Iron-Sulfur Clusters in Chemistry and Biology (eBook)

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Tracey Rouault, NIH Bethesda, Maryland, USA

Contents 9
Preface 5
Contributing authors 21
1 Iron-sulfur proteins: a historical perspective 25
1.1 Framing the scene 25
1.2 The early days of “nonheme iron” 25
1.3 Of proteins and analogues 26
1.4 Beyond electron shuttles 30
1.5 How are FeS clusters synthesized in cells? 31
Acknowledgment 32
References 32
2 Chemistry of iron-sulfur clusters 35
2.1 Introduction 35
2.2 Electronic structure of Fe-S complexes 36
2.2.1 Spin-polarization and strong metal-ligand bonds 36
2.2.2 Spin-coupling and metal-metal bonds 38
2.2.3 Spin resonance delocalization in mixed-valence iron pairs 38
2.3 Unique properties of Fe-S clusters 39
2.3.1 Stable rigid clusters mean low reorganization energy 39
2.3.2 Polynuclear clusters mean multiple valency 40
2.3.3 Resonance delocalization and [Fe4S4(Cys)4] cluster conversion 40
2.4 Summary 42
Acknowledgments 42
References 42
3 Quantitative interpretation of EPR spectroscopy with applications for iron-sulfur proteins 45
3.1 Introduction 45
3.2 Basic EPR theory 46
3.3 g Factor anisotropy 48
3.4 Hyperfine structure 48
3.5 Ligand interactions 50
3.6 Spin Hamiltonian 51
3.7 Basic EPR instrumentation 52
3.8 Simulation of powder spectra 53
3.9 Quantitative aspects 55
3.10 Examples 57
3.10.1 S = 1/2 systems 57
3.10.2 Spin systems with S = 3/2, 5/2, 7/2, etc. 61
3.10.3 Spin systems with S = 1, 2, 3, etc 66
3.11 Conclusion 70
References 70
4 The utility of Mössbauer spectroscopy in eukaryotic cell biology and animal physiology 73
4.1 Introduction 73
4.2 Transitions associated with MBS 73
4.3 Coordination chemistry of iron 75
4.4 Electron spin angular momentum and EPR spectroscopy 77
4.5 High-spin vs low-spin FeII and FeIII complexes 77
4.6 Isomer shift (d) and quadrupole splitting (.EQ) 77
4.7 Effects of a magnetic field 78
4.8 Slow vs fast relaxation limit 79
4.9 MB properties of individual Fe centers found in biological systems 80
4.10 Magnetically interacting Fe aggregates 82
4.11 Insensitivity of MBS and a requirement for 57Fe enrichment 83
4.12 Invariance of spectral intensity among Fe centers 84
4.12.1 Mitochondria 84
4.12.2 Vacuoles 87
4.12.3 Whole yeast cells 88
4.12.4 Human mitochondria and cells 89
4.12.5 Blood 89
4.12.6 Heart 91
4.12.7 Liver 91
4.12.8 Spleen 92
4.12.9 Brain 92
4.13 Limitations of MBS and future directions 94
Acknowledgments 95
References 96
5 The interstitial carbide of the nitrogenase M-cluster: insertion pathway and possible function 101
5.1 Introduction 101
5.2 Proposed role of NifB in carbide insertion 103
5.3 Accumulation of a cluster intermediate on NifB 104
5.4 Investigation of the insertion of carbide into the M-cluster 106
5.5 Tracing the fate of carbide during substrate turnover 109
References 110
6 The iron-molybdenum cofactor of nitrogenase 113
6.1 Introduction 113
6.2 The metal clusters of nitrogenase 114
6.3 Structure of FeMoco 115
6.4 Redox properties of FeMoco 117
6.5 An overlooked detail: the central light atom 118
6.6 The nature of X 120
6.7 Insights into the electronic structure of FeMoco 124
6.8 A central carbon – consequences and perspectives 125
Acknowledgments 127
References 127
7 Biotin synthase: a role for iron-sulfur clusters in the radical-mediated generation of carbon-sulfur bonds 131
7.1 Introduction 131
7.2 Sulfur atoms in biomolecules 132
7.3 Biotin chemistry and biosynthesis 133
7.4 The biotin synthase reaction 135
7.5 The structure of biotin synthase and the radical SAM superfamily 137
7.6 The [4Fe-4S]2+ cluster and the radical SAM superfamily 141
7.7 The [2Fe-2S]2+ cluster and the sulfur insertion reaction 144
7.8 Characterization of an intermediate containing 9-MDTB and a [2Fe-2S]+ cluster 145
7.9 Other important aspects of the biotin synthase reaction 146
7.10 A role for iron-sulfur cluster assembly in the biotin synthase reaction 147
7.11 Possible mechanistic similarities with other sulfur insertion radical SAM enzymes 149
Acknowledgment 151
References 151
8 Molybdenum-containing iron-sulfur enzymes 157
8.1 Introduction 157
8.2 The xanthine oxidase family 158
8.2.1 D. gigas aldehyde:ferredoxin oxidoreductase 159
8.2.2 Bovine xanthine oxidoreductase 161
8.2.3 Aldehyde oxidases 169
8.2.4 CO dehydrogenase 172
8.2.5 4-Hydroxybenzoyl-CoA reductase 176
8.3 The DMSO reductase family 177
8.3.1 DMSO reductase and DMS dehydrogenase 179
8.3.2 Polysulfide reductase 189
8.3.3 Ethylbenzene dehydrogenase 193
8.3.4 Formate dehydrogenases 194
8.3.5 Bacterial nitrate reductases 204
8.3.6 Arsenite oxidase and arsenate reductase 212
8.3.7 Pyrogallol:phloroglucinol transhydroxylase 216
8.4 Prospectus 218
References 219
9 The role of iron-sulfur clusters in the biosynthesis of the lipoyl cofactor 235
9.1 Introduction 235
9.2 Discovery of LA 235
9.3 Functions of the lipoyl cofactor 236
9.3.1 Primary metabolism 236
9.3.2 Antioxidant 238
9.4 Pathways for lipoyl cofactor biosynthesis 239
9.4.1 Exogenous pathway 239
9.4.2 Endogenous pathway 240
9.5 Characterization of LipA 241
9.5.1 Discovery of LipA 241
9.5.2 In vivo characterization of LipA 241
9.5.3 LipA is an iron-sulfur enzyme 243
9.5.4 LipA is an RS enzyme 244
9.5.5 Product inhibition of LipA 248
9.5.6 LipA contains two [4Fe-4S] clusters 249
9.5.7 Two distinct roles for the iron-sulfur clusters 250
9.5.8 A unique intermediate 251
9.5.9 A proposed mechanism for the biosynthesis of the lipoyl cofactor 253
9.6 Conclusions 255
Acknowledgment 255
References 255
10 Iron-sulfur clusters and molecular oxygen: function, adaptation, degradation, and repair 263
10.1 Introduction 263
10.2 Fe-S clusters – reasons for their abundance 264
10.2.1 Origin of Fe-S clusters 264
10.2.2 Functions of Fe-S clusters 265
10.3 Oxygen and Fe-S clusters 267
10.3.1 Properties of molecular oxygen and its partially reduced species 267
10.3.2 Oxidative damage to Fe-S clusters 269
10.3.3 Molecular mechanisms of oxidative damage to Fe4S4 clusters 270
10.3.4 Fe3S4 to Fe2S2 cluster conversion in FNR 271
10.3.5 X-ray crystallographic studies 271
10.3.6 Alternative reactions can occur and compete 273
10.3.7 Structural changes 274
10.4 Adaptation to oxygen 274
10.4.1 Switch between metabolisms or restriction to niches 276
10.4.2 O2-tolerant NiFe hydrogenases 277
10.4.3 Protective systems against ROS 280
10.4.4 Evolutionary replacement of Fe-S clusters to keep essential functions in aerobic organisms 281
10.5 Conclusions 282
References 283
11 A retrospective on the discovery of [Fe-S] cluster biosynthetic machineries in Azotobacter vinelandii 291
11.1 Introduction 291
11.2 An introduction to nitrogenase 293
11.3 Approaches to identify gene-product and product-function relationships 297
11.4 FeMoco and development of the scaffold hypothesis for complex [Fe-S] cluster formation 297
11.5 An approach for the analysis of nif gene product function 300
11.5.1 Phenotypes associated with loss of NifS or NifU function indicate their involvement in nitrogenase-associated [Fe-S] cluster formation 301
11.5.2 NifS is a cysteine desulfurase 302
11.5.3 Extension of the scaffold hypothesis to NifU function 306
11.5.4 Discovery of isc system for [Fe-S] cluster formation and functional cross-talk among [Fe-S] cluster biosynthetic systems 312
11.6 The Isc system is essential in A. vinelandii 314
11.7 There is limited functional cross-talk between the Nif and Isc systems 315
11.8 Closing remarks 316
Acknowledgments 316
References 316
12 A stress-responsive Fe-S cluster biogenesis system in bacteria – the suf operon of Gammaproteobacteria 321
12.1 Introduction to Fe-S cluster biogenesis 321
12.2 Sulfur trafficking for Fe-S cluster biogenesis 322
12.3 Iron donation for Fe-S cluster biogenesis 323
12.4 Fe-S cluster assembly and trafficking 325
12.5 Iron and oxidative stress are intimately intertwined 327
12.6 Stress-response Fe-S cluster biogenesis in E. coli 330
12.7 Sulfur trafficking in the stress-response Suf pathway 331
12.8 Stress-responsive iron donation for the Suf pathway 335
12.8.1 SufD 335
12.8.2 Iron storage proteins 337
12.8.3 Other candidates 338
12.9 Unanswered questions about Suf and Isc roles in E. coli 339
Acknowledgment 339
References 340
13 Sensing the cellular Fe-S cluster demand: a structural, functional, and phylogenetic overview of Escherichia coli IscR 349
13.1 Introduction 349
13.2 General properties of IscR 350
13.3 [2Fe-2S]-IscR represses Isc expression via a negative feedback loop 352
13.4 IscR adjusts synthesis of the Isc pathway based on the cellular Fe-S demand 354
13.5 IscR has a global role in maintaining Fe-S homeostasis 356
13.6 Fe-S cluster ligation broadens DNA site specificity for IscR 357
13.7 Phylogenetic analysis of IscR 359
13.8 Binding to two classes of DNA sites allows IscR to differentially regulate transcription in response to O2 363
13.9 Roles of IscR beyond Fe-S homeostasis 365
13.10 Additional aspects of IscR regulation 365
13.11 Summary 366
Acknowledgments 366
References 366
14 Fe-S assembly in Gram-positive bacteria 371
14.1 Introduction 371
14.2 Fe-S proteins in Gram-positive bacteria 371
14.3 Fe-S cluster assembly orthologous proteins 373
14.3.1 Clostridia-ISC system 373
14.3.2 Actinobacteria-SUF 378
14.3.3 Bacilli-SUF 379
14.4 Concluding remarks and remaining questions 386
References 387
15 Fe-S cluster assembly and regulation in yeast 391
15.1 Introduction 391
15.2 Yeast and Fe-S cluster assembly – evolutionary considerations 391
15.2.1 Nfs1 and the surprise of Isd11 392
15.2.2 Scaffold proteins in yeast mitochondria 393
15.2.3 Frataxin’s roles throughout evolution 394
15.2.4 Ssq1 is a specialized Hsp70 chaperone arising by convergent evolution 395
15.2.5 Atm1 and CIA components 395
15.2.6 Yeast components are conserved with their human counterparts 396
15.2.7 Yeast Fe-S cluster assembly mutants modeling aspects of human diseases 397
15.3 Yeast genetic screens pointing to the Fe-S cluster assembly apparatus 398
15.3.1 Misregulation of iron uptake 398
15.3.2 Suppression of µsod1 amino acid auxotrophies 399
15.3.3 tRNA modification and the SPL1-1 allele 400
15.3.4 tRNA thiolation and resistance to killer toxin 400
15.3.5 Cytoplasmic aconitase maturation 400
15.3.6 Ribosome assembly 401
15.3.7 Synthetic lethality with the pol3-13 allele 401
15.3.8 Factors needed for Yap5 response to high iron 402
15.3.9 Screening of essential genes coding for mitochondrial proteins 403
15.4 Mitochondrial Fe-S cluster assembly 403
15.4.1 Mitochondrial cysteine desulfurase 405
15.4.2 Formation of the Isu Fe-S cluster intermediate in mitochondria 409
15.4.3 Roles of frataxin 410
15.4.4 Bypass mutation in Isu 411
15.4.5 Transfer of the mitochondrial Isu Fe-S cluster intermediate 412
15.4.6 Role of Grx5 412
15.4.7 The switch between cluster synthesis and cluster transfer 413
15.5 Role of glutathione 414
15.5.1 Glutathione and monothiol glutaredoxins in mitochondria 415
15.5.2 Glutathione and monothiol glutaredoxins Grx3 and Grx4 outside of mitochondria 416
15.6 Role of Atm1, an ABC transporter of the mitochondrial inner membrane 417
15.6.1 Cells lacking Atm1 lose mtDNA 418
15.7 Relationship between Fe-S cluster biogenesis and iron homeostasis 420
15.8 Conclusion and missing pieces 426
Acknowledgments 427
References 427
16 The role of Fe-S clusters in regulation of yeast iron homeostasis 435
16.1 Introduction 435
16.2 Iron acquisition and trafficking in yeast 435
16.3 Regulation of iron homeostasis in S. cerevisiae 438
16.3.1 Aft1/Aft2 low-iron transcriptional regulators and target genes 438
16.3.2 Yap5 high-iron transcriptional regulator and target genes 440
16.3.3 Links among mitochondrial Fe-S cluster biogenesis, the Grx3/Grx4/ Fra2/Fra1 signaling pathway, and Aft1/Aft2 regulation 441
16.3.4 Fe-S cluster binding by Grx3/4 and Fra2 is important for their function in S. cerevisiae iron regulation 442
16.3.5 Working model for Fe-dependent regulation of Aft1/2 via the Fra1/Fra2/ Grx3/Grx4 signaling pathway 444
16.3.6 Yap5 regulation and mitochondrial Fe-S cluster biogenesis 446
16.4 Regulation of iron homeostasis in S. pombe 447
16.4.1 Fep1 and Php4 transcriptional repressors and target genes 447
16.4.2 Roles for Grx4 in regulation of Fep1 and Php4 activity 450
16.4.3 Molecular basis of iron-dependent control of Fep1 activity 452
16.4.4 Molecular basis of iron-dependent control of Php4 activity 453
16.5 Summary 454
Acknowledgments 455
References 455
17 Biogenesis of Fe-S proteins in mammals 461
17.1 Introduction 461
17.2 The Fe-S regulatory switch of IRP1 461
17.3 IRP2, a highly homologous gene, also post-transcriptionally regulates iron metabolism, but iron sensing occurs through the regulation of its degradation rather than through an Fe-S switch mechanism 465
17.4 Identification of the mammalian cysteine desulfurase and two scaffold proteins: implications for compartmentalization of the process 466
17.5 Sequential steps in Fe-S biogenesis – an initial Fe-S assembly process on a scaffold, followed by Fe-S transfer to recipient proteins, aided by a chaperone-co-chaperone system 467
17.6 Mitochondrial iron overload in response to defects in Fe-S biogenesis raises important questions about how mitochondrial iron homeostasis is regulated 470
17.7 Perspectives and future directions 471
References 472
18 Iron-sulfur proteins and human diseases 479
18.1 Introduction 479
18.2 Oxidative susceptibility of Fe-S proteins 480
18.2.1 Aconitases: targets of oxidative stress in disease and aging 482
18.3 Diseases associated with genetic defects in Fe-S proteins 485
18.3.1 Mitochondrial respiratory complexes and human diseases 485
18.3.2 FECH deficiency causes erythropoietic protoporhyria (MIM 177000) 490
18.3.3 DNA repair Fe-S proteins and human disorders 491
18.4 Diseases associated with genetic defects in Fe-S cluster biogenesis 493
18.4.1 A GAA trinucleotide repeat expansion in FXN is the major cause of the neurodegenerative disorder Friedreich ataxia 496
18.4.2 Mutations in ABCB7 cause X-linked sideroblastic anemia with ataxia 500
18.4.3 Mutations in glutaredoxin 5 cause an autosomal recessive pyridoxine-refractory sideroblastic anemia 501
18.4.4 Mutations in ISCU cause myopathy with lactic acidosis (MIM 255125) 502
18.4.5 NUBPL mutations cause childhood-onset mitochondrial encephalomyopathy and respiratory complex I deficiency (MIM252010) 505
18.4.6 Mutations in NFU1 cause multiple mitochondrial dysfunctions syndrome 1 (MIM 605711) 506
18.4.7 Mutations in BOLA3 cause multiple mitochondrial dysfunctions syndrome 2 (MIM 614299) 509
18.4.8 IBA57 deficiency causes severe myopathy and encephalopathy 510
18.4.9 A mutation in ISD11 causes deficiencies of respiratory complexes 510
18.5 Fe-S cluster biogenesis and iron homeostasis 511
18.6 Therapeutic strategies 512
Acknowledgments 514
References 514
19 Connecting the biosynthesis of the molybdenum cofactor, Fe-S clusters, and tRNA thiolation in humans 537
19.1 Introduction 537
19.2 Pathways for the formation of Moco and thiolated tRNAs in humans 539
19.2.1 Moco biosynthesis in mammals 539
19.2.2 The role of tRNA thiolation in the cell 549
19.3 The connection between sulfur-containing biomolecules and their distribution in different compartments in the cell 551
19.3.1 Sulfur transfer in mitochondria 551
19.3.2 Sulfur transfer in the cytosol 553
19.3.3 Role of NFS1, ISD11, URM1, and MOCS2A in the nucleus 556
Acknowledgments 558
References 558
20 Iron-sulfur proteins and genome stability 565
20.1 Introduction 565
20.2 The importance of genome stability 565
20.3 Link between FeS cluster biogenesis and genome stability 566
20.4 FeS proteins in DNA replication 568
20.4.1 DNA primase and DNA polymerase a 569
20.4.2 DNA polymerases d and e 570
20.4.3 DNA2 571
20.5 FeS proteins in DNA repair 572
20.5.1 DNA glycosylases 573
20.5.2 The Rad3 family of helicases 575
20.6 Summary 579
References 579
21 Eukaryotic iron-sulfur protein biogenesis and its role in maintaining genomic integrity 565
21.1 Introduction 587
21.2 Biogenesis of mitochondrial Fe-S proteins 592
21.2.1 Step 1: De novo Fe-S cluster assembly on the Isu1 scaffold protein 592
21.2.2 Step 2: Chaperone-dependent release of the Isu1-bound Fe-S cluster 593
21.2.3 Step 3: Late-acting ISC assembly proteins function in [4Fe-4S] cluster synthesis and in target-specific Fe-S cluster insertion 595
21.3 The role of the mitochondrial ABC transporter Atm 1 in the biogenesis of cytosolic and nuclear Fe-S proteins and in iron regulation 598
21.4 The role of the CIA machinery in the biogenesis of cytosolic and nuclear Fe-S proteins 600
21.4.1 Step 1: The synthesis of a [4Fe-4S] on the scaffold complex Cfd1-Nbp35 600
21.4.2 Step 2: Transfer of the [4Fe-4S] cluster to target apo-proteins 600
21.5 Specialized functions of the human CIA-targeting complex components 601
21.5.1 Dedicated biogenesis of cytosolic and nuclear Fe-S proteins 601
21.5.2 The dual role of CIA2A in iron homeostasis 602
21.6 Fe-S protein assembly and the maintenance of genomic stability 603
21.6.1 Late-acting CIA factors in DNA metabolism 604
21.6.2 XPD and the Rad3 family of DNA helicases 605
21.6.3 Fe-S proteins involved in DNA replication 606
21.6.4 DNA glycosylases as Fe-S proteins 607
21.7 Biochemical functions of Fe-S clusters in DNA metabolic enzymes 607
21.8 Interplay among Fe-S proteins, genome stability, and tumorigenesis 609
21.9 Summary 611
Acknowledgments 612
References 612
22 Iron-sulfur cluster assembly in plants 623
22.1 Introduction 623
22.2 Iron uptake, translocation, and distribution 623
22.3 Fe-S cluster assembly 625
22.3.1 SUF system in plastids 627
22.3.2 ISC system in mitochondria 630
22.3.3 CIA system in cytosol 632
22.4 Regulation of cellular iron homeostasis by Fe-S cluster biosynthesis 634
22.5 Conservation of Fe-S cluster assembly genes across the green lineage 634
22.6 Potential significance to agriculture 636
Acknowledgments 637
References 637
23 Origin and evolution of Fe-S proteins and enzymes 643
23.1 Introduction 643
23.2 Fe-S chemistry and the origin of life 643
23.3 The ubiquity and antiquity of biological Fe-S clusters 646
23.4 Early energy conversion 650
23.5 Evolution of complex Fe-S cluster containing proteins 654
23.6 The path from minerals to Fe-S proteins and enzymes 656
References 657
Index 661