptors......Page 242
3.1.3 The TonB-ExbB-ExbD System......Page 244
3.1.4 Transport across the Periplasm and Cytoplasmic Membranes......Page 245
3.1.6 The Ferric Dicitrate System of E. coli – an Example......Page 246
3.2.1 The FeoABC System. G-Protein-Coupled Transport......Page 247
3.2.2 ZIP-Like Transporters......Page 248
3.2.4 The EfeUOB System of E. coli......Page 249
3.2.6 Metal ABC Systems......Page 251
4.2 Ferritins and Bacterioferritins......Page 252
5.1 Cellular Iron and the ‘Iron Proteome’......Page 254
5.2.1 Introduction......Page 255
5.2.2 The Fur Modulon and Global Control......Page 256
5.4 Fur Family Members......Page 259
5.5.1 DtxR-IdeR......Page 260
6 Iron Replacement......Page 261
7.2.1 Transferrin and Lactoferrin as Iron Sources......Page 262
7.2.2 Heme as an Iron Source......Page 263
8 Final Remarks......Page 264
Abbreviations......Page 265
References......Page 266
Chapter 8: The Iron Metallome in Eukaryotic Organisms......Page 274
1 Introduction......Page 275
2.1 Intracellular Concentrations, Oxidation State, and Speciation......Page 276
2.2 Subcellular Distribution......Page 278
2.3.1 Bioavailability......Page 279
2.3.2 Intracellular Labile Iron Pools......Page 280
2.4.1 Oxidative Stress and Formation of Reactive Oxygen Species......Page 281
3.1.1 Heme-Containing Proteins......Page 282
3.1.2 Iron-Sulfur Cluster-Containing Proteins......Page 283
3.2.1 Assembly and Insertion of Heme Cofactors......Page 284
3.2.2 Assembly and Insertion of Iron-Sulfur Clusters......Page 286
3.2.3 Assembly and Insertion of Non-Heme Iron Cofactors......Page 290
4.1.1 Iron Uptake and Transport in S. cerevisiae......Page 291
4.1.2 Iron Uptake and Transport in Mammalian Cells......Page 293
4.3.1 Yeast Vacuoles......Page 295
4.3.4 Nucleus......Page 296
5.1.1.2 S. cerevisiae Aft1/Aft2:......Page 297
5.1.1.3 S. cerevisiae Yap5:......Page 298
5.2.1 Iron-Responsive mRNA-Binding Proteins in Yeast......Page 299
5.2.2 Iron-Responsive mRNA-Binding Proteins in Mammalian Cells......Page 300
5.3.1 Post-Translational Iron Regulation in S. cerevisiae......Page 301
5.3.2.1 Hepcidin:......Page 302
5.3.2.3 FBXL5 Regulation of IRP2:......Page 304
6 Concluding Remarks and Future Directions......Page 305
Abbreviations......Page 306
References......Page 307
Chapter 9: Heme Uptake and Metabolism in Bacteria......Page 312
1 Introduction......Page 313
2.1 d-Aminolevulinic Acid, the First Committed Precursor for Tetrapyrroles......Page 314
3.1 Heme Sources......Page 317
3.2 Heme Scavenging from the Extracellular Milieu......Page 318
3.2.1.2 Outer Membrane Receptor Proteins:......Page 319
3.2.1.3 Structure and Properties of the Hemophore HasA:......Page 321
3.2.1.4 The Heme Loading Mechanism of HasA:......Page 323
3.2.1.6 A Model for Delivery of Heme from HasAs to HasR:......Page 325
3.2.1.7 Heme Uptake by Porphyromonas gingivalis May Involve Hemophores:......Page 327
3.2.1.8 HxuA from Haemophilus influenzae Is also a Hemophore:......Page 328
3.2.2.1 Staphylococcus aureus:......Page 329
3.2.2.3 Structural Characterization of S . aureus NEAT Domains:......Page 330
3.2.2.4 On the Mechanism of Hemin Acquisition from Methemoglobin by IsdH:......Page 332
3.2.2.5 The Mechanism of Hemin Transfer:......Page 333
3.2.2.6 Bacillus anthracis:......Page 335
3.2.2.7 Streptococcus pyogenes:......Page 336
3.3.1 Periplasmic-Binding Proteins......Page 337
3.3.1.1 Structurally Characterized Heme-Binding Periplasmic-Binding Proteins Belong to Class III:......Page 339
3.3.1.2 Are Class III Periplasmic-Binding Proteins Flexible?......Page 341
3.3.2 Across the Inner Membrane in Gram-Negative Bacteria......Page 342
4.1.1 Heme Degradation in Gram-Negative Bacteria......Page 345
4.1.1.1 The Catalytic Cycle of Heme Degradation by Canonical Heme Oxygenase:......Page 346
4.1.1.2 Activation of Heme Reactivity by Canonical Heme Oxygenase:......Page 347
4.1.1.3 The Different Nature of the Coupled Oxidation versus Heme Oxygenation Reactions:......Page 349
4.1.1.4 The Regioselectivity of Heme Oxidation:......Page 350
4.1.2 Heme Degradation in Gram-Positive Bacteria......Page 352
4.1.3 Does a Bacterial Dechelatase exist?......Page 353
4.2 Cytosolic Heme Chaperones......Page 354
5 Conclusions and Outlook......Page 356
Abbreviations......Page 357
References......Page 358
Chapter 10: Cobalt and Corrinoid Transport and Biochemistry......Page 366
2.1 Cobalt Transporters......Page 367
2.2 Corrinoid Transport and Metabolism in Bacteria......Page 369
2.3 Cobalamin Transport in Eukaryotes......Page 375
3.1 Nitrile Hydratase......Page 376
3.2 Methionine Aminopeptidase......Page 381
4.1 Methylmalonyl-Coenzyme A Mutase......Page 384
4.2 Isobutyryl-Coenzyme A Mutase......Page 387
4.3 Novel Activities Catalyzed by Coenzyme B 12 -Dependent Isomerases......Page 389
5.1 Organization and Common Features of G-Proteins Belonging to the G3E Family......Page 391
5.2 MeaB Is a Chaperone for Methylmalonyl-Coenzyme A Mutase......Page 395
5.3 Biochemical Properties of MMAA, a Human Ortholog of MeaB......Page 396
5.4 The Chaperoning Role of MeaB: The Interplay between Three Proteins......Page 397
Abbreviations and Definitions......Page 399
References......Page 401
Chapter 11: Nickel Metallomics: General Themes Guiding Nickel Homeostasis......Page 408
1 Introduction......Page 409
1.1 The Chemistry of Nickel......Page 410
2 Nickel Transport......Page 411
2.1.2 Secondary Nickel Transporters......Page 412
2.2 Nickel Export......Page 414
3.1 [NiFe]-Hydrogenase......Page 415
3.1.1 HypA......Page 417
3.1.2 HypB......Page 418
3.1.3 SlyD......Page 419
3.2 Urease......Page 420
3.2.1 UreE......Page 421
3.3 Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase......Page 422
3.4 Superoxide Dismutase......Page 424
3.6 Glyoxalase I......Page 425
4 Nickel Storage Proteins......Page 426
5 Nickel-Based Genetic Regulation......Page 427
5.1.1 E. coli NikR......Page 428
5.1.2 H. pylori NikR......Page 429
5.2 RcnR......Page 430
5.4 Nur......Page 431
5.5 Additional Nickel-Responsive Genetic Regulators......Page 433
6 The View From The Top......Page 434
Abbreviations and Definitions......Page 440
References......Page 441
Chapter 12: The Copper Metallome in Prokaryotic Cells......Page 450
1 Evolution of Copper Use and Homeostasis in Prokaryotes......Page 451
2 Prokaryotic Copper Uptake......Page 453
3 Copper Proteins......Page 455
3.1 Cytochrome Oxidase......Page 456
3.2 Multicopper Oxidases......Page 457
3.3 Plastocyanin/Azurin Family of Blue (Type 1) Copper Proteins......Page 458
3.5 Methane Monooxygenases......Page 459
3.6 Enzymes Involved in Nitrogen Metabolism......Page 461
4.1 P 1B -Type ATPases......Page 462
4.2 Cus-Like Resistance-Nodulation Cell Division Systems......Page 464
4.3 CueP and Other Periplasmic Systems......Page 466
4.4 Pco-Like Systems......Page 467
5.1 Copper-Dependent Transcriptional Activators......Page 468
5.2 Copper-Dependent Transcriptional Repressors......Page 469
5.3 Two-Component Regulatory Systems......Page 471
6 Copper Omics......Page 472
7 Concluding Remarks and Future Directions......Page 474
Abbreviations......Page 475
References......Page 476
Chapter 13: The Copper Metallome in Eukaryotic Cells......Page 484
1 Overview of Copper Homeostasis in Eukaryotic Cells......Page 485
2 Copper Homeostasis: Saccharomyces cerevisiae......Page 486
2.2 Membrane Transporters......Page 487
2.3 Copper Chaperones......Page 489
2.4 Sequestration and Regulation......Page 491
3 Copper Homeostasis: Mammals......Page 492
3.1 Mammalian Copper Transport......Page 493
3.2 Copper Chaperones......Page 496
3.3 Mammalian Copper Enzymes......Page 497
3.5 Sequestration and Regulation......Page 499
4 Copper Homeostasis: Photosynthetic Organisms......Page 500
Abbreviations......Page 503
References......Page 504
Chapter 14: Zinc and the Zinc Proteome......Page 512
1 Introduction......Page 513
2.3 Impact......Page 514
3.2 Signatures of Zinc-Binding Sites in Proteins......Page 515
3.3 Zinc Proteomes......Page 518
4.1 Catalytic Zinc......Page 523
5.1 The Proteins Controlling Cellular Zinc Homeostasis......Page 524
5.2 Zinc Buffering and Muffling......Page 526
5.3 Zinc(II) Ions in Cellular Regulation......Page 527
6.1 Quantitative Zinc Proteomics......Page 528
6.3 Functional Zinc Proteomics......Page 529
6.4 Evolution of Zinc Proteomes......Page 530
References......Page 531
Chapter 15: Metabolism of Molybdenum......Page 535
1 Introduction......Page 536
2.1 Molybdenum Uptake......Page 537
2.2 The Molybdenum Cofactor......Page 539
2.3.1 Step 1: Conversion of Guanosine 5'-Triphosphate to Cyclic Pyranopterin Monophosphate......Page 540
2.3.3 Step 3: Adenlyation of Molybdopterin......Page 541
2.3.4 Step 4: Molybdenum Insertion and Crosstalk to Copper Metabolism......Page 542
2.4 Storage, Transfer and Insertion of the Molybdenum Cofactor......Page 543
3 Molybdenum Enzymes......Page 545
3.2 Sulfite Oxidase......Page 546
3.4 Xanthine Oxidoreductase......Page 547
3.6 Post-translational Sulfuration of Xanthine Oxidoreductase and Aldehyde Oxidase......Page 548
4.1 Molybdenum Deficiencies in Plants......Page 549
5 Molybdenum Metabolism Is Linked to Iron Metabolism......Page 550
6.1 Molybdenum versus Tungsten......Page 551
6.3 Metal Enzymes and Pterin-Based Cofactors for Molybdenum and Tungsten......Page 552
6.4 Iron Molybdenum Cofactor and Nitrogenase......Page 554
Abbreviations and Definitions......Page 555
References......Page 556
Chapter 16: Comparative Genomics Analysis of the Metallomes......Page 561
1 Introduction......Page 562
2.1 Identification of Metal Utilization Traits and Metalloprotein Families......Page 564
2.3 Comparative Analyses of Metal Utilization and Interaction......Page 566
3.1 Molybdenum Transport and Molybdenum Cofactor Biosynthesis......Page 567
3.2 Molybdoenzymes......Page 570
3.3 Comparative Genomics of Molybdenum Utilization......Page 572
4.1 Overview of Copper Trafficking and Homeostasis......Page 575
4.2 Cuproproteins......Page 579
4.3 Comparative Genomics of Copper Utilization......Page 583
5.1 Nickel and Cobalt Uptake......Page 585
5.2 Nickel-Dependent Proteins......Page 588
5.3.1 Vitamin B 12 Uptake and Biosynthesis......Page 589
5.3.2 Vitamin B 12 -Dependent Proteins......Page 590
5.4 Comparative Genomics of Nickel, Cobalt, and Vitamin B 12 Utilization......Page 594
6.1 Comparative Genomics of Zinc-Dependent Metalloproteomes......Page 597
6.2 Advances in Comparative Genomics of Other Metals......Page 599
7 Comparative Genomics of Metal Dependency in Biology......Page 600
Abbreviations and Definitions......Page 604
References......Page 606
Index......Page 613