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Inorganics
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Assembly and Reactivity of Iron–Sulfur Clusters
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Assembly and Reactivity of Iron–Sulfur Clusters

A special issue of Inorganics (ISSN 2304-6740). This special issue belongs to the section "Bioinorganic Chemistry".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 23728

Special Issue Editor

Dr. Sandrine Ollagnier de Choudens

E-Mail Website
Guest Editor
Laboratoire de Chimie et Biologie des Métaux - UMR 5249, Département des Interfaces pour l’Energie, la Santé et l’Environnement, Institut de Recherche Interdisciplinaire de Grenoble, 38054 Grenoble Cedex, France
Interests: metalloenzymes; iron–sulfur clusters; mechanisms; antibacterials; biocatalysis; bioinorganic chemistry; biochemistry

Special Issue Information

Dear Colleagues,

Clusters of nonheme iron and inorganic sulfide (Fe–S clusters) are one of the most ubiquitous and functionally versatile prosthetic groups in nature. Since the discovery of ferredoxins (1960s), the number of Fe–S proteins has proliferated, and new functions have emerged, revealing remarkable functional and structural diversity of these inorganic cofactors. The formation of intracellular Fe–S clusters does not occur spontaneously; specialized multiprotein machineries present in all types of organisms are required to support their biosynthesis.

This Special Issue aims to collect research and review contributions focused on recent advances in molecular mechanisms underlying the maturation of Fe–S proteins and in chemical mechanisms of Fe–S proteins/enzymes involved in fundamental biological processes. A preference will be given to novel function/reactivity of iron–sulfur clusters and on recent and original outcomes concerning Fe–S biogenesis in humans and bacteria. We invite you to contribute your research or review articles concerning the assembly and reactivity of Fe–S clusters, which we expect will make an important impact in the bio-inorganic chemistry field (metalloproteins/metalloenzymes).

Dr. Sandrine Ollagnier de Choudens
Guest Editor

Manuscript Submission Information

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Keywords

  • Iron
  • Sulfur
  • Iron–sulfur clusters (Fe–S)
  • Reactivity of Fe–S
  • Biogenesis of Fe–S
  • Biocatalysis of Fe–S
  • Chemical mechanisms
  • Inorganic cofactors
  • Fe–S metalloproteins/metalloenzymes

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Published Papers (6 papers)

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Research

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16 pages, 38123 KiB  
Article
Structural Insights into a Fusion Protein between a Glutaredoxin-like and a Ferredoxin-Disulfide Reductase Domain from an Extremophile Bacterium
by Flavien Zannini, Sandrine Mathiot, Jérémy Couturier, Claude Didierjean and Nicolas Rouhier
Inorganics 2022, 10(2), 24; https://doi.org/10.3390/inorganics10020024 - 17 Feb 2022
Viewed by 2592
Abstract
In eukaryotic photosynthetic organisms, ferredoxin–thioredoxin reductases (FTRs) are key proteins reducing several types of chloroplastic thioredoxins (TRXs) in light conditions. The electron cascade necessary to reduce oxidized TRXs involves a pair of catalytic cysteines and a [4Fe–4S] cluster present at the level of [...] Read more.
In eukaryotic photosynthetic organisms, ferredoxin–thioredoxin reductases (FTRs) are key proteins reducing several types of chloroplastic thioredoxins (TRXs) in light conditions. The electron cascade necessary to reduce oxidized TRXs involves a pair of catalytic cysteines and a [4Fe–4S] cluster present at the level of the FTR catalytic subunit, the iron–sulfur cluster receiving electrons from ferredoxins. Genomic analyses revealed the existence of FTR orthologs in non-photosynthetic organisms, including bacteria and archaea, referred to as ferredoxin-disulfide reductase (FDR) as they reduce various types of redoxins. In this study, we describe the tridimensional structure of a natural hybrid protein formed by an N-terminal glutaredoxin-like domain fused to a FDR domain present in the marine bacterium Desulfotalea psychrophila Lsv54. This structure provides information on how and why the absence of the variable subunit present in FTR heterodimer which normally protects the Fe–S cluster is dispensable in FDR proteins. In addition, modelling of a tripartite complex based on the existing structure of a rubredoxin (RBX)–FDR fusion present in anaerobic methanogen archaea allows recapitulating the electron flow involving these RBX, FDR and GRX protein domains. Full article
(This article belongs to the Special Issue Assembly and Reactivity of Iron–Sulfur Clusters)
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15 pages, 2601 KiB  
Article
Prediction of the Iron–Sulfur Binding Sites in Proteins Using the Highly Accurate Three-Dimensional Models Calculated by AlphaFold and RoseTTAFold
by Béatrice Golinelli-Pimpaneau
Inorganics 2022, 10(1), 2; https://doi.org/10.3390/inorganics10010002 - 22 Dec 2021
Cited by 10 | Viewed by 5234
Abstract
AlphaFold and RoseTTAFold are deep learning-based approaches that predict the structure of proteins from their amino acid sequences. Remarkable success has recently been achieved in the prediction accuracy of not only the fold of the target protein but also the position of its [...] Read more.
AlphaFold and RoseTTAFold are deep learning-based approaches that predict the structure of proteins from their amino acid sequences. Remarkable success has recently been achieved in the prediction accuracy of not only the fold of the target protein but also the position of its amino acid side chains. In this article, I question the accuracy of these methods to predict iron–sulfur binding sites. I analyze three-dimensional models calculated by AlphaFold and RoseTTAFold of Fe–S–dependent enzymes, for which no structure of a homologous protein has been solved experimentally. In all cases, the amino acids that presumably coordinate the cluster were gathered together and facing each other, which led to a quite accurate model of the Fe–S cluster binding site. Yet, cysteine candidates were often involved in intramolecular disulfide bonds, and the number and identity of the protein amino acids that should ligate the cluster were not always clear. The experimental structure determination of the protein with its Fe–S cluster and in complex with substrate/inhibitor/product is still needed to unambiguously visualize the coordination state of the cluster and understand the conformational changes occurring during catalysis. Full article
(This article belongs to the Special Issue Assembly and Reactivity of Iron–Sulfur Clusters)
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Review

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25 pages, 2866 KiB  
Review
Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis
by Ingie Elchennawi and Sandrine Ollagnier de Choudens
Inorganics 2022, 10(10), 174; https://doi.org/10.3390/inorganics10100174 - 18 Oct 2022
Cited by 6 | Viewed by 2531
Abstract
Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive [...] Read more.
Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB. Full article
(This article belongs to the Special Issue Assembly and Reactivity of Iron–Sulfur Clusters)
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21 pages, 2231 KiB  
Review
The Intriguing Role of Iron-Sulfur Clusters in the CIAPIN1 Protein Family
by Simone Ciofi-Baffoni and Claudia Andreini
Inorganics 2022, 10(4), 52; https://doi.org/10.3390/inorganics10040052 - 13 Apr 2022
Cited by 2 | Viewed by 3302
Abstract
Iron-sulfur (Fe/S) clusters are protein cofactors that play a crucial role in essential cellular functions. Their ability to rapidly exchange electrons with several redox active acceptors makes them an efficient system for fulfilling diverse cellular needs. They include the formation of a relay [...] Read more.
Iron-sulfur (Fe/S) clusters are protein cofactors that play a crucial role in essential cellular functions. Their ability to rapidly exchange electrons with several redox active acceptors makes them an efficient system for fulfilling diverse cellular needs. They include the formation of a relay for long-range electron transfer in enzymes, the biosynthesis of small molecules required for several metabolic pathways and the sensing of cellular levels of reactive oxygen or nitrogen species to activate appropriate cellular responses. An emerging family of iron-sulfur cluster binding proteins is CIAPIN1, which is characterized by a C-terminal domain of about 100 residues. This domain contains two highly conserved cysteine-rich motifs, which are both involved in Fe/S cluster binding. The CIAPIN1 proteins have been described so far to be involved in electron transfer pathways, providing electrons required for the biosynthesis of important protein cofactors, such as Fe/S clusters and the diferric-tyrosyl radical, as well as in the regulation of cell death. Here, we have first investigated the occurrence of CIAPIN1 proteins in different organisms spanning the entire tree of life. Then, we discussed the function of this family of proteins, focusing specifically on the role that the Fe/S clusters play. Finally, we describe the nature of the Fe/S clusters bound to CIAPIN1 proteins and which are the cellular pathways inserting the Fe/S clusters in the two cysteine-rich motifs. Full article
(This article belongs to the Special Issue Assembly and Reactivity of Iron–Sulfur Clusters)
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18 pages, 1974 KiB  
Review
Mitochondrial De Novo Assembly of Iron–Sulfur Clusters in Mammals: Complex Matters in a Complex That Matters
by Tyler L. Perfitt and Alain Martelli
Inorganics 2022, 10(3), 31; https://doi.org/10.3390/inorganics10030031 - 26 Feb 2022
Cited by 4 | Viewed by 4868
Abstract
Iron–sulfur clusters (Fe–S or ISC) are essential cofactors that function in a wide range of biological pathways. In mammalian cells, Fe–S biosynthesis primarily relies on mitochondria and involves a concerted group of evolutionary-conserved proteins forming the ISC pathway. In the early stage of [...] Read more.
Iron–sulfur clusters (Fe–S or ISC) are essential cofactors that function in a wide range of biological pathways. In mammalian cells, Fe–S biosynthesis primarily relies on mitochondria and involves a concerted group of evolutionary-conserved proteins forming the ISC pathway. In the early stage of the ISC pathway, the Fe–S core complex is required for de novo assembly of Fe–S. In humans, the Fe–S core complex comprises the cysteine desulfurase NFS1, the scaffold protein ISCU2, frataxin (FXN), the ferredoxin FDX2, and regulatory/accessory proteins ISD11 and Acyl Carrier Protein (ACP). In recent years, the field has made significant advances in unraveling the structure of the Fe–S core complex and the mechanism underlying its function. Herein, we review the key recent findings related to the Fe–S core complex and its components. We highlight some of the unanswered questions and provide a model of the Fe–S assembly within the complex. In addition, we briefly touch on the genetic diseases associated with mutations in the Fe–S core complex components. Full article
(This article belongs to the Special Issue Assembly and Reactivity of Iron–Sulfur Clusters)
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24 pages, 5158 KiB  
Review
The Redox Active [2Fe-2S] Clusters: Key-Components of a Plethora of Enzymatic Reactions—Part I: Archaea
by Maddalena Corsini and Piero Zanello
Inorganics 2022, 10(1), 14; https://doi.org/10.3390/inorganics10010014 - 17 Jan 2022
Cited by 1 | Viewed by 3567
Abstract
The earliest forms of life (i.e., Archaea, Bacteria, and Eukarya) appeared on our planet about ten billion years after its formation. Although Archaea do not seem to possess the multiprotein machinery constituted by the NIF (Nitrogen Fixation), ISC (Iron Sulfur Cluster), SUF (sulfur [...] Read more.
The earliest forms of life (i.e., Archaea, Bacteria, and Eukarya) appeared on our planet about ten billion years after its formation. Although Archaea do not seem to possess the multiprotein machinery constituted by the NIF (Nitrogen Fixation), ISC (Iron Sulfur Cluster), SUF (sulfur mobilization) enzymes, typical of Bacteria and Eukarya, some of them are able to encode Fe-S proteins. Here we discussed the multiple enzymatic reactions triggered by the up-to-date structurally characterized members of the archaeal family that require the crucial presence of structurally characterized [2Fe-2S] assemblies, focusing on their biological functions and, when available, on their electrochemical behavior. Full article
(This article belongs to the Special Issue Assembly and Reactivity of Iron–Sulfur Clusters)
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