text:
Elisabeth Rathgeb-Schnierer
email: rathgeb-schnierer@mathematik.uni-kassel.de

Renata Cavalho

Judy Sayers

Darina Jirotkova

Introduction to the papers of TWG02: Arithmetic and number systems

Introduction

Working Group 2 was formed in 2011 in Rzeszów, Poland (CERME 7) as a forum for presenting and discussing theoretical and empirical research on the teaching and learning of arithmetic and number systems. The scope of the working group comprises grades 1-12 and emphasizes researchbased specifications of domain-specific goals, analysis of learning processes and learning outcomes in domain-specific learning environments and classroom cultures, new approaches to the design of meaningful and rich learning environments and assessments as well as research on teachers' professional development.

According to the great variety in the field of learning arithmetic and number systems, the group intensively discussed fifteen papers and one poster addressing research for different ages and different approaches1 . The key themes were number sense and structure sense, estimation and estimation tasks, flexibility in mental calculation, derived fact based strategies of multiplication in low-achieving students, understanding of rational numbers and ratio, didactical models as scaffolds for the evolution of mathematical knowledge as well as teachers' knowledge about rational numbers, ratio and place value according to big numbers.

In comparison to former working groups, we had an even greater variety of themes, and therefore the challenges and opportunities to identify common ideas and approaches in the papers presented. Two papers put the emphasis on teaching arithmetic, five on learning arithmetic, five followed a design based research approach with combining teaching and learning, and two papers focused on teachers' professional development.

Teaching arithmetic and number systems

The topics of the two papers focusing teaching were diverse. One paper reflected the role and function of didactical models, the other analyzed and compared textbooks.

Marita Barabash and Raisa Guberman presented a theoretical study on didactical models (DMs) to support students' development of mathematical concepts and ideas. The authors discuss didactical models as a mathematical model (supporting the development of appropriate and consistent concepts) as well as a learning tool (providing an experience of using models). In this sense, DMs may help to cope some discontinuity in mathematics teaching across different levels.

With the focus on a foundational number sense, Anna Löwenhielm Gosia Marschall, Judy Sayers and Paul Andrews analyzed and compared how English and Swedish textbook tasks facilitate children's learning of those number-related competences that require instruction. Analyses identified both similarities and differences. Swedish pre-school curriculum seems to have prompted a conceptually focused textbook, while the strongly framed English pre-school curriculum seems to have precipitated a procedurally focused textbook.

Learning arithmetic and number systems

The subject area "learning arithmetic and number systems" includes papers on number sense, structure sense, and understanding of rational numbers and ratio.

Students' development of structure sense in arithmetic is the focus of Andrea Maffia and Maria Alessandra Mariotti. Structure sense can be mobilized by students to compare and to transform arithmetical expressions, however sometimes it can lead to mathematical inconsistency that pupils might not be aware of. Their paper provides evidence of this type of phenomenon through syntactical transformations.

The assessment of students' ability in number estimation is the topic of a study conducted with Brazilian second and third graders. Beatriz Vargas Dorneles, Mariana Lima Duro, Nohemy Marcela Bedoya Rios, Camila Peres Nogues and Clarissa dos Santos Pereira compare a Number Line Estimation Task and a Numeroisty Task. Results show that the Number Line Estimation Task is more accurate in assessing students' performance in estimation.

Luciana Corso and Beatriz Vargaz Dorneles put the emphasis on number sense and investigate the relation between three domains: working memory (especially the central executive and the phonological component), number sense and arithmetical performance. Based on different valid instruments, data was collected regarding each single component. The analyses reveal a significant correlation between the central executive component of working memory and number sense.

Ayşenur Yılmaz and Mine Işıksal-Bostan examine to what extent middle-grade students agree on statements about the ordering of two negative integers given within a real-life context, and what kind of procedural and conceptual strategies do middle-grade students generate to order those numbers. The results reveal that students did not explain the concept of ordering in daily life considering their conceptual meanings, and have problems in their procedural knowledge repertoire.

Ozur Soyak examines students' difficulties in proportional reasoning in rate and ratio problems. Students' difficulties are caused by the confusion of unit rate identification and by algorithmically based mistakes. A lack of understanding in the unit of measurement, the difference between additive and multiplicative reasoning, and some errors in the computation process seems to underlie such difficulties. The study suggests emphasizing proportional reasoning in the learning process.

Teaching and learning arithmetic and number systems

This time we had a considerable amount of papers following a design based research approach. All studies were characterized by designing a teaching and learning arrangement and investigating students learning and understanding according to this specific context.

With the focus on students' development, Laura Korton explores a teaching-learning arrangement for the inclusive mathematics classroom to foster flexible mental calculation. The approach considered both the level of design (consideration for use) and the level of research (quest for fundamental understanding). Initial findings appear to suggest positive outcomes when Mutual Learning processes are integrated.

Michael Gaidoschik, Kora Maria Deweis and Silvia Guggenbichler exhibit results of an ongoing design research project. Based on a specific instructional design that emphasizes conceptual understanding and derived fact strategies, the study investigates the exhibited strategies in basic multiplication of lower-achieving students. Within the analyses three different strategy types could be developed. Results also show the influence of the instructional context.

Cristina Morais and Lurdes Serrazinha describe an approach to develop conceptual understanding of decimal numbers by using and adapting the hundred square model. Within a teaching experiment 3 rd and 4 th grade students worked with three different models focusing on part-whole meaning. Results indicate that models promote students understanding of rational numbers, and suggest the decimat as an important part-whole model.

Helena Gil Guerreiro and Lurdes Serrazina discuss an approach to focus students' conceptual understanding of rational numbers based on teaching percentages in elementary school. Within a teaching experiment, the authors collected data by logbook, audio and video-recording, and analyzed qualitatively. Results suggest that this specific approach supports to understand multiplicative relations and rational numbers.

The pilot study of Carlos Valenzuela García, Olimpia Figueras, David Arnau and Juan Gutierrez-Soto contributes to the development of better mental objects for fractions. Using a Theoretical Model for fractions, they designed and developed a seven stage teaching sequence based on the use of applets created with GeoGebra and the number line as a conceptual and didactical resource. Results of the first two stages suggest students' preferences to represent fractions as proper fractions (unit segment). The majority of the participants paid more attention to the graphical aspects of the applet.

Teachers' professional development

The two papers in this field focused on teachers' knowledge and its impact on students' learning.

Frédérick Tempier and Christine Chambris paper aims to reveal teachers understanding of place value related to larger numbers, and its impact on teaching and students understanding. Based on the "Theory of Didactic Transposition" the authors investigate the relations between all three aspects. The qualitative analyses of a teachers' lesson compared with the results of a questionnaire of students' knowledge provide interesting insights in teaching large numbers.

Gulseren Karagoz Akar conducted a single case study on teachers reasoning about ratio. Using a theoretical framework based on the concepts within (state) ratios and between (state) ratios, the teachers' conceptions of ratio are discussed. The results suggest different levels of reasoning in between-state ratios (as an operator and a combination of two extensive quantities), but some lack understanding about in between-state ratios as a single intensive quantity.

Summary and outcomes

The great variety of papers provided a fruitful base for interesting and often animated discussions in a supportive quizzical environment. We agreed that we were able to broaden our own perspectives in terms of new perspectives on different mathematics educational research domains, and different uses of terms, concepts and theoretical frameworks. In our discussions, we went far beyond the specific themes of the single papers and covered general aspects that influence our work as international and interdisciplinary group of researchers. Those were  the synergy of cognitive science and mathematics education,  the similarity and differences in research paradigms and approaches,  the intercultural differences,  the different terminologies and the relevance of creating common terminologies and  the necessity to clarify concepts and theoretical frameworks.

This spectrum of research focus in the papers reflect the number of open questions that still persist in the teaching and learning of arithmetic and number systems, and in need of further research. The intense group discussions raised further awareness amongst the group and questioned some positions that were taken for granted in both the field and in specific contexts. With the commonly perused aim improving mathematics education in the field of arithmetic and number systems in all academic levels, we perceived common ideas as a base for further research and discussion: (1) The importance of number sense regarding different age levels, number systems and perspectives form different domains. (2) The necessity to develop models for fostering flexible relational thinking about numbers. (3) The requirement to enhance our notion of number literacy as interaction of various components.

For our further work, the group agreed on enhancing the exchange of research on arithmetic and number systems from cognitive psychologists and mathematics education researchers, and work on specifying terms for both fields to agree on.

Fourteen papers were resubmitted after the conference and are published in the proceedings.Thematic Working Group 02Proceedings of CERME10

Proceedings of CERME10


Marie-Pierre Golinelli-Cohen
email: marie-pierre.golinelli@cnrs.fr

Cécile Bouton
email: cecile.bouton@cnrs.fr.

Fe-S Proteins Acting as Redox Switch: New Key Actors of Cellular Adaptive Responses

Keywords: Fe-S cluster, sensor, redox state, cellular adaptive response

Iron-sulfur (Fe-S) clusters are inorganic prosthetic groups composed of only iron and inorganic sulfur atoms with variable nuclearities. Found in all kingdoms of life, they perform numerous critical functions in fundamental processes (e.g. respiration, photosynthesis, nitrogen fixation). Organisms develop different pathways to sense their local environment such as nutrient availability, level of oxidative stress or of an element such as iron, and to respond and adapt to changes. The chemistry of Fe-S clusters makes them ideal for sensing various redox environmental signals and subsequently for mediating appropriate cellular responses. Fe-S cluster-containing sensors can lose their cluster, accommodate another type of cluster (e.g. interconversion between [4Fe-4S] and [2Fe-2S] clusters) or receive/give electrons (change in the redox state of the cluster). The present review focuses on the latter sensing mechanism, which controls the activity of Fe-S proteins in response to redox signals by change in the redox state of its cluster. Proteins using this mechanism can be found in bacteria, yeasts as well as mammals and are involved in enzyme protection (FeSII), Fe-S cluster transfer/repair (mitoNEET), DNA repair (Base Excision Repair (BER) glycosylases and helicases), and regulation of gene expression (ThnY, AirS, SoxR). In all these proteins, when the Fe-S cluster is reduced, proteins are in a "dormant state". When their cluster perceives a signal that induces its oxidation, they switch to an "active state". This sensing mechanism efficiently helps cells to turn on survival pathways quickly and recover from stressful conditions.

INTRODUCTION

Iron-sulfur (Fe-S) cluster-containing proteins are thought to have been present in the very early forms of anaerobic life. This inorganic prosthetic group is composed of iron and inorganic sulfur atoms with variable nuclearities and geometries and is extremely widespread in nature. Since their discovery in the 1960s [1], they have been found in proteins of every kingdom of life and have been shown to perform numerous critical functions in cellular processes as fundamental for life as respiration and photosynthesis [START_REF] Beinert | Iron-sulfur clusters: nature's modular, multipurpose structures[END_REF]. Organisms often use iron-containing proteins as sensors of the environment. The iron can be directly bound to the protein (Ferric uptake regulator (Fur), PerR…), involved in heme (Dissimilative Nitrate respiration Regulator (DNR), Dos…) but also in an Fe-S cluster [START_REF] Fleischhacker | Iron-containing transcription factors and their roles as sensors[END_REF]. Indeed, the chemistry of Fe-S clusters confers on these cofactors a remarkable plasticity and makes them ideal for sensing redox environmental signals such as gases, e.g. O 2 and NO, the level of Fe and Fe-S clusters, reactive oxygen species (ROS), and redox cycling compounds, and subsequently for mediating adaptive cellular responses. In response to a signal, Fe-S cluster-containing sensors can lose their cluster (e.g. cytosolic aconitase, IscR, NreB...), interconvert between Fe-S cluster types (e.g. [4Fe-4S] cluster converted into [2Fe-2S] cluster, Fumarate and Nitrate reduction Regulator (FNR), WhiB3, RirA...) or be chemically modified (Nitric oxide Sensing Rrf2-type regulator Repressor NsrR…) [START_REF] Miller | Bacterial iron-sulfur cluster sensors in mammalian pathogens[END_REF][START_REF] Mettert | Fe-S proteins that regulate gene expression[END_REF][START_REF] Crack | Bacterial iron-sulfur regulatory proteins as biological sensor-switches[END_REF]. Finally, Fe-S clusters can also receive and give electrons (modulation of the iron oxidation state). Such a cluster redox modulation also stands for a potential sensing mechanism, controlling Fe-S-associated protein activity in response to redox signals. Several examples will be examined in this review, which focuses on how Fe-S cluster-containing sensor proteins act as redox switches and control a cell's rapid and efficient response to a change in its environment. cofactors such as organic groups (e.g. flavin) or other metal atoms including nickel, molybdenum, vanadium, and selenium. Fe-S clusters incorporated into proteins have different atom compositions, cluster structures and core oxidation states. The most common configurations are the [2Fe-2S], [3Fe-4S] and [4Fe-4S] core units. Interestingly, the [2Fe-2S] unit can be considered as the basic building block for the two other types of clusters; the [4Fe-4S] cluster being assembled from two [2Fe-2S] units and the [3Fe-4S] cluster from the loss of one iron of the [4Fe-4S] cluster. The tetrahedral coordination of each iron site is performed by cluster inorganic sulfides (S 2-) and proteinbased ligands, generally, thiolate groups provided by cysteine residues. However, aspartate, histidine, serine, glutamine, arginine, or small molecules (i.e. glutathione, substrate molecule, water …) are occasionally ligand at one unique iron site [START_REF] Johnson | Structure, function, and formation of biological iron-sulfur clusters[END_REF][START_REF] Meyer | Iron-sulfur protein folds, iron-sulfur chemistry, and evolution[END_REF][START_REF] Beinert | Iron-sulfur proteins: ancient structures, still full of surprises[END_REF]. Fe-S clusters are typically redox active, in other words they can be found in different oxidation states. Thus, each iron ion of the cluster can be either in the oxidized state, Fe(III)(ferric ion), or in the reduced state, Fe(II)(ferrous ion). [2Fe-2S] clusters are generally found only in two redox states: the oxidized form, [2Fe-2S] 2+ , with two ferric ions and the reduced form, [2Fe-2S] + , with one ferric ion and one ferrous ion. The all-ferrous form, [2Fe-2S] 0 , has been observed only in the case of the Rieske center [START_REF] Leggate | Formation and characterization of an all-ferrous Rieske cluster and stabilization of the [2Fe-2S] core by protonation[END_REF]. The [4Fe-4S] cluster can be typically found in three redox states: 3+ with three ferric ions and one ferrous ion, 2+ with two ferric ions and two ferrous ions and 1+ with one ferric ion and three ferrous ions. The all-ferrous [4Fe-4S] 0 state was obtained in vitro using strong reducing reagents with very few proteins including nitrogenase [12]. Typically, each [4Fe-4S] protein can be found only in two redox states. The +1 and +2 levels are found in the low potential [4Fe-4S] proteins whereas the +2 and +3 levels are found in the high potential [4Fe-4S] proteins HiPIP. Finally, the [3Fe-4S] cluster can be found in the oxidized form with a global +1 charge (three ferric ions) and in the reduced form with a global charge of 0 (two ferric ions and one ferrous ion) [START_REF] Pandelia | Mossbauer spectroscopy of Fe/S proteins[END_REF].

Functions of Fe-S proteins

Fe-S proteins are capable of mediating biological electron transport (coupled or not to proton transfer), either through small soluble electron carriers such as ferredoxins or in membrane-bound redox enzymatic systems such as photosynthetic and respiratory electron transport chains. However, it was soon demonstrated that Fe-S clusters could also constitute the site for substrate binding and activation in a wide range of enzymes. Among these, the most characterized example is [4Fe-4S]-containing aconitase [START_REF] Lauble | Steric and conformational features of the aconitase mechanism[END_REF]. Three of the four iron atoms of the cluster are coordinated by three cysteines of the polypeptide chain and the fourth iron binds one molecule of substrate (citrate) and acts as a Lewis acid for the activation of the substrate. A similar approach is used by the members of the fast-growing and diverse radical-SAM superfamily including the biotin synthase BioB, the hydrogenase biosynthetic enzyme HydE, and the thiamine pyrimidine biosynthetic enzyme ThiC [START_REF] Shisler | Emerging themes in radical SAM chemistry[END_REF].

Fe-S proteins are also involved in iron or Fe-S cluster storage as in polyferredoxins from anaerobic bacteria and archaea [START_REF] Reeve | A hydrogenase-linked gene in Methanobacterium thermoautotrophicum strain delta H encodes a polyferredoxin[END_REF], in disulfide reduction as in thioredoxin reductase in chloroplasts for example [START_REF] Lu | The thioredoxin superfamily in oxidative protein folding[END_REF], in sulfur donation as in biotin synthase [START_REF] Fugate | Biotin synthase: insights into radical-mediated carbon-sulfur bond formation[END_REF], in ribosome synthesis (ABCE1) and in Fe-S cluster biogenesis (IscU, IscA…) or repair (mitoNEET) [START_REF] Beilschmidt | Mammalian Fe-S cluster biogenesis and its implication in disease[END_REF][START_REF] Ferecatu | The drug diabetes MitoNEET governs a novel trafficking pathway to rebuild an Fe-S cluster into cytosolic aconitase/Iron Regulatory Protein 1[END_REF]. Until recently, zinc, a redox inactive metal, was considered as the metal of choice for nucleic acid-binding proteins (Znfinger proteins). Actually, few DNA-binding proteins (the glycosylases MutY and endonuclease III) were known to contain an Fe-S cluster and it was considered that, in these proteins, the Fe-S cluster played only a structural role similar to that of Zn in Zn-finger proteins. Moreover, strong in vitro evidence suggested that they may also use their clusters to search cooperatively for damaged DNA bases within the genome [START_REF] Lukianova | A role for iron-sulfur clusters in DNA repair[END_REF][START_REF] Boal | DNA repair glycosylases with a [4Fe-4S] cluster: a redox cofactor for DNA-mediated charge transport?[END_REF](this review). Nevertheless, during the last decade, a growing number of DNA-binding proteins including DNA helicase XPD family members, replicative DNA polymerases, the helicase-nuclease Dna2 and RNA-binding proteins including some tRNA modifying enzymes were characterized as Fe-S proteins [START_REF] Fuss | Emerging critical roles of Fe-S clusters in DNA replication and repair[END_REF][START_REF] Kimura | Iron-sulfur proteins responsible for RNA modifications[END_REF]. Thus, Fe-S proteins play a major role in copying the genome and maintaining its integrity. The exact function of Fe-S clusters in the majority of these proteins has yet to be uncovered, which will be a major issue in the coming years. Finally, Fe-S proteins are also involved in transcriptional or translational regulation of gene expression [START_REF] Mettert | Fe-S proteins that regulate gene expression[END_REF]. To sense different types of environmental stimuli, distinct sensing mechanisms are used, involving cluster assembly, conversion, or redox chemistry (redox switch, this review). This activity was first described in the case of the mammalian cytosolic aconitase (holoform of the protein), the apo-protein of which, iron-regulatory protein 1 (IRP-1), binds to mRNA iron-responsive elements and regulates the expression of several proteins involved in cellular iron metabolism [START_REF] Anderson | Mammalian iron metabolism and its control by iron regulatory proteins[END_REF]. In the case of the bacterial FNR, an oxygen-sensing transcriptional regulator, the conversion of the DNA-binding dimeric [4Fe-4S] 2+ form to a monomeric [2Fe-2S] 2+ form is used to control the expression of genes involved in the respiratory pathways [START_REF] Crack | Iron-sulfur clusters as biological sensors: the chemistry of reactions with molecular oxygen and nitric oxide[END_REF]. Finally, as discussed below, intracellular oxidative stress converts the reduced inactive SoxR into a transcriptional activator of soxS gene, which is responsible for activating the transcription of numerous enzymes in the oxidative stress response [START_REF] Kobayashi | Oxidative stress sensing by the iron-sulfur cluster in the transcription factor, SoxR[END_REF].

Fe-S cluster proteins acting as redox switches 2.1. Enzyme protection: case of the FeSII protein (Shethna protein II)

Nitrogen is an essential component of all living organisms because it is present in nucleic acids, proteins and many other biological molecules. Although molecular nitrogen (N 2 ) gas is abundant in air, it cannot be readily used by most organisms. Typically, they use ammonia as substrate for insertion of nitrogen in molecules. Thus, the reduction of N 2 to ammonia (nitrogen fixation) is a key process for the synthesis of many organic compounds and is one of the most common ways to make nitrogen available for plants.

Biological nitrogen fixation is catalyzed by the nitrogenase present in some microorganisms known as diazotrophs, mainly bacteria such as Azotobacter species [START_REF] Kim | Nitrogenase and biological nitrogen fixation[END_REF]. Nitrogenase is composed of two proteins, the Fe protein and the MoFe protein. Both proteins contain complex Fe-S clusters and are irreversibly inactivated by oxygen within minutes by irreversible oxidation of their clusters [START_REF] Goldberg | Mechanism of nitrogenase switchoff by oxygen[END_REF]. Azotobacter species are obligatory aerobic nitrogen-fixing organisms and they develop two main mechanisms to protect nitrogenase from in vivo inactivation by oxygen. When this organism fixes N 2 during energy-supplemented growth, its respiratory system increases to reduce the concentration of intracellular dioxygen (respiratory protection). But, in the case of oxygen stress or under substrate-limiting conditions, this protection ceases to be effective, and nitrogenase is rapidly and reversibly inhibited (temporary conformational protection) [START_REF] Robson | Characterization of an oxygen-stable nitrogenase complex isolated from Azotobacter chroococcum[END_REF]. Thus, in crude A. vinelandii extracts, nitrogenase is more resistant to O 2 than the purified enzyme. Analysis of this O 2 -insensitive inactive nitrogenase form shows that the two components of nitrogenase are complexed to a small [2Fe-2S] protein known as FeSII or Shethna protein II [START_REF] Robson | Characterization of an oxygen-stable nitrogenase complex isolated from Azotobacter chroococcum[END_REF][START_REF] Shethna | Non heme (iron-sulfur) proteins of Azotobacter vinelandii[END_REF][START_REF] Bulen | Nitrogenase complex and its components[END_REF]. FeSII protein is not essential for anaerobic nitrogen fixation of A. vinelandii [START_REF] Moshiri | The FeSII protein of Azotobacter vinelandii is not essential for aerobic nitrogen fixation, but confers significant protection to oxygen-mediated inactivation of nitrogenase in vitro and in vivo[END_REF] but strains lacking FeSII lose viability upon carbon substrate deprivation in the presence of oxygen [START_REF] Maier | Role of the Azotobacter vinelandii nitrogenaseprotective shethna protein in preventing oxygen-mediated cell death[END_REF].

In vitro studies show that only the oxidized holo-FeSII can form a complex with the two components of nitrogenase (oxidation state-dependent interaction) [START_REF] Scherings | On the formation of an oxygen-tolerant three-component nitrogenase complex from Azotobacter vinelandii[END_REF]. This complex is more resistant to oxygen than nitrogenase alone, but is inactive ("switch off state") [START_REF] Wang | Complex formation and O2 sensitivity of Azotobacter vinelandii nitrogenase and its component proteins[END_REF][START_REF] Schlesier | A Conformational Switch Triggers Nitrogenase Protection from Oxygen Damage by Shethna Protein II (FeSII)[END_REF]. In favorable redox conditions, the cluster of FeSII is reduced and the protein dissociates from nitrogenase and its activity recovers [START_REF] Scherings | On the formation of an oxygen-tolerant three-component nitrogenase complex from Azotobacter vinelandii[END_REF]. A similar protective mechanism was described in a few other diazotrophs such as Gluconacetobacter diazotrophicus, which plays a major role in the supply of nitrogen to sugar cane [START_REF] Ureta | Evidence for conformational protection of nitrogenase against oxygen in Gluconacetobacter diazotrophicus by a putative FeSII protein[END_REF]. The crystallographic structure of A. vinelandii FeSII [START_REF] Schlesier | A Conformational Switch Triggers Nitrogenase Protection from Oxygen Damage by Shethna Protein II (FeSII)[END_REF] shows that this small dimeric protein is present in the crystal in two distinct states that differ only in the conformation of an extended loop in close proximity to the Fe-S cluster ("Nloop" from Gly59 to Pro96) whereas, in the "closed state", the cluster is shielded by a helix of the N-loop. When in the "open state", the helix moves away from the cluster, revealing a new protein surface and increasing the solvent accessibility of the cluster. Gel filtration analysis demonstrates that the oxidized form has a larger hydrodynamic radius than the reduced form. Thus, the "open form" was attributed to the oxidized form and the "closed form" to the reduced one. A model of the complex between FeSII and nitrogenase was built from each crystal structure and clearly, only the "open state" (oxidized) FeSII was able to insert into the cleft between the two components of nitrogenase, leaving the Fe-S cluster accessible to the solvent and to reduction. Thus, the oxidation of the cluster of FeSII protein induces a conformational change that allows the FeSII protein to bind reversibly to nitrogenase and to protect it from oxygen with a still ill-defined mechanism (simple induction of conformational switch of the complex or a more active role in the protection of nitrogenase) (Fig. 1). After stress relief, reduced FeSII dissociates from nitrogenase, the activity of which is restored.

Fe-S repair proteins: case of the NEET proteins

NEET proteins are present in all the kingdoms of life. They are characterized by the presence of at least one highly conserved 39-amino-acid motif called CDGSH Iron-Sulfur Domain (CISD) and involved in the coordination of a [2Fe-2S] cluster coordinated by 3 cysteines and one histidine. In mammals, this family is composed of three members: mitoNEET (CISD1), Miner1 (CISD2, ERIS, Noxp70 or NAF-1), and Miner2 (CISD3). MitoNEET and Miner1 are dimers that assemble one cluster per monomer whereas Miner2 is monomeric and assembles two clusters. In plants and bacteria, NEET orthologs are similar to mitoNEET/Miner1 and Miner2, respectively [START_REF] Lin | Structure and molecular evolution of CDGSH iron-sulfur domains[END_REF][START_REF] Nechushtai | Characterization of Arabidopsis NEET reveals an ancient role for NEET proteins in iron metabolism[END_REF]. MitoNEET is anchored to the mammalian outer mitochondrial membrane (OMM) by its N-terminus with the major part of the protein, including the C-terminal [2Fe-2S]binding domain, located in the cytosol [START_REF] Wiley | MitoNEET is an iron-containing outer mitochondrial membrane protein that regulates oxidative capacity[END_REF]. This is the first identified Fe-S protein of the OMM. Its biological activity is still debated [START_REF] Tamir | Structurefunction analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease[END_REF], but several studies have shown that this protein is involved in the regulation of iron and ROS homeostasis [START_REF] Ferecatu | The drug diabetes MitoNEET governs a novel trafficking pathway to rebuild an Fe-S cluster into cytosolic aconitase/Iron Regulatory Protein 1[END_REF][START_REF] Wiley | MitoNEET is an iron-containing outer mitochondrial membrane protein that regulates oxidative capacity[END_REF][START_REF] Kusminski | MitoNEET-driven alterations in adipocyte mitochondrial activity reveal a crucial adaptive process that preserves insulin sensitivity in obesity[END_REF][START_REF] Landry | Redox control of human mitochondrial outer membrane protein MitoNEET [2Fe-2S] clusters by biological thiols and hydrogen peroxide[END_REF], in cell proliferation in human breast cancer [START_REF] Sohn | NAF-1 and mitoNEET are central to human breast cancer proliferation by maintaining mitochondrial homeostasis and promoting tumor growth[END_REF], and in lipid accumulation in adipocytes without insulin resistance [START_REF] Kusminski | MitoNEET-driven alterations in adipocyte mitochondrial activity reveal a crucial adaptive process that preserves insulin sensitivity in obesity[END_REF]. Miner1 is anchored by its Nterminus at the endoplasmic reticulum (ER) membranes and at contact sites between mitochondria and ER (MAM) [START_REF] Wiley | Wolfram Syndrome protein, Miner1, regulates sulphydryl redox status, the unfolded protein response, and Ca2+ homeostasis[END_REF]. Miner1 could be involved in neuronal development [START_REF] Boucquey | Noxp20 and Noxp70, two new markers of early neuronal differentiation, detected in teratocarcinomaderived neuroectodermic precursor cells[END_REF], in the regulation of autophagy through its interaction with Bcl2 [START_REF] Chang | Antagonism of Beclin 1-dependent autophagy by BCL-2 at the endoplasmic reticulum requires NAF-1[END_REF] and of apoptosis [START_REF] Holt | Activation of apoptosis in NAF-1-deficient human epithelial breast cancer cells[END_REF], in the homeostasis of intracellular calcium [START_REF] Wang | Cisd2 modulates the differentiation and functioning of adipocytes by regulating intracellular Ca2+ homeostasis[END_REF], in the maintenance of the integrity of mitochondria and lifespan [START_REF] Chen | Cisd2 deficiency drives premature aging and causes mitochondria-mediated defects in mice[END_REF] and in the inflammatory response [START_REF] Lin | CISD2 serves a novel role as a suppressor of nitric oxide signalling and curcumin increases CISD2 expression in spinal cord injuries[END_REF]. Recessive mutations in CISD2 gene coding for Miner1 are the cause of Wolfram syndrome 2 (or WFS-2), a neurological disease characterized by at least optical atrophy and diabetes [START_REF] Amr | A homozygous mutation in a novel zinc-finger protein, ERIS, is responsible for Wolfram syndrome 2[END_REF][START_REF] Rondinelli | Wolfram syndrome 2: a novel CISD2 mutation identified in Italian siblings[END_REF][START_REF] Mozzillo | A novel CISD2 intragenic deletion, optic neuropathy and platelet aggregation defect in Wolfram syndrome type 2[END_REF]. Finally, like mitoNEET, a strong link was noted between a high level of expression of Miner1 and fast proliferation of various cancer cells [START_REF] Salem | Mitochondrial biogenesis in epithelial cancer cells promotes breast cancer tumor growth and confers autophagy resistance[END_REF], which makes Miner1 a new marker of negative prognosis for various cancers [START_REF] Wang | Overexpressed CISD2 has prognostic value in human gastric cancer and promotes gastric cancer cell proliferation and tumorigenesis via AKT signaling pathway[END_REF]. Miner2 is less characterized than the two other NEET proteins. It seems to be mostly localized to the mitochondria, and it might also be involved in cellular proliferation [START_REF] Wiley | MitoNEET is an iron-containing outer mitochondrial membrane protein that regulates oxidative capacity[END_REF][START_REF] Perez-Ramirez | Genomics and epigenetics: A study of ependymomas in pediatric patients[END_REF]. Crystallographic studies of the overexpressed soluble Cterminal domains of mitoNEET and Miner1 revealed a similar unique folding for both proteins. Both form dimers with two distinct domains, a β-cap and an Fe-S cluster binding domain. Both structures slightly differ in the β-cap domain. Each monomer accommodates one [2Fe-2S] cluster coordinated by three cysteines and one histidine [START_REF] Hou | Crystallographic studies of human MitoNEET[END_REF][START_REF] Lin | Crystal structure of human mitoNEET reveals distinct groups of iron sulfur proteins[END_REF][START_REF] Paddock | MitoNEET is a uniquely folded 2Fe 2S outer mitochondrial membrane protein stabilized by pioglitazone[END_REF][START_REF] Wiley | The outer mitochondrial membrane protein mitoNEET contains a novel redox-active 2Fe-2S cluster[END_REF][START_REF] Conlan | The novel 2Fe-2S outer mitochondrial protein mitoNEET displays conformational flexibility in its N-terminal cytoplasmic tethering domain[END_REF] and they have very similar UV-visible absorption spectra. The cluster of mitoNEET is pH labile and redox-active with a midpoint redox potential of roughly 0 mV at pH 7 [START_REF] Wiley | The outer mitochondrial membrane protein mitoNEET contains a novel redox-active 2Fe-2S cluster[END_REF][START_REF] Conlan | The novel 2Fe-2S outer mitochondrial protein mitoNEET displays conformational flexibility in its N-terminal cytoplasmic tethering domain[END_REF][START_REF] Bak | Redox characterization of the FeS protein MitoNEET and impact of thiazolidinedione drug binding[END_REF][START_REF] Tirrell | Resonance Raman studies of the (His)(Cys)3 2Fe-2S cluster of MitoNEET: comparison to the (Cys)4 mutant and implications of the effects of pH on the labile metal center[END_REF]. The reduced form, which is very likely present in quiescent mammalian cells holds a [2Fe-2S] + [START_REF] Landry | Redox control of human mitochondrial outer membrane protein MitoNEET [2Fe-2S] clusters by biological thiols and hydrogen peroxide[END_REF][START_REF] Wiley | The outer mitochondrial membrane protein mitoNEET contains a novel redox-active 2Fe-2S cluster[END_REF][START_REF] Golinelli-Cohen | Redox Control of the Human Iron-Sulfur Repair Protein MitoNEET Activity via its Iron-Sulfur Cluster[END_REF] and is extremely stable and cannot lose its cluster. The latter can be reversibly oxidized by hydrogen peroxide and reduced by biological thiols implying a redox sensory function of mitoNEET [START_REF] Landry | Redox control of human mitochondrial outer membrane protein MitoNEET [2Fe-2S] clusters by biological thiols and hydrogen peroxide[END_REF][START_REF] Landry | Reduction of mitochondrial protein mitoNEET [2Fe-2S] clusters by human glutathione reductase[END_REF]. Recently, we have shown that the cluster of the oxidized mitoNEET is relatively stable and that oxygen strongly increases its lability [START_REF] Golinelli-Cohen | Redox Control of the Human Iron-Sulfur Repair Protein MitoNEET Activity via its Iron-Sulfur Cluster[END_REF]. In vitro, mitoNEET and Miner1 are both able to transfer their Fe-S cluster to an apo-protein receptor (an Fe-S protein that has lost its Fe-S cluster) of various origins [START_REF] Ferecatu | The drug diabetes MitoNEET governs a novel trafficking pathway to rebuild an Fe-S cluster into cytosolic aconitase/Iron Regulatory Protein 1[END_REF][START_REF] Tamir | Structurefunction analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease[END_REF][START_REF] Golinelli-Cohen | Redox Control of the Human Iron-Sulfur Repair Protein MitoNEET Activity via its Iron-Sulfur Cluster[END_REF][START_REF] Lipper | Cancer-Related NEET Proteins Transfer 2Fe-2S Clusters to Anamorsin, a Protein Required for Cytosolic Iron-Sulfur Cluster Biogenesis[END_REF]. The His ligand is critical for cluster release and transfer [START_REF] Zuris | Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein[END_REF][START_REF] Dicus | Binding of histidine in the (Cys)3(His)1-coordinated [2Fe-2S] cluster of human mitoNEET[END_REF][START_REF] Tan | His-87 ligand in mitoNEET is crucial for the transfer of iron sulfur clusters from mitochondria to cytosolic aconitase[END_REF]. In cellulo, mitoNEET can transfer its cluster to the human IRP-1/cytosolic Fe-S aconitase, a key regulator of cellular iron homeostasis after oxidative damage of its cluster. We proposed that mitoNEET is involved in the repair of oxidatively damaged IRP-1/aconitase and possibly in a more general repair pathway of damaged cytosolic Fe-S protein [START_REF] Ferecatu | The drug diabetes MitoNEET governs a novel trafficking pathway to rebuild an Fe-S cluster into cytosolic aconitase/Iron Regulatory Protein 1[END_REF]. Initial studies on mitoNEET/Miner1 suggested that the transfer can occur only if the cluster is oxidized [START_REF] Zuris | Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein[END_REF]. Recently, by decoupling the oxygen effect from the cluster redox effect, we have proven that only oxidized mitoNEET cluster triggers its transfer to a model receptor protein, independently of the presence or absence of oxygen and without major protein rearrangement between the two redox state of the protein [START_REF] Golinelli-Cohen | Redox Control of the Human Iron-Sulfur Repair Protein MitoNEET Activity via its Iron-Sulfur Cluster[END_REF]. Then, we proposed a model (Fig. 2) for a new Fe-S cluster repair pathway involving mitoNEET. In the absence of stress, mitoNEET would be reduced. Oxidative stress damages Fe-S clusters of proteins and oxidizes the mitoNEET Fe-S cluster. If the damaged Fe-S cluster protein is not degraded after loss of its cluster (i.e. IRP-1/caconitase), oxidized mitoNEET can then transfer its cluster to the damaged protein. This newly discovered repair pathway might allow very fast recovery of key Fe-S protein activity after stress.

DNA repair enzymes

2.3.1. BER glycosylases Cellular DNA is constantly attacked by damaging agents including ROS. Cells have developed efficient DNA repair pathways in order to maintain genome integrity. BER is a highly conserved pathway from prokaryotes to eukaryotes involved in removing a large variety of DNA lesions including oxidation, deamination, depurination, alkylation and single-strand break. DNA glycosylases are key components of this repair pathway. They first search for and detect DNA damage among the vast excess of undamaged bases and then cleave the glycosidic bond between damaged base and sugar, leaving an abasic site that is further processed by downstream enzymes to restore the undamaged DNA [START_REF] Wallace | Base excision repair: a critical player in many games[END_REF]. Several BER glycosylases assemble a [4Fe-4S] cluster including the E. coli endonuclease III (Endo III) [START_REF] Cunningham | Endonuclease III is an iron-sulfur protein[END_REF][START_REF] Thayer | Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure[END_REF] and MutY [START_REF] Guan | MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily[END_REF][START_REF] Michaels | MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III[END_REF], Microccus luteus UV endonuclease [START_REF] Piersen | Purification and cloning of Micrococcus luteus ultraviolet endonuclease, an N-glycosylase/abasic lyase that proceeds via an imino enzyme-DNA intermediate[END_REF], Methanobacterium thermoautotrophicum G:T-specific thymine glycosylase [START_REF] Horst | Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF[END_REF], Thermotoga maritima methylpurine glycosylase [START_REF] Begley | A new member of the endonuclease III family of DNA repair enzymes that removes methylated purines from DNA[END_REF], and uracil DNA glycosylases (UDG) from thermophile and hyperthermophilic organisms [START_REF] Lukianova | A role for iron-sulfur clusters in DNA repair[END_REF][START_REF] Fuss | Emerging critical roles of Fe-S clusters in DNA replication and repair[END_REF][START_REF] Hinks | An iron-sulfur cluster in the family 4 uracil-DNA glycosylases[END_REF]. Until now, their human homologs have not been studied extensively but, clearly, mammalian hNTH1 and MUTYH, homologs of Endo III and MutY respectively, assemble a [4Fe-4S] cluster [START_REF] Pope | Insight into the functional consequences of hMYH variants associated with colorectal cancer: distinct differences in the adenine glycosylase activity and the response to AP endonucleases of Y150C and G365D murine MYH[END_REF][START_REF] Engstrom | A zinc linchpin motif in the MUTYH glycosylase interdomain connector is required for efficient repair of DNA damage[END_REF][START_REF] Luncsford | A structural hinge in eukaryotic MutY homologues mediates catalytic activity and Rad9-Rad1-Hus1 checkpoint complex interactions[END_REF][START_REF] Aspinwall | Cloning and characterization of a functional human homolog of Escherichia coli endonuclease III[END_REF]. The first BER glycosylase reported as an Fe-S-containing protein is Endo III from E. coli. The purified enzyme contains a single [4Fe-4S] 2+ that cannot be reduced under physiological conditions or oxidized without cluster degradation. Thus, the Fe-S cluster was thought to be redoxinactive [START_REF] Cunningham | Endonuclease III is an iron-sulfur protein[END_REF]. The apo-form of MutY is globally folded but is completely inactive and its activity can be restored by chemical cluster reconstitution [START_REF] Porello | A substrate recognition role for the [4Fe-4S]2+ cluster of the DNA repair glycosylase MutY[END_REF]. Moreover, mutagenesis of the cluster ligands decreases their DNA-binding affinity [START_REF] Golinelli | Site-directed mutagenesis of the cysteine ligands to the [4Fe-4S] cluster of Escherichia coli MutY[END_REF]. The crystal structures of E. coli Endo III [START_REF] Kuo | Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III[END_REF], E. coli MutY [START_REF] Guan | MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily[END_REF] and Thermus thermophilus UDG [START_REF] Hoseki | Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8[END_REF] show that the polypeptide forms a solvent exposed loop (iron-sulfur cluster loop, FCL) between two cysteines involved in the coordination of the cluster. This loop contains numerous positively charged residues. The crystal structures of these enzymes bound to DNA substrate reveal that the cluster is necessary to properly position conserved basic residues from the FCL to interact with the DNA phosphate backbone [START_REF] Fromme | Structure of a trapped endonuclease III-DNA covalent intermediate[END_REF][START_REF] Fromme | Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase[END_REF][START_REF] Kosaka | Crystal structure of family 5 uracil-DNA glycosylase bound to DNA[END_REF]. The importance of these residues of FCL in enzyme binding to substrate and activity was confirmed by sitedirected mutagenesis [START_REF] Thayer | Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure[END_REF][START_REF] Engstrom | An iron-sulfur cluster loop motif in the Archaeoglobus fulgidus uracil-DNA glycosylase mediates efficient uracil recognition and removal[END_REF][START_REF] Chepanoske | Positively charged residues within the iron-sulfur cluster loop of E. coli MutY participate in damage recognition and removal[END_REF]. Thus, the Fe-S cluster clearly plays, at least, a structural role in these Fe-S clustercontaining glycosylases. Interestingly, MutY lacks the [4Fe-4S] cluster in bacteria such as Lactobacillaes as well as in the protozoan genus Entamoeba. In these organisms, loss of the cluster is compensated for by bulky amino acids that stabilize the structure in a similar manner [START_REF] Trasvina-Arenas | Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY[END_REF]. The pioneering work of Barton and David's laboratories has led to a reexamination of the role of the Fe-S cluster in these glycosylases [START_REF] Lukianova | A role for iron-sulfur clusters in DNA repair[END_REF][START_REF] Boal | DNA repair glycosylases with a [4Fe-4S] cluster: a redox cofactor for DNA-mediated charge transport?[END_REF]. Using DNA-modified gold electrodes, they first showed that the binding of [4Fe-4S] 2+ -MutY to DNA shifts the redox potential of the +3/+2 couple into the physiological range (roughly 80 mV vs. Normal Hydrogen Electrode, NHE) and makes the cluster more easily oxidized (redox active cluster) [START_REF] Boon | DNAmediated charge transport for DNA repair[END_REF]. Thus, the binding of the protein to DNA allows the oxidation of its cluster and the release of an electron. Similar observations were made with Endo III and UDG [START_REF] Boal | DNA-bound redox activity of DNA repair glycosylases containing [4Fe-4S] clusters[END_REF]. Moreover, they observed that the DNAbinding affinity of the [4Fe-4S] 2+ -MutY is much lower than that of the oxidized form (DNA-binding affinity controlled by the redox state of the cluster) [START_REF] Boal | DNA-bound redox activity of DNA repair glycosylases containing [4Fe-4S] clusters[END_REF]. Guanine radicals are frequent oxidative DNA lesions generated by ROS. Interestingly, by their very high redox potential, they facilitate the oxidation of DNA-bound MutY and initiate the binding of MutY in the vicinity of oxidized DNA [START_REF] Yavin | Protein-DNA charge transport: redox activation of a DNA repair protein by guanine radical[END_REF]. The intact double helix structure of DNA, with π-stacked base pairs, allows charge transfer (CT) along DNA between two redox partners over at least 200 Å and displays sensitivity to mismatched or damaged base pairs such as abasic sites that disturb the π-staked array. Interestingly, MutY and EndoIII exhibit a diminished electrochemical signal with an electrode modified with DNA containing an abasic site [START_REF] Boon | DNAmediated charge transport for DNA repair[END_REF][START_REF] Boal | DNA-bound redox activity of DNA repair glycosylases containing [4Fe-4S] clusters[END_REF], suggesting that DNA-mediated CT is necessary for the redox-controlled activity of MutY and EndoIII through Fe-S clusters [START_REF] Boon | DNAmediated charge transport for DNA repair[END_REF][START_REF] Boal | DNA-bound redox activity of DNA repair glycosylases containing [4Fe-4S] clusters[END_REF][START_REF] Yavin | Electron trap for DNA-bound repair enzymes: a strategy for DNA-mediated signaling[END_REF]. Taken together, a model for BER enzymes scanning DNA for damaged bases using DNA-mediated CT has been proposed (Fig. 3). A highly oxidizing guanine radical in DNA oxidizes a cluster of MutY and initiates binding of the enzyme to the DNA. The electron released during this oxidation process can reduce a distally bound protein using DNA-mediated CT by intact DNA between the two proteins. The newly reduced protein then dissociates from the DNA. As a consequence, local concentrations of MutY/EndoIII remain low where DNA is not damaged. If DNA is damaged, the CT cannot occur and both proteins remain bound to DNA on both sides of the lesion (higher local concentration of glycosylases around the DNA damage) and can slide along DNA using a processive mechanism without dissociation of the enzyme and, subsequently, repair the damage [START_REF] Francis | Escherichia coli MutY and Fpg utilize a processive mechanism for target location[END_REF]. This mechanism allows glycosylases, only 30-500 copies of which are found per bacterial cell, to localize DNA damage rapidly and relocate in the surrounding vicinity [START_REF] Boal | DNA repair glycosylases with a [4Fe-4S] cluster: a redox cofactor for DNA-mediated charge transport?[END_REF][START_REF] Boal | Redox signaling between DNA repair proteins for efficient lesion detection[END_REF][START_REF] Romano | Mutants of the base excision repair glycosylase, endonuclease III: DNA charge transport as a first step in lesion detection[END_REF].

XPD/XPD-like helicases and AddB-type nucleases

XPD is an ATP-dependent super-family 2 DNA helicase with 5'-3' polarity. In eukaryotes, it is a component of the transcription factor TFIIH complex and is involved in DNA repair by the Nucleotide Excision Repair (NER) pathway. XPD opens the DNA around the lesion in an ATPdependent fashion and then additional NER factors are recruited. The presence of a [4Fe-4S] cluster was first shown in XPD from the archaea Sulfolobus acidocaldarius [START_REF] Rudolf | The DNA repair helicases XPD and FancJ have essential iron-sulfur domains[END_REF] then XPD-like helicases were further found in all kingdoms of life including Rad3 in yeast [START_REF] Pugh | The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNAdouble-stranded DNA junction[END_REF], E. coli DinG [START_REF] Ren | Redox control of the DNA damageinducible protein DinG helicase activity via its iron-sulfur cluster[END_REF] and human Rtel1 [START_REF] Landry | The N-terminal domain of human DNA helicase Rtel1 contains a redox active iron-sulfur cluster[END_REF]. Typically, the cluster is essential for the helicase activity and to couple ATP hydrolysis to DNA translocation [102-104, 106, 107]. Moreover, an Fe-S cluster was also found in AddB-type nuclease of the AddAB helicase-nuclease complex from Bacillus subtilis [START_REF] Yeeles | An iron-sulfur cluster is essential for the binding of broken DNA by AddAB-type helicasenucleases[END_REF], as well as in the yeast bifunctional helicase-nuclease protein Dna2 involved in Okazaki fragment processing during DNA replication [START_REF] Pokharel | Cross talk between the nuclease and helicase activities of Dna2: role of an essential iron-sulfur cluster domain[END_REF]. Crystal structures of archaeal XPD [START_REF] Liu | Structure of the DNA repair helicase XPD[END_REF][START_REF] Wolski | Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD[END_REF][START_REF] Fan | XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations[END_REF][START_REF] Constantinescu-Aruxandei | Mechanism of DNA loading by the DNA repair helicase XPD[END_REF] and of bacterial AddAB bound to DNA [START_REF] Saikrishnan | Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex[END_REF] show that the cluster is involved in the formation of a FCL-type domain between two ligands of the Fe-S cluster similar to the one found in Fe-S cluster-containing glycosylases. Moreover, crystal structures revealed a four-domain organization of the helicases with the two motor domains (HD1 and HD2), ARCH and Fe-S domains with the HD1, ARCH and Fe-S domains forming a channel critical for ssDNA translocation during XPD helicase unwinding [START_REF] Wolski | The XPD helicase: XPanDing archaeal XPD structures to get a grip on human DNA repair[END_REF]. Thus, the cluster plays a structural role in maintaining local conformations that are critical for enzyme activity, but is also redox active (redox potential of the +2/+1 couple around 400 mV vs. NHE) [START_REF] Ren | Redox control of the DNA damageinducible protein DinG helicase activity via its iron-sulfur cluster[END_REF][START_REF] Landry | The N-terminal domain of human DNA helicase Rtel1 contains a redox active iron-sulfur cluster[END_REF][START_REF] Fan | XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations[END_REF]. Actually, in vitro reduction of the [4Fe-4S] 2+ cluster of E. coli DinG reversibly switches off its helicase activity [START_REF] Ren | Redox control of the DNA damageinducible protein DinG helicase activity via its iron-sulfur cluster[END_REF]. Moreover, both the cluster and the helicase activity are resistant to high concentrations of hydrogen peroxide, whereas exposure to NO reversibly inactivates the enzyme in vitro by formation of a DinG-bound dinitrosyl iron complex (DNIC). Thus, these results suggest that the cluster might also act as a sensor of intracellular redox potential to modulate its helicase activity [START_REF] Ren | Redox control of the DNA damageinducible protein DinG helicase activity via its iron-sulfur cluster[END_REF]. Finally, experiments using DNA-modified electrodes showed that DNA binding shifts the 3+/2+ redox potential of the helicase to roughly 80 mV, a redox potential similar to the one previously measured for the Fe-S clustercontaining glycosylases [START_REF] Mui | ATP-stimulated, DNA-mediated redox signaling by XPD, a DNA repair and transcription helicase[END_REF]. Moreover, redistribution of XPD around DNA damage, which inhibits CT, was observed [START_REF] Sontz | DNA charge transport as a first step in coordinating the detection of lesions by repair proteins[END_REF]. Then, the model of DNA scanning and repair by Fe-S cluster-containing glycosylases using DNAmediated CT was extended to XPD-type helicases and even to UvrC, a NER endonuclease containing an Fe-S cluster [START_REF] Grodick | DNA-mediated charge transport signaling within the cell[END_REF]. In this extended model, XPD-type helicase, EndoIII/MutY glycosylase and UvrC have similar redox potentials and cooperate at long range using DNA-mediated CT for repair protein redistribution around DNA damage [START_REF] Sontz | DNA charge transport as a first step in coordinating the detection of lesions by repair proteins[END_REF][START_REF] Grodick | DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for genomic integrity[END_REF][START_REF] Arnold | DNA Charge Transport: from Chemical Principles to the Cell[END_REF]. This DNA-mediated signaling among different DNA repair pathway enzymes was also demonstrated to be critical to maintenance of the integrity of the bacterial genome under stress conditions [START_REF] Grodick | DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for genomic integrity[END_REF]. Finally, it was shown that all replicative DNA polymerases (POLα, POLδ, POLε), but also the primase subunit PRIM2, assemble an Fe-S cluster [START_REF] Netz | Eukaryotic DNA polymerases require an iron-sulfur cluster for the formation of active complexes[END_REF][START_REF] Weiner | An iron-sulfur cluster in the C-terminal domain of the p58 subunit of human DNA primase[END_REF]. Preliminary studies showed that PRIM2 is able to also mediate DNA CT [START_REF] Holt | Cracking Open a Molecular Calculator: DNA Charge Transport and Primase[END_REF]. Thus, it was proposed that DNA-mediated CT might be a mechanism largely used by all these Fe-S cluster-containing DNA synthesis and repair enzymes to interrogate DNA integrity, to communicate rapidly and to coordinate their activities efficiently by modulating the redox state of their cluster [START_REF] Fuss | Emerging critical roles of Fe-S clusters in DNA replication and repair[END_REF].

Regulators of gene expression

2.4.1.ThnY/ThnR, regulators of the tetralin degradation pathway In response to the presence of the organic solvent tetralin (1,2,3,4-tetrahydronaphthalene), the expression of the thnA genes of the Gram-negative Sphingomonas macrogolitabida strain TFA allows the utilization of this compound as a carbon and energy source (tetralin biodegradation) [START_REF] Andujar | Identification of an extradiol dioxygenase involved in tetralin biodegradation: gene sequence analysis and purification and characterization of the gene product[END_REF][START_REF] Moreno-Ruiz | Identification and functional characterization of Sphingomonas macrogolitabida strain TFA genes involved in the first two steps of the tetralin catabolic pathway[END_REF]. The catabolism pathway involves the ferredoxin reductase ThnA4, the Rieske-type ferredoxin ThnA3, and the dioxygenase ThnA1/ThnA2 forming an electron transfer chain from the NAD(P)H to the tetralin substrate [START_REF] Moreno-Ruiz | Identification and functional characterization of Sphingomonas macrogolitabida strain TFA genes involved in the first two steps of the tetralin catabolic pathway[END_REF]. The regulation of the expression of the four thnA genes is complex and involves two proteins of the catabolic pathway, ThnA4 and ThnA3, the LysR-type transcriptional activator ThnR and ThnY. ThnY is an Fe-S flavoprotein containing an FAD-binding site and a plant ferredoxin-like [2Fe-2S] cluster, sharing homology with bacterial oxygenase-coupled NAD(P)H-dependent ferredoxin reductases (enzymes that play an important role in the degradation of aromatic compounds) [START_REF] Martinez-Perez | Regulation of tetralin biodegradation and identification of genes essential for expression of thn operons[END_REF][START_REF] Ledesma-Garcia | ThnY is a ferredoxin reductase-like iron-sulfur flavoprotein that has evolved to function as a regulator of tetralin biodegradation gene expression[END_REF][START_REF] Lopez-Sanchez | Tetralin-induced and ThnR-regulated aldehyde dehydrogenase and betaoxidation genes in Sphingomonas macrogolitabida strain TFA[END_REF]. Clearly, ThnR and ThnY are both essential for tetralin biodegradation [START_REF] Martinez-Perez | Regulation of tetralin biodegradation and identification of genes essential for expression of thn operons[END_REF][START_REF] Lopez-Sanchez | Tetralin-induced and ThnR-regulated aldehyde dehydrogenase and betaoxidation genes in Sphingomonas macrogolitabida strain TFA[END_REF]. ThnR activates thnA gene transcription by binding to promoter regions [START_REF] Lopez-Sanchez | Tetralin-induced and ThnR-regulated aldehyde dehydrogenase and betaoxidation genes in Sphingomonas macrogolitabida strain TFA[END_REF]. In vitro, oxidized ThnY binds to ThnR and enhances the DNA-binding affinity of ThnR by modifying the structure of the ThnR-DNA complex, most likely through direct interaction with ThnR [START_REF] Ledesma-Garcia | ThnY is a ferredoxin reductase-like iron-sulfur flavoprotein that has evolved to function as a regulator of tetralin biodegradation gene expression[END_REF]. Mutations of residues involved in the coordination of the Fe-S cluster or in the FAD-binding region of ThnY allow the transcription of the thnA genes in response to compounds other than tetralin (loss of the specificity of the pathway), suggesting that ThnY cofactors are important for tetralin response specificity [START_REF] Ledesma-Garcia | The ferredoxin ThnA3 negatively regulates tetralin biodegradation gene expression via ThnY, a ferredoxin reductase that functions as a regulator of the catabolic pathway[END_REF]. Finally, it has been proposed that the redox state of the ThnY cluster might modulate the protein activity under the regulation of the ferredoxin ThnA3 [START_REF] Ledesma-Garcia | ThnY is a ferredoxin reductase-like iron-sulfur flavoprotein that has evolved to function as a regulator of tetralin biodegradation gene expression[END_REF]. Interestingly, similar poor substrate specificity was observed in a strain deleted for ThnA3, a protein of the catabolic pathway [START_REF] Ledesma-Garcia | The ferredoxin ThnA3 negatively regulates tetralin biodegradation gene expression via ThnY, a ferredoxin reductase that functions as a regulator of the catabolic pathway[END_REF]. Moreover, in the absence of a good substrate for the dioxygenase or in conditions when reduced ThnA3 presumably accumulates, the expression of thnA genes is blocked, indicating communication between the regulatory and catabolic pathways [START_REF] Ledesma-Garcia | The ferredoxin ThnA3 negatively regulates tetralin biodegradation gene expression via ThnY, a ferredoxin reductase that functions as a regulator of the catabolic pathway[END_REF][START_REF] Martinez-Perez | Integrated response to inducers by communication between a catabolic pathway and its regulatory system[END_REF]. The whole regulatory cascade leading to the specific expression of thnA genes only in the presence of tetralin was recently described (Fig. 4) [START_REF] Ledesma-Garcia | Redox proteins of hydroxylating bacterial dioxygenases establish a regulatory cascade that prevents gratuitous induction of tetralin biodegradation genes[END_REF]. It is proposed that in presence of tetralin, the catabolic pathway is very efficient and that electrons from NAD(P)H are transferred to ThnA4, then to ThnA3 and finally to the dioxygenase ThnA1/ThnA2, which degrades the substrate. In this case, the substrate acts as an electron sink. ThnY is mostly oxidized, binds to ThnR and stimulates its binding to DNA. Conversely, at low tetralin concentration or in the presence of a non-optimal substrate for the dioxygenase, electrons from NAD(P)H that accumulate in ThnA3 are redirected towards ThnY (ThnY reduction) instead of the dioxygenase. The binding of reduced ThnY to ThnR is thus impaired and thnA gene expression is not induced by ThnR.

The bacterial redox-sensor histidine kinase, AirS

Bacteria frequently sense numerous environmental signals and respond rapidly through sophisticated informationprocessing two-component signaling (TCS) pathways that exhibit complex dynamics on different timescales. Typically, these pathways involve a sensor histidine kinase that autophosphorylates in response to a given stimulus, and then transfers its phosphate group to a cognate response regulator that initiates appropriate cellular responses [START_REF] Salazar | Temporal and evolutionary dynamics of twocomponent signaling pathways[END_REF]. Among them, the FixL/NreB O 2 -sensor kinase family members are iron-containing proteins [START_REF] Taabazuing | Oxygen sensing strategies in mammals and bacteria[END_REF]. The FixL subfamily uses heme as sensor while the NreB subfamily, including NreB and AirS, uses an Fe-S cluster. Staphylococcus aureus is a facultative anaerobe, which is able to invade almost every kind of tissue and to adapt to diverse hypoxic conditions, including the highly hypoxic environment at the onset of inflammation. Thus, bacteria have different sensing mechanisms, including TCS pathways, to adapt to oxygen availability and to use either nitrate respiration or carbohydrate fermentation [START_REF] Somerville | At the crossroads of bacterial metabolism and virulence factor synthesis in Staphylococci[END_REF][START_REF] Hall | Sensing and Adapting to Anaerobic Conditions by Staphylococcus aureus[END_REF]. The AirS-AirR TCS of S. aureus (AirS is the kinase; AirR is the transcriptional regulator), also known as YhcSR, is essential for growth of the bacteria in culture [START_REF] Sun | Identification of a novel essential two-component signal transduction system, YhcSR, in Staphylococcus aureus[END_REF] and for its pathogenesis [START_REF] Hall | The AirSR two-component system contributes to Staphylococcus aureus survival in human blood and transcriptionally regulates sspABC operon[END_REF]. It is a global key regulator that controls the transcription of more than 350 genes [START_REF] Sun | AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus[END_REF], including regulation of the nitrate respiratory pathway [START_REF] Yan | The essential two-component system YhcSR is involved in regulation of the nitrate respiratory pathway of Staphylococcus aureus[END_REF], of cell wall synthesis [START_REF] Sun | Modulation of cell wall synthesis and susceptibility to vancomycin by the two-component system AirSR in Staphylococcus aureus NCTC8325[END_REF], and of various virulence factors [START_REF] Sun | AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus[END_REF]. It is also involved in the resistance to ROS induced by the host immune system by upregulation of the production of the antioxidant molecule staphyloxanthin [START_REF] Hall | The Staphylococcus aureus AirSR Two-Component System Mediates Reactive Oxygen Species Resistance via Transcriptional Regulation of Staphyloxanthin Production[END_REF] and, more generally, it contributes to bacterial survival in human blood [START_REF] Hall | The AirSR two-component system contributes to Staphylococcus aureus survival in human blood and transcriptionally regulates sspABC operon[END_REF].

In vitro studies demonstrate that the membrane-bound histidine kinase AirS coordinates a [2Fe-2S] cluster with four cysteine ligands acting both as an oxygen-and a redoxsensor [START_REF] Sun | AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus[END_REF]. Under anaerobic conditions (Fig. 5), AirS cluster is in the reduced state [2Fe-2S] 1+ and AirS kinase activity is low (low concentration of phosphorylated AirR). The unphosphorylated AirR represses transcription of genes involved in bacterial virulence, including the quorum-sensing TCS Agr, the virulence TCS SaeRS, and some other stress-associated factors [START_REF] Sun | AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus[END_REF]. Oxidation of the cluster to the [2Fe-2S] 2+ state leads to efficient AirS kinase activity (optimal phosphorylation of AirR). However, prolonged exposure to oxygen, intense host-generated ROS, or contact with reactive nitrogen species (RNS) leads to inactive AirS (Apo-AirS and DNIC forms for oxidative and NO stresses, respectively [START_REF] Sun | AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus[END_REF]), and accumulation of unphosphorylated AirR. Thus, AirS is capable of sensing oxygen and redox signals through its Fe-S cluster, which is essential for its kinase activity. This redox-dependent kinase activity of AirS allows AirRS TCS to play an important role in appropriately coordinating and rapidly synchronizing virulence determinant production in response to the host environment.

SoxR

The SoxRS system found in enteric bacteria such as E. coli is another two-part regulatory system [START_REF] Wu | Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli[END_REF][START_REF] Amabile-Cuevas | Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon[END_REF]. It is involved in a global response to exogenous oxidative and nitrosative stresses by controlling the expression of more than 100 genes involved in redox homeostasis, damage repair, multidrug resistance, and heavy metal detoxification [START_REF] Pomposiello | Identification of SoxS-regulated genes in Salmonella enterica serovar typhimurium[END_REF][START_REF] Blanchard | Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks[END_REF]. First, SoxR is activated in response to an oxidative stress in a superoxide-independent manner [START_REF] Gu | The SoxRS response of Escherichia coli is directly activated by redox-cycling drugs rather than by superoxide[END_REF], and switches on the transcription of the global regulator SoxS, which activates the soxRS regulon [START_REF] Nunoshiba | Two-stage control of an oxidative stress regulon: the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene[END_REF][START_REF] Wu | Two-stage induction of the soxRS (superoxide response) regulon of Escherichia coli[END_REF]. SoxS homologs do not exist in nonenteric bacteria such as Pseudomonas aeruginosa and Streptomyces coelicolor. Thus, in these antibiotic producer bacteria, SoxR is believed to regulate directly the transcription of a small set of genes that protect the bacterium against excreted endogenous redox-active antibiotics involved in quorum-sensing, inhibition of competitor bacteria, and bacterial virulence during infection [START_REF] Palma | Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response[END_REF][START_REF] Dietrich | Redox-active antibiotics control gene expression and community behavior in divergent bacteria[END_REF][START_REF] Mahavihakanont | Novel roles of SoxR, a transcriptional regulator from Xanthomonas campestris, in sensing redox-cycling drugs and regulating a protective gene that have overall implications for bacterial stress physiology and virulence on a host plant[END_REF][START_REF] Burbank | OxyR and SoxR modulate the inducible oxidative stress response and are implicated during different stages of infection for the bacterial phytopathogen Pantoea stewartii subsp. stewartii[END_REF][START_REF] Naseer | RNA-Seq analysis reveals a sixgene SoxR regulon in Streptomyces coelicolor[END_REF]. SoxR is a small protein of the MerR family of transcriptional sensors that forms a dimer in solution and assembles a [2Fe-2S] cluster fully coordinated by cysteine residues in the C-terminal domain of each monomer [START_REF] Hidalgo | An iron-sulfur center essential for transcriptional activation by the redox-sensing SoxR protein[END_REF][START_REF] Wu | Overproduction and physical characterization of SoxR, a [2Fe-2S] protein that governs an oxidative response regulon in Escherichia coli[END_REF]. The crystal structure of SoxR alone or in complex with soxS promoter DNA showed a protein folding similar that of other MerR proteins (DNA-binding domain, sensor domain, and coiled-coil dimerization domain), but with cluster irons exposed to the solvent with an asymmetric electrostatic environment [START_REF] Watanabe | Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA[END_REF]. The Fe-S cluster present in the sensor domain of SoxR can be found in the +1 and +2 oxidation states, with a midpoint potential around -285mV vs. NHE [START_REF] Gaudu | SoxR, a [2Fe-2S] transcription factor, is active only in its oxidized form[END_REF][START_REF] Ding | The redox state of the [2Fe-2S] clusters in SoxR protein regulates its activity as a transcription factor[END_REF]. SoxR can bind DNA with similar affinity independently of the absence (apo-form) or presence of the Fe-S cluster [START_REF] Hidalgo | An iron-sulfur center essential for transcriptional activation by the redox-sensing SoxR protein[END_REF], and of its redox state (oxidized vs. reduced). Still, only the oxidized holo-SoxR can activate the transcription of SoxS [START_REF] Gaudu | SoxR, a [2Fe-2S] transcription factor, is active only in its oxidized form[END_REF][START_REF] Ding | The redox state of the [2Fe-2S] clusters in SoxR protein regulates its activity as a transcription factor[END_REF]. During normal aerobic growth, the SoxR cluster is clearly reduced in E. coli [START_REF] Ding | In vivo kinetics of a redox-regulated transcriptional switch[END_REF]. Using DNA-modified electrodes, it was proposed that the binding of SoxR to its cognate DNA shifts its redox potential to +200 mV [START_REF] Gorodetsky | DNA binding shifts the redox potential of the transcription factor SoxR[END_REF]. As a consequence, only a strongly oxidizing environment would be able to oxidize the cluster quickly and to activate SoxR and the transcription of the soxS operon [START_REF] Gu | The SoxRS response of Escherichia coli is directly activated by redox-cycling drugs rather than by superoxide[END_REF]. Interestingly, SoxR from different organisms exhibit various sensitivities to redox-cycling agents depending on the redox potential of their Fe-S cluster, which is affected by changes in a few residues around the cluster [START_REF] Sheplock | Species-specific residues calibrate SoxR sensitivity to redox-active molecules[END_REF]. It has been also reported that SoxR can be activated by DNA-guanine radicals and DNA-mediated charge transfer [START_REF] Lee | DNA-mediated redox signaling for transcriptional activation of SoxR[END_REF], which can provide rational bases for rapid activation of SoxR. Finally, SoxR can be activated by exposure to macrophage-generated NO followed by nitrosylation of its Fe-S cluster resulting in SoxR-bound DNIC [START_REF] Ding | Direct nitric oxide signal transduction via nitrosylation of iron-sulfur centers in the SoxR transcription activator[END_REF][START_REF] Fujikawa | Mechanistic studies on formation of the dinitrosyl iron complex of the [2Fe-2S] cluster of SoxR protein[END_REF][START_REF] Lo | A study of NO trafficking from dinitrosyl-iron complexes to the recombinant E. coli transcriptional factor SoxR[END_REF]. SoxR cluster oxidation induces a protein conformational change with interdomain reorganization [START_REF] Kobayashi | Protein conformational changes of the oxidative stress sensor, SoxR, upon redox changes of the [2Fe-2S] cluster probed with ultraviolet resonance Raman spectroscopy[END_REF] and significant distortion and underwinding of the SoxR-bound DNA [START_REF] Fujikawa | Redox-dependent DNA distortion in a SoxR protein-promoter complex studied using fluorescent probes[END_REF] that improves RNA polymerase binding and further increases transcription [START_REF] Hidalgo | Binuclear [2Fe-2S] clusters in the Escherichia coli SoxR protein and role of the metal centers in transcription[END_REF][START_REF] Hidalgo | Spacing of promoter elements regulates the basal expression of the soxS gene and converts SoxR from a transcriptional activator into a repressor[END_REF]. When the stress is over, the SoxR cluster is rapidly reduced by rsxABCDGE and rseC gene products [START_REF] Koo | A reducing system of the superoxide sensor SoxR in Escherichia coli[END_REF] and SoxS is subject to proteolytic degradation [START_REF] Griffith | Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons[END_REF], ensuring that the system's response remains dependent on the signal (Fig. 6). Recently, it was proposed that the Streptomyces venezuelae NsrR homolog RsrR for Redox sensitive response Regulator assembles a redox active [2Fe-2S]. It is believed that its cluster controls its DNA-binding ability in a similar manner to SoxR (the oxidized form binds DNA more efficiently) and regulates NADH/NAD(P)H and glutamate/glutamine pathways [START_REF] Munnoch | Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily[END_REF].

REMARKS AND CONCLUSION

Upon hyperactivation or insult, cells classically respond by activating different pathways that promote protection such as activation of the heat shock pathway or of the unfolded protein response pathway, and eventually, cell defense, survival and recovery. However, if this typical adaptive response fails, cell death programs are activated to eliminate damaged cells. In this review, we have examined Fe-S proteins with different cluster nuclearity ([2Fe-2S] or [4Fe-4S]) from organisms as diverse as bacteria, yeast and mammals, with disparate cellular functions including enzyme protection (FeSII), Fe-S cluster repair (mitoNEET), DNA repair (BER glycosylases and helicases), and transcriptional regulation (ThnY, AirS and SoxR) (Fig. 7). Despite all these differences, a common point emerges: they are inactive when their Fe-S cluster is in the reduced state, which confers on the protein a state of dormancy. Upon sensing a signal (typically change of oxygen tension or oxidative stress), the cluster becomes oxidized and the protein turns to the "active state". This general mechanism appears to be a very efficient way for the cell to turn on survival pathways to recover quickly from stressful conditions. An emblematic example is given by the bacterial nitrogenase, which is irreversibly inactivated by oxygen due destruction of its Fe-S cluster. As developed above, by forming a reversible complex with nitrogenase during oxidative stress, FeSII allows fast recovery of nitrogenase activity by simple dissociation of the complex as the stress disappears. Likewise, in mammals, the cytosolic aconitase loses its Fe-S cluster after suffering from oxidative or nitrosative stress. In the absence of mitoNEET, the Fe-S cluster biogenesis pathway would have to synthesize a new cluster before supplying it to aconitase. Instead, the reduced cluster of dormant mitoNEET can benefit from oxidative stress to become oxidized and quickly to replenish Fe-S-damaged aconitase with an intact [4Fe-4S] cluster. These last two examples are illustrative of general situations in which cells keep protective responses silent, but are ready to be activated promptly as soon as a single electron is transferred to Fe-S cluster. Such rapid and efficient stress response systems underline once again how the exceptional electronic properties of Fe-S clusters are being used by living organisms and permit subtle tuning of Fe-S proteins properties. In conclusion, Fe-S cluster proteins acting as redox switch appear as new key actors of very efficient and rapid cellular reactions that help cells to restore their activity after a change in environment. Therefore, ThnR unable to form a complex with reduced ThnY does not induce the transcription of thn genes. Tetralin

LIST OF ABBREVIATIONS

Figure 4 .

 4 Figure 4. Regulation by ThnY of the catabolic pathway dedicated to the biodegradation of tetralin in Sphingomonas macrogolitabida. Biodegradation of tetralin is performed by the dioxygenase ThnA1/ThnA2, which receives electrons from NAD(P)H via the ferredoxin reductase ThnA4 and the ferredoxin ThnA3. (1)In the presence of tetralin substrate, ThnA3 is mostly oxidized. The Fe-S clustercontaining ThnY remains oxidized, binds to ThnR, and the transcription of thn genes is activated. (2) In absence of tetralin, ThnA3 is reduced and transfers electrons to ThnY (accumulation of reduced ThnY). Therefore, ThnR unable to form a complex with reduced ThnY does not induce the transcription of thn genes.

Figure 5 .

 5 Figure 5. Regulation of Staphylococcus aureus virulence by the kinase AirS.Under anaerobic conditions, the [2Fe-2S]-containing AirS is reduced and its kinase activity is low. In moderate oxidative conditions, the AirS Fe-S cluster is oxidized and exhibits efficient kinase activity. It phosphorylates AirR, a major transcriptional regulator of more than 350 genes involved in bacterial survival and virulence. However, under conditions of prolonged exposure to oxygen, ROS or RNS, the AirS cluster is lost (apoform due to oxygen exposure or ROS) or modified (DNIC-modified form due to RNS), and AirS has no kinase activity.

Figure 6 .

 6 Figure 6. SoxR, a bacterial two-stage control system for cell survival under physiological stress. The redox-sensor SoxR is a homodimer, which holds one [2Fe-2S] cluster per monomer. During normal aerobic growth, SoxR [2Fe-2S] clusters are reduced and the protein binds a specific promoter region of its target gene soxS and inactivates its transcription. During oxidative stress, the redox cycling compounds produced cause oxidation of SoxR [2Fe-2S] clusters, resulting in a conformational change of the protein.The active oxidized form of SoxR remodels the conformation of the soxS promoter in a way that allows RNA polymerase to initiate transcription of SoxS. The increased levels of SoxS protein then activate the various soxRS regulon genes.

Figure 7 .

 7 Figure 7. Fe-S cluster-containing redox switches are key components of efficient cellular responses to change in cellular environments.

( 1 )( 2 )

 12 Figure 1

FIGURE LEGENDS Figure 1. Protection of bacterial nitrogenase by oxidized FeSII protein.

  Composed of two Fe-S cluster-containing proteins (Fe and MoFe proteins), nitrogenase can be irreversibly inactivated by oxygen due to cluster oxidation. FeSII protein is involved in a pathway to protect nitrogenase against oxidative damage. In oxidative conditions, the [2Fe-2S] cluster of FeSII becomes oxidized. This change in the redox state of the cluster induces a major conformational change ("open conformation") that allows FeSII to form a protective but inactive complex with nitrogenase. After stress relief, FeSII returns to its reduced form ("closed conformation"), the complex dissociates, and nitrogenase activity is restored.

	BER	Base excision repair
	CISD	CDGSH Iron-Sulfur Domain
	CT	Charge transfer
	DNIC	Dinitrosyl iron complex
	Endo III	Endonuclease III
	FCL	Iron-sulfur cluster loop
	FNR	Fumarate and Nitrate reduction Regulator
	IRP-1	Iron-Regulatory Protein-1
	NER	Nucleotide Excision Repair
	NHE	Normal Hydrogen Electrode
	OMM	Outer mitochondrial membrane
	RNS	Reactive nitrogen species
	ROS TCS Figure 2. Fe-S cluster repair process of cytosolic aconitase/IRP1 by mitoNEET after oxidative Reactive oxygen species Two-component signaling UDG stress. Under physiological redox conditions, mitoNEET is believed to accommodate a very stable [2Fe-Uracil DNA glycosylase 2S] + cluster, and the cytosolic aconitase/IRP1 assembles a redox sensitive [4Fe-4S] cluster, which is
	essential for aconitase activity. When cells are exposed to an oxidative or nitrosative stress, the [4Fe-4S]
	is completely disassembled revealing the IRP1 regulatory function. At the same time, the mitoNEET

[2Fe-2S] cluster is oxidized (+2 state). Upon cessation of oxidative stress, mitoNEET [2Fe-2S] 2+ transfers its clusters to apo-IRP1, which is converted back into aconitase. Unfolded apo-mitoNEET might be recycled into holo-mitoNEET through the iron-sulfur cluster (ISC) assembly machinery, so as to repeat the steps described above. Figure 3.

Search for DNA lesions by DNA repair proteins using their Fe-S clusters and DNA- mediated charge transfer

  . A reduced (2+ state) DNA repair enzyme (BER glycosylase or helicase) loosely binds DNA (step 1). After transfer of one electron to a highly oxidizing guanine cation radical, the oxidized form (3+ state) tightly binds DNA (step 2). Then, a second DNA repair enzyme of similar redox potential (2+ state) loosely binds to DNA (step 3). If DNA is intact between the two proteins (in the absence of DNA damage, step 4), the first enzyme can receive one electron (reduction of the first enzyme, 2+ state) from the second one via DNA-mediated charge transfer and dissociates from DNA. If DNA is damaged between the two enzymes, they cannot exchange electrons (in the presence of damage to DNA, step 4). The second enzyme then transfers its electron to another enzyme localized in the distal side of the lesion (step 5). Both enzymes are oxidized (3+ state), bind DNA efficiently, and can slide along DNA to find and repair the lesion.

ACKNOWLEDGEMENTS

We are grateful to Cécile Mons and Drs. Jean-Claude Drapier, Ewen Lescop (ICSN) and Laurence Vernis (Institut Curie) for many fruitful discussions and for critical reading of the manuscript. Funding information: Work on mitoNEET by MPGC and CB was supported by the Fondation pour la Recherche Médicale (ING20101220983) and the Agence Nationale de la Recherche (ANR-13BSV8-0017-01).

CONFLICT OF INTEREST

The authors declare that they have no conflicts of interest with the contents of this article.