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Iron-sulfur cluster biosynthesis



Leader
 
Dr. Sandrine Ollagnier-de Choudens
CNRS researcher
iRTSV/LCBM
CEA Grenoble
17 rue des Martyrs
38 054 Grenoble cedex 09
Phone: (33) 4 38 78 91 15
Fax: (33) 4 38 78 91 24
 
Iron-sulfur cluster biosynthesis
 
Iron-sulfur clusters are ubiquitous ancient prosthetic groups that are required to sustain fundamental life processes including electron transfer, redox and non redox catalysis, gene regulation and protein structure stabilization. Even though enzymatic systems involved in the formation of iron-sulfur clusters have been identified and characterized, the molecular mechanisms by which clusters are assembled are still unknown.

Escherichia coli contains two machineries involved in iron-sulfur cluster biosynthesis. The first one, referred to as ISC (Iron-Sulfur-Cluster), is essential for general biogenesis of iron-sulfur clusters in bacteria under normal growth conditions. Homologues of these proteins have also been identified in eucaryotes suggesting a highly conserved mechanism. The second machinery, SUF (SulFUr), works under iron limitation and oxidative stress. These two systems are endowed with properties allowing the correct assembly of iron and sulfur atoms to form a cluster (Figure 1). In our laboratory we aim to understand at a fundamental level, the mechanistic features of the processes used to insert iron and sulfur atoms into target-proteins. This is achieved by combining the methods of biochemistry, protein chemistry and spectroscopy.



Figure 1: Iron-sulfur clusters machineries in Escherichia coli

In 2001, we started to investigate the process of iron-sulfur cluster biogenesis with the characterization of the IscA protein. We identified it as an [Fe-S] scaffold protein: a protein able to assemble [Fe-S] clusters and to transfer them efficiently to apo-target proteins. Since 2003, we have worked mainly on the SUF system in collaboration with F. Barras’ group (CNRS, Marseille) who is specialized in bacterial genetic and microbiology. In this context, we structurally and functionally characterized the SufA, SufS and SufE proteins (Figure 2). The former displays properties similar to the IscA protein. SufS and SufE proteins form a complex that is endowed with an important cysteine desulfurase activity that provides sulfur for the biogenesis of [Fe-S] clusters. Based on this result, a new two-component cysteine desulfurase class could be identified that was later extended by our work on the CsdA-CsdE complex.
More recently, our researches showed a direct sulfur transfer from SufE to SufA and from SufE to SufB, through a transpersulfuration reaction, leading to the formation of persulfide (cys-S-SH) and polysulfide (cys-S-(S)
n-SH) species located at the conserved cysteine residues (Figure 2). Also recently, we were able to identify a potential iron donor for the [Fe-S] cluster assembly, the bacterial frataxin homologous CyaY.



Figure 2: Summary of knowledge on the SUF system and our objectives for future years (indicated by the « ? » symbol).

For the future, we will pursue the following objectives using different approaches mentioned in the introduction:

1- Identify the SufBCD function (role of the ATPase activity, role of the [Fe-S] cluster on SufB);

2- Structural and functional characterization of the as-isolated SufA protein containing its metallic cofactor [Fe-S]; Comparison to the in vitro results;

3- Unravel the molecular mechanism by which iron-sulfur clusters are assembled within scaffold protein, using SufA as a model. Identify whether iron or sulfide, is incorporated first at the active site and identify which transfer mechanisms to the target proteins are involved.

 
PhD on the subject:
 
Carine Rousset.
Structural and Functional studies of Quinolinate Synthase: an iron-sulfur protein as a key target of antibacterial agents.
[Abstract]
[Thesis on-line]

Maïté Sendra.
Mechanistic studies of iron-sulfur cluster assembly in Escherichia coli: Which role for SufA?
[Abstract] [Thesis on-line]
 
Publications
 

Wollers S, Layer G, Garcia-Serres R, Signor L, Clemancey M, Latour JM, Fontecave M and Ollagnier de Choudens S
Iron-sulfur (Fe-S) cluster assembly: The SufBCD complex is a new type of Fe-S scaffold with a flavin redox cofactor.
Journal of Biological Chemistry, 2010, 285(30): 23331-23431

Gupta V, Sendra M, Naik SG, Chahal HK, Huynh BH, Outten FW, Fontecave M and Ollagnier de Choudens S
Native Escherichia coli SufA, coexpressed with SufBCDSE, purifies as a [2Fe-2S] protein and acts as an Fe-S transporter to Fe-S target enzymes.
Journal of the American Chemical Society, 2009, 131(17): 6149-6153

Chandor-Proust A, Berteau O, Douki T, Gasparutto D, Ollagnier de Choudens S, Fontecave M and Atta M
DNA repair and free radicals: New insights into the mechanism of spore photoproduct lyase revealed by single amino acid substitution.
Journal of Biological Chemistry, 2008, 283(52): 36361-36368

Fontecave M and Ollagnier-de-Choudens S
Iron-sulfur cluster biosynthesis in bacteria: Mechanisms of cluster assembly and transfer.
Archives of Biochemistry and Biophysics, 2008, 474(2): 226-237

Rousset C, Fontecave M and Ollagnier de Choudens S
The [4Fe-4S] cluster of quinolinate synthase from Escherichia coli: Investigation of cluster ligands.
FEBS Letters, 2008, 582(19): 2937-2944

Layer G, Gaddam SA, Ayala-Castro CN, Ollagnier-de Choudens S, Lascoux D, Fontecave M and Outten FW
SufE transfers sulfur from SufS to SufB for iron-sulfur cluster assembly.
Journal of Biological Chemistry, 2007, 282(18): 13342-13350

Loiseau L, Gerez C, Bekker M, Ollagnier-de Choudens S, Py B, Sanakis Y, Teixeira de Mattos J, Fontecave M and Barras F
ErpA, an iron sulfur (Fe-S) protein of the A-type essential for respiratory metabolism in Escherichia coli.
Proceedings of the National Academy of Sciences USA, 2007, 104(34): 13626-13631

Sendra M, Ollagnier de Choudens S, Lascoux D, Sanakis Y and Fontecave M
The SUF iron-sulfur cluster biosynthetic machinery: Sulfur transfer from the SUFS-SUFE complex to SUFA.
FEBS Letters, 2007, 581(7): 1362-1368

Layer G, Ollagnier de Choudens S, Sanakis Y and Fontecave M
Iron-sulfur cluster biosynthesis: Characterization of Escherchia coli CyaY as an iron donor for the assembly of [2Fe-2S] clusters in the scaffold IscU.
Journal of Biological Chemistry, 2006, 281(24): 16256-16263

Fontecave M, Ollagnier-de Choudens S, Py B and Barras F
Mechanisms of iron-sulfur cluster assembly: The SUF machinery.
Journal of Biological Inorganic Chemistry, 2005, 10(7): 713-721

Loiseau L, Ollagnier-de Choudens S, Lascoux D, Forest E, Fontecave M and Barras F
Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting Fe-S cluster biogenesis in Escherichia coli.
Journal of Biological Chemistry, 2005, 280(29): 26760-26769

Ollagnier-de Choudens S, Sanakis Y and Fontecave M
SufA/IscA: reactivity studies of a class of scaffold proteins involved in Fe-S cluster assembly.
Journal of Biological Inorganic Chemistry, 2004, 9(7): 828-838

Loiseau L, Ollagnier-de Choudens S, Nachin L, Fontecave M and Barras F
Biogenesis of Fe-S cluster by the bacterial Suf system: SufS and SufE form a new type of cysteine desulfurase.
Journal of Biological Chemistry, 2003, 278(40): 38352-38359

Ollagnier-de Choudens S, Lascoux D, Loiseau L, Barras F, Forest E, and Fontecave M
Mechanistic studies of the SufS-SufE cysteine desulfurase: Evidence for sulfur transfer from SufS to SufE.
FEBS Letters, 2003, 555(2): 263-267

Ollagnier-de Choudens S, Nachin L, Sanakis Y, Loiseau L, Barras F and Fontecave M
SufA from Erwinia chrysanthemi. Characterization of a scaffold protein required for iron-sulfur cluster assembly.
Journal of Biological Chemistry, 2003, 278(20): 17993-18001

Ollagnier-de Choudens S, Mattioli T, Takahashi Y and Fontecave M
Iron-sulfur cluster assembly: Characterization of IscA and evidence for a specific and functional complex with ferredoxin.
Journal of Biological Chemistry, 2001, 276(25): 22604-22607

 
Biosynthesis of NAD: NadA protein as an antibacterial target?
 
Nicotinamide adenine dinucleotide (NAD) plays a crucial role as a cofactor in numerous essential redox biological reactions. In fact, in all living organisms, NAD derives from quinolinic acid, the biosynthetic pathway of which differs among organisms. In most eukaryotes and some bacteria, quinolinic acid is produced via the degradation of tryptophan whereas in Escherichia coli it is synthesized from L-aspartate and dihydroxyacetone phosphate (DHAP) as the result of the concerted action of two enzymes, the L-aspartate oxidase, a flavin adenine dinucleotide (FAD)-dependent flavoenzyme encoded by the nadB gene, and the quinolinate synthetase, a [4Fe-4S] enzyme encoded by the nadA gene (Figure 3). Beside the de novo synthesis of NAD, a salvage pathway exists that enables NAD to be recycled. The presence of distinctly different pathways in most prokaryotes and eukaryotes for the biosynthesis of quinolinic acid and the absence of the salvage pathway for some suggests that NadA might prove to be a key target for the design of antibacterial agents.



Figure 3: Reaction catalyzed by the Quinolinate synthase.

Quinolinate synthase from Escherichia coli and Mycobacterium tuberculosis are available in our laboratory in their active [4Fe-4S] form. Our future objectives are the following:

1- Three-dimensional structure determination (in collaboration with Juan Fontecilla's laboratory),
2- Design of molecules that inhibit NadA protein (substrate analogues, analogues of the reaction intermediates) (collaboration with Olivier Hamelin),
3- Identification of the [4Fe-4S] ligands.

We were also involved in the characterization of the plant quinolinate synthase from Arabidopsis thaliana (in collaboration with M and E Pilon-Smith, Colorado, USA). This is a fascinating system since the protein results from the fusion of a SufE domain and a NadA domain. This may have a functional significance with the SufE domain specifically devoted to shuttle the sulfur between the plant cysteine desulfurase (CpNifS) and the NadA domain allowing the assembly of the catalytically essential [4Fe-4S] cluster. We are interested to study at a molecular level the assembly of the [4Fe-4S] cluster on the NadA domain through the intraproteic sulfur transfer from the SufE domain to the NadA domain in the presence of iron, L-cysteine and CpNifS. This study may help to unravel the [Fe-S] assembly process.

 
Publications
 
Murthy UMN, Ollagnier-de-Choudens S, Sanakis Y, Abdel-Ghany SE, Rousset C, Ye H, Fontecave M, Pilon-Smits EA and Pilon M
Characterization of Arabidopsis thaliana SuFE2 and SuFE3: Functions in chloroplast iron-sulfur cluster assembly and NAD synthesis.
Journal of Biological Chemistry, 2007, 282(25): 18254-18264

Ollagnier-de Choudens S, Loiseau L, Sanakis Y, Barras F and Fontecave M
Quinolinate synthetase, an iron-sulfur enzyme in NAD biosynthesis.
FEBS Letters, 2005, 579(17): 3737-3743
 
DNA repair and Spore Photoproduct Lyase
 
The overwhelming majority of DNA photoproducts in UV-irradiated spores is a unique thymine dimer called spore photoproduct (SP). In Bacilli and Clostridii bacteria this lesion is specifically repaired by the spore photoproduct lyase (SPL). This enzyme belongs to the Radical-SAM enzyme superfamily and directly reverts SP to two unmodified thymines. We are unravelling the mechanism of the reaction catalyzed by this fascinating enzyme that uses a radical chemistry to repair DNA lesions (see Dr. Mohamed Atta).
 
Biosynthesis of sulfur containing compounds and formation of C-S bonds