دانلود کتاب Iron-Sulfur Clusters in Chemistry and Biology. Volume 2: Biochemistry, Biosynthesis and Human Diseases

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Iron-Sulfur Clusters in Chemistry and Biology. Volume 2: Biochemistry, Biosynthesis and Human Diseases
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Preface
Tracey A. Rouault biography
Contents
List of contributing authors
1. A retrospective on the discovery of [Fe-S] cluster biosynthetic machineries in Azotobacter vinelandii
1.1 Introduction
1.2 An introduction to nitrogenase
1.3 Approaches to identify gene-product and product-function relationships
1.4 FeMoco and development of the scaffold hypothesis for complex [Fe-S] cluster formation
1.5 An approach for the analysis of nif gene product function
1.5.1 Phenotypes associated with loss of NifS or NifU function indicate their involvement in nitrogenase-associated [Fe-S] cluster formation
1.5.2 NifS is a cysteine desulfurase
1.5.3 Extension of the scaffold hypothesis to NifU function
1.5.3.1 Physiological characterization of nifU mutants
1.5.3.2 In vitro NifS-assisted formation of [Fe-S] clusters on NifU
1.5.3.3 Activation of Fe protein using cluster-loaded NifU
1.5.3.4 [Fe-S] clusters are assembled on NifU in vivo
1.5.4 Discovery of isc system for [Fe-S] cluster formation and functional cross-talk among [Fe-S] cluster biosynthetic systems
1.6 The Isc system is essential in A. vinelandii
1.7 There is limited functional cross-talk between the Nif and Isc systems
1.8 Closing remarks
Acknowledgments
References
2. The ISC system and the different facets of Fe-S biology in bacteria
2.1 Introduction
2.2 The ISC system, the general housekeeping system for Fe-S biogenesis
2.2.1 Description and function
2.2.2 The putative role of Fxn in early Fe-S biogenesis by the ISC system
2.2.3 Stress represses ISC functions and enhances SUF pathway activity
2.3 Genetic regulation of ISC synthesis
2.4 The role of the ISC system in antibiotic resistance
2.4.1 The proton motive force link
2.4.2 The DNA repair connection
2.5 The role of the ISC system in bacterial pathogenesis
2.6 Conclusions
References
3. A stress-responsive Fe-S cluster biogenesis system in bacteria – the suf operon of Gammaproteobacteria
3.1 Introduction to Fe-S cluster biogenesis
3.2 Sulfur trafficking for Fe-S cluster biogenesis
3.3 Iron donation for Fe-S cluster biogenesis
3.4 Fe-S cluster assembly and trafficking
3.5 Iron and oxidative stress are intimately intertwined
3.6 Stress-response Fe-S cluster biogenesis in E. coli
3.7 Sulfur trafficking in the stress-response Suf pathway
3.8 Stress-responsive iron donation for the Suf pathway
3.8.1 SufD
3.8.2 Iron storage proteins
3.8.3 Other candidates
3.9 Unanswered questions about Suf and Isc roles in E. coli
Acknowledgment
References
4. Sensing the cellular Fe-S cluster demand: a structural, functional, and phylogenetic overview of Escherichia coli IscR
4.1 Introduction
4.2 General properties of IscR
4.3 [2Fe-2S]-IscR represses Isc expression via a negative feedback loop
4.4 IscR adjusts synthesis of the Isc pathway based on the cellular Fe-S deman
4.5 IscR has a global role in maintaining Fe-S homeostasis
4.6 Fe-S cluster ligation broadens DNA site specificity for IscR
4.7 Phylogenetic analysis of IscR
4.8 Binding to two classes of DNA sites allows IscR to differentially regulate transcription in response to O2
4.9 Roles of IscR beyond Fe-S homeostasis
4.10 Additional aspects of IscR regulation
4.11 Summary
Acknowledgments
References
5. Fe-S assembly in Gram-positive bacteria
5.1 Introduction
5.2 Fe-S proteins in Gram-positive bacteria
5.3 Fe-S cluster assembly orthologous proteins
5.3.1 Clostridia-ISC system
5.3.2 Actinobacteria-SUF
5.3.3 Bacilli-SUF
5.3.3.1 Sulfurtransferase reaction of SufS
5.3.3.2 Sulfur acceptor SufU
5.3.3.3 Cysteine desulfurases involved in the biosynthesis of other thio-cofactors
5.3.3.4 Additional proteins involved in Fe-S metabolism
5.4 Concluding remarks and remaining questions
References
6. Fe-S cluster assembly and regulation in yeast
6.1 Introduction
6.2 Yeast and Fe-S cluster assembly – evolutionary considerations
6.2.1 Nfs1 and the surprise of Isd11
6.2.2 Scaffold proteins in yeast mitochondria
6.2.3 Frataxin’s roles throughout evolution
6.2.4 Ssq1 is a specialized Hsp70 chaperone arising by convergent evolution
6.2.5 Atm1 and CIA components
6.2.6 Yeast components are conserved with their human counterparts
6.2.7 Yeast Fe-S cluster assembly mutants modeling aspects of human diseases
6.3 Yeast genetic screens pointing to the Fe-S cluster assembly apparatus
6.3.1 Misregulation of iron uptake
6.3.2 Suppression of ∆sod1 amino acid auxotrophies
6.3.3 tRNA modification and the SPL1-1 allele
6.3.4 tRNA thiolation and resistance to killer toxin
6.3.5 Cytoplasmic aconitase maturation
6.3.6 Ribosome assembly
6.3.7 Synthetic lethality with the pol3-13 allele
6.3.8 Factors needed for Yap5 response to high iron
6.3.9 Screening of essential genes coding for mitochondrial proteins
6.4 Mitochondrial Fe-S cluster assembly
6.4.1 Mitochondrial cysteine desulfurase
6.4.2 Formation of the Isu Fe-S cluster intermediate in mitochondria
6.4.3 Roles of frataxin
6.4.4 Bypass mutation in Isu
6.4.5 Transfer of the mitochondrial Isu Fe-S cluster intermediate
6.4.6 Role of Grx5
6.4.7 The switch between cluster synthesis and cluster transfer
6.5 Role of glutathione
6.5.1 Glutathione and monothiol glutaredoxins in mitochondria
6.5.2 Glutathione and monothiol glutaredoxins Grx3 and Grx4 outside of mitochondria
6.6 Role of Atm1, an ABC transporter of the mitochondrial inner membrane
6.6.1 Cells lacking Atm1 lose mtDNA
6.7 Relationship between Fe-S cluster biogenesis and iron homeostasis
6.8 Conclusion and missing pieces
Acknowledgments
References
7. The role of Fe-S clusters in regulation of yeast iron homeostasis
7.1 Introduction
7.2 Iron acquisition and trafficking in yeast
7.3 Regulation of iron homeostasis in S. cerevisiae
7.3.1 Aft1/Aft2 low-iron transcriptional regulators and target genes
7.3.2 Yap5 high-iron transcriptional regulator and target genes
7.3.3 Links between mitochondrial Fe-S cluster biogenesis, the Grx3/Grx4/Fra2/Fra1 signaling pathway, and Aft1/Aft2 regulation
7.3.4 Fe-S cluster binding by Grx3/4 and Fra2 is important for their function in S. cerevisiae iron regulation
7.3.5 Working model for Fe-dependent regulation of Aft1/2 via the Fra1/Fra2/Grx3/Grx4 signaling pathway
7.3.6 Yap5 regulation and mitochondrial Fe-S cluster biogenesis
7.4 Regulation of iron homeostasis in S. pombe
7.4.1 Fep1 and Php4 transcriptional repressors and target genes
7.4.2 Roles for Grx4 in regulation of Fep1 and Php4 activity
7.4.3 Molecular basis of iron-dependent control of Fep1 activity
7.4.4 Molecular basis of iron-dependent control of Php4 activity
7.5 Summary
Acknowledgments
References
8. Biogenesis of Fe-S proteins in mammals
8.1 Introduction
8.2 The Fe-S regulatory switch of IRP1
8.3 IRP2, a highly homologous gene, also posttranscriptionally regulates iron metabolism, but iron sensing occurs through regulation of its degradation rather than through a Fe-S switch mechanism
8.4 Identification of the mammalian cysteine desulfurase and two scaffold proteins: implications for compartmentalization of the process
8.5 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-cochaperone system
8.6 Mitochondrial iron overload in response to defects in Fe-S biogenesis raises important questions about how mitochondrial iron homeostasis is regulated
8.7 Perspectives and future directions
References
9. Delivery of iron-sulfur clusters to recipient proteins: the role of chaperone and cochaperone proteins
9.1 Introduction
9.2 A specialized chaperone-cochaperone system ensures efficient Fe-S cluster delivery
9.3 Transfer of Fe-S clusters to recipient proteins: the ATPase cycle
9.4 The mammalian Fe-S transfer system
9.5 Recent progress: identification of molecular features that guide selection of recipient Fe-S proteins by the Fe-S transfer complex
9.6 SDHAF1, a member of the LYR motif family, assists Fe-S cluster incorporation into SDHB
9.7 Potential role of LYR motif proteins in Fe-S cluster biogenesis
9.8 Molecular features of peptides containing the LYR motif that affect binding to HSC20
9.9 Conclusions and future perspectives
References
10. Iron-sulfur proteins and human diseases
Abstract
10.1 Introduction
10.2 Oxidative susceptibility of Fe-S proteins
10.2.1 Aconitases: targets of oxidative stress in disease and aging
10.3 Diseases associated with genetic defects in Fe-S proteins
10.3.1 Mitochondrial respiratory complexes and human diseases
10.3.1.1 Diseases associated with complex II deficiencies
10.3.1.2 Mutations in SDHB, an Fe-S protein, in paraganglioma-pheochromocytoma syndrome, renal cell carcinoma, Carney-Stratakis syndrome/GIST, and infantile leukoencephalopathy
10.3.1.2.1 Paraganglioma-pheochromocytoma syndrome
10.3.1.2.2 Renal cell carcinoma
10.3.1.2.3 Carney-Stratakis syndrome/GIST
10.3.1.2.4 Infantile leukoencephalopathy
10.3.2 FECH deficiency causes erythropoietic protoporhyria (MIM 177000)
10.3.3 DNA repair Fe-S proteins and human disorders
10.3.3.1 Mutations in XPD in XP, TTD, and combined XP with Cockayne’s syndrome
10.3.3.2 Mutations in FANCJ in Fanconi anemia
10.3.4 Diseases associated with genetic defects in radical S-adenosylmethionine enzymes
10.3.5 DNA polymerase delta 1 (POLD1) in mandibular hypoplasia, deafness, progeroid features, and lipodystrophy (MDPL) and cancer
10.3.6 CDGSH iron sulfur domain (CISD) proteins
10.4 Diseases associated with genetic defects in Fe-S cluster biogenesis
10.4.1 A GAA trinucleotide repeat expansion in FXN is the major cause of the neurodegenerative disorder Friedreich ataxia
10.4.2 Mutations in ABCB7 cause x-linked sideroblastic anemia with ataxia
10.4.3 Mutations in GLRX 5 cause an autosomal recessive pyridoxine-refractory sideroblastic anemia
10.4.4 Mutations in ISCU cause myopathy with lactic acidosis (MIM 255125)
10.4.5 NUBPL mutations cause childhood-onset mitochondrial encephalomyopathy and respiratory complex I deficiency (MIM 252010)
10.4.6 Mutations in NFU1 cause multiple mitochondrial dysfunctions syndrome 1 (MIM 605711)
10.4.7 Mutations in BOLA3 cause MMDS 2 (MIM 614299)
10.4.8 IBA57 deficiency causes severe myopathy and encephalopathy
10.4.9 A mutation in ISD11 causes deficiencies of respiratory complexes
10.4.10 Infantile mitochondrial complex II/III deficiency (IMC23D) caused by a missense mutation in NFS1
10.4.11 Mutations in HSPA9 in patients with congenital sideroblastic anemia and myelodysplastic syndrome
10.5 Fe-S cluster biogenesis and iron homeostasis
10.6 Therapeutic strategies
Acknowledgments
References
11. Friedreich ataxia
11.1 Introduction
11.2 Clinical presentation and genetics
11.2.1 Signs and symptoms
11.2.2 Identification of the disease gene
11.2.3 Mitochondrial dysfunction
11.3 Iron metabolism and dysregulation
11.3.1 Mitochondrial iron accumulation
11.3.2 Oxidative stress
11.3.3 ISC biogenesis
11.3.4 Precise function of frataxin
11.3.5 Cellular consequences of frataxin deficiency
11.4 Summary
References
12. Connecting the biosynthesis of the molybdenum cofactor, Fe-S clusters, and tRNA thiolation in humans
12.1 Introduction
12.2 Pathways for the formation of Moco and thiolated tRNAs in humans
12.2.1 Moco biosynthesis in mammals
12.2.1.1 Conversion of 5′-GTP to cPMP
12.2.1.2 Conversion of cPMP to MPT
12.2.1.3 Insertion of molybdate into MPT and further modification of Moco
12.2.1.4 Finishing Moco biosynthesis: maturation and insertion into complex molybdoenzymes
12.2.2 The role of tRNA thiolation in the cell
12.3 The connection between sulfur-containing biomolecules and their their distribution in different compartments in the cell
12.3.1 Sulfur transfer in mitochondria
12.3.2 Sulfur transfer in the cytosol
12.3.3 Role of NFS1, ISD11, URM1, and MOCS2A in the nucleus
Acknowledgments
References
13. Iron-sulphur proteins and genome stability
13.1 The importance of genome stability
13.2 Link between iron-sulphur cluster biogenesis and genome stability
13.3 FeS proteins in DNA replication
13.3.1 DNA primase and DNA polymerase alpha
13.3.2 DNA polymerases delta and epsilon
13.3.3 DNA2
13.4 FeS proteins in DNA repair
13.4.1 DNA glycosylases
13.4.1.1 ROS and DNA damage
13.4.1.2 Base excision repair and DNA glycosylases
13.4.1.3 Endo III and MutY
13.4.1.4 Damage detection by DNA-mediated charge transfer
13.4.2 The Rad3 family of helicases
13.4.2.1 A conserved family of helicases with links to human disease
13.4.2.2 The FeS cluster in XPD
13.4.2.3 Mutations in the FeS cluster binding region of XPD, FANCJ, and ChlR1
13.4.2.4 Possible functions of the FeS cluster in Rad3-like helicases
13.5 Outlook
References
14. Eukaryotic iron-sulfur protein biogenesis and its role in maintaining genomic integrity
14.1 Introduction
14.2 Biogenesis of mitochondrial Fe-S proteins
14.2.1 Step 1: De novo Fe-S cluster assembly on the Isu1 scaffold protein
14.2.2 Step 2: Chaperone-dependent release of the Isu1-bound Fe-S cluster
14.2.3 Step 3: Late-acting ISC assembly proteins function in [4Fe-4S] cluster synthesis and in target-specific Fe-S cluster insertion
14.3 The role of the mitochondrial ABC transporter Atm1 in the biogenesis of cytosolic and nuclear Fe-S proteins and in iron regulation
14.4 The role of the CIA machinery in the biogenesis of cytosolic and nuclear Fe-S proteins
14.4.1 Step 1: The synthesis of a [4Fe-4S] on the scaffold complex Cfd1-Nbp35
14.4.2 Step 2: Transfer of the [4Fe-4S] cluster to target apo-proteins
14.5 Specialized functions of the human CIA-targeting complex components
14.5.1 Dedicated biogenesis of cytosolic and nuclear Fe-S proteins
14.5.2 The dual role of CIA2A in iron homeostasis
14.6 Fe-S protein assembly and the maintenance of genomic stability
14.6.1 Late-acting CIA factors in DNA metabolism
14.6.2 XPD and the Rad3 family of DNA helicases
14.6.3 Fe-S proteins involved in DNA replication
14.6.4 DNA glycosylases as Fe-S proteins
14.7 Biochemical functions of Fe-S clusters in DNA metabolic enzymes
14.8 Interplay among Fe-S proteins, genome stability, and tumorigenesis
14.9 Summary
Acknowledgments
References
15. DNA signaling by iron-sulfur cluster proteins
15.1 Introduction
15.2 DNA-mediated signaling in BER
15.3 Assessing redox signaling by [4Fe-4S] proteins in vitro and in vivo
15.4 DNA CT in other repair pathways
15.5 A role for CT in eukaryotic DNA replication?
15.6 DNA-binding [4Fe-4S] proteins in human disease
15.7 Conclusions
Acknowledgments
16. Iron-sulfur cluster assembly in plants
16.1 Introduction
16.2 Iron uptake, translocation, and distribution
16.3 Fe-S cluster assembly
16.3.1 SUF system in plastids
16.3.2 ISC system in mitochondria
16.3.3 CIA system in cytosol
16.4 Regulation of cellular iron homeostasis by Fe-S cluster biosynthesis
16.5 Conservation of Fe-S cluster assembly genes across the green lineage
16.6 Potential significance to agriculture
Acknowledgments
References
17. Origin and evolution of Fe-S proteins and enzymes
17.1 Introduction
17.2 Fe-S chemistry and the origin of life
17.3 The ubiquity and antiquity of biological Fe-S clusters
17.4 Early energy conversion
17.5 Evolution of complex Fe-S cluster containing proteins
17.6 The path from minerals to Fe-S proteins and enzymes
References
Index