Elucidating the mechanisms of [4Fe-4S] cluster insertions into the cytosolic iron-sulfur protein assembly component Nar1
Joseph J. Braymer
Philipps-Universität Marburg
A majority of metal or bioinorganic cofactor transfer reactions are governed by protein interactions, yet mechanistic detail remains unclear for many metalloproteins in how they pass cofactors from one protein to the next, especially at sites buried within proteins. This applies to one of the most ubiquitous types of cofactors found in bacteria, archaea, and eukaryotes, namely iron sulfur (Fe/S) clusters. In the model eukaryotic organism Saccharomyces cerevisiae, 18 mitochondrial Fe/S cluster (ISC) assembly proteins and 11 cytosolic Fe/S protein assembly (CIA) components create an extensive cellular protein network, which synthesizes, traffics, and inserts Fe/S clusters into target apoproteins.
An interesting aspect of the CIA machinery in eukaryotes is that many of the trafficking factors themselves bind more than one Fe/S cluster and it remains poorly understood how the CIA components themselves are matured. For example, Nar1 is peculiar because it has been proposed to be a [4Fe-4S] cluster trafficking mediator of the CIA pathway via a labile [4Fe-4S] cluster and at the same time a target apoprotein that requires a buried, non-transferable [4Fe-4S] cluster. Furthermore, Nar1 is homologous to bacterial and algal [FeFe]-hydrogenases, but doesn’t have the characteristic hydrogenase function. Why a hydrogenase-like protein has evolved as an essential eukaryotic Fe/S cluster trafficking protein remains a challenging question to address in the Fe/S cluster biogenesis field. Our aim is to assign the molecular function of Nar1 in the CIA pathway, which would advance our understanding of how Fe/S clusters can be transferred or inserted into apoproteins. Subsequently, this will also enhance our understanding of the CIA machinery and how disruptions in cytosolic Fe/S cofactor trafficking lead to Fe/S protein assembly diseases.
Collaborations:
- Antonio Pierik, TU Kaiserslautern
- Thomas Happe, Ruhr-Universit Bochum
- Holger Dobbek, Humboldt Universität Berlin
- Seigo Shima, Philipps-Universität Marburg
- Roland Lill, Philipps-Universität Marburg
Project description
James Birrell and Ingrid Span
Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr
Heinrich-Heine-Universität Düsseldorf
The main objective of the proposed research is to provide structural insight into the catalytic cycle of the [FeFe] hydrogenase and in particular the conformational flexibility of the unique iron-sulfur cluster cofactor, the H-cluster, at the heart of the enzyme.
We have already established the production of the protein in various states as well as crystallization conditions for DdHydAB in the Hoxair state. As a next step, we intend to characterize various states of the enzyme and correlate the conformational changes observed by crystallography with the electronic structure determined by spectroscopy. In addition, we will correlate structural and spectroscopic information obtained in crystallo with functional studies and theoretical calculations.
The specific aims are to characterize the electronic and three-dimensional structures of
- the Hoxair state to locate the sulfur in the active site
- the Htrans state in crystallo by mild reduction of the DdHydAB crystals
- the reduced states Hred and HredH+ at high and low pH values, respectively, obtained by activation of DdHydAB crystals by exposure to hydrogen
- the Hhyd state that corresponds to a “super-reduced” and activated DdHydAB generated by treatment with high concentrations of sodium dithionite
- the Hox-blue and Hox states produced by oxidation of activated DdHydAB crystals under nitrogen atmosphere at low and high pH
The results obtained by structural biology, IR and EPR spectroscopies, and theoretical calculations will be combined to obtain detailed insights into the mechanism of [FeFe] hydrogenase. Collecting structural and spectroscopic data on the identical sample in the crystal form will allow for the rationalization of intermediates in the catalytic cycle. This will ultimately lead to an improved understanding of how the catalytic cycle of this bidirectional enzyme operates. The new insights will significantly contribute to a fundamental understanding of [FeFe] hydrogenases and inspire further studies in basic research as well as the development of synthetic molecular catalysts.
Iron-sulfur cluster electronic structural evolution and its contribution to diverse functionality
Serena DeBeer and Frank Neese
Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr
This project represents a dedicated effort to combine the results of advanced X-ray spectroscopic methods with state-of-the-art quantum chemical calculations in order to obtain insight into the electronic structural evolution through a series of iron-sulfur clusters ranging from relatively straightforward Fe-S monomers all the way to the intimidatingly complex FeMoco active site of nitrogenase. The prime target for the experimental part of this proposal is to develop 2p3d resonant X-ray emission (RXES) spectroscopy, a two-dimensional form of inelastic X-ray scattering, into a major tool for the investigation of complex systems, such as Fe/S clusters. The small amount of data that has been collected so far indicates that the information content of this method is very high, but the complexity of the underlying theory has so far prevented very detailed assignments to be made and electronic structure related conclusions to be drawn. Hence, we plan to closely combine RXES experiments (as well as other, more established techniques) in conjunction with high-level ab initio electronic structure methods. The calculations will largely be based on the density matrix renormalization group (DMRG) formalism, the only available method that is able to deal with the complexity of oligonuclear open-shell, mixed-valence transition metal complexes such as that presented by Fe/S clusters. The validity and scope of applicability of model Hamiltonians such as the widely used Heisenberg-Double Exchange (HDE) Hamiltonian will be established alongside the analysis of the experimental data. Taken together, we believe that the present project will arrive at experimentally validated electronic structure descriptions of Fe/S clusters at an unprecedented level of detail. The consequences of these electronic structure intricacies on the reactivity of these clusters will be discussed.
Collaborations
| F. Meyer | M. Boll | G. Fritz |
| O. Einsle | O. Lenz | S. Shima |
| C. Schulzke | R. Lill | C. Berndt |
CooC2/AcsF and Cfd1/Nbp35: maturation of complex Fe/S-clusters by MinD-type ATPases
Holger Dobbek
Humboldt Universität Berlin
Anaerobic bacteria and archaea use homologous enzymes to convert CO2 and H2 to acetyl-CoA and methane, which determine since the dawn of life the global carbon cycle on earth.
In recent years, we have discovered and investigated a Ni insertase for the central enzyme acetyl-CoA synthase (ACS). While one or more maturation enzymes are known for all other central Ni enzymes; so far no enzyme supporting the maturation of Ni,Ni-[4Fe4S] cluster, called Cluster A, has been described. We could show that the maturation protein CooC2, a MinD-family ATPase, forms a specific complex with the Ni-deficient ACS, that this protein complex binds two Ni ions with high affinity and finally that the active ACS is liberated by the addition of Mg-ATP to the complex. Bioinformatic analyzes suggest that the CooC ATPases can be divided into three subclasses: one subclass contains ATPases for the maturation of the [NiFe4S4] center of the carbon monoxide dehydrogenases; one subclass, with CooC2 as the first example described functionally, consists of ATPases responsible for the maturation of the ACS; the role of the third subclass is unknown.
In the first funding period we want to investigate: (I) whether the homologous enzymes from archaea have the same function as the bacterial CooC2 protein. This is particularly interesting since the ACS from Archaea differs in size and association with CODH and CoFeSP from the bacterial enzyme: compared to the bacterial enzymes it misses the N-terminal domain, but is present in a multi-enzyme complex of 2.5 MDa. We want to investigate (II), how the high affinity for Ni is generated in the CooC2-apoACS complex and which role ATP plays in the maturation. In addition to apo- and holo-ACS, we can produce two stable maturation intermediates giving us the rare opportunity to “watch” the stepwise assembly of a complex Ni, Fe, S-cluster. Furthermore, (III) we want to compare the insertion strategy of CooC2 with a different type MinD metal-insertase, Cfd1/Nbp35, a key complex of cytosolic Fe/S cluster maturation machinery. In order to achieve the three objectives, integration in the SPP and the interaction with other groups of the SPP are indispensable.
Collaborations:
AG Pierik (EPR spectroscopy)
AG Schünemann (Mössbauer spectroscopy)
AG Zebger (Vibrational spectroscopy)
AG Leimkühler (Metal analysis)
AG Lill (Cfd1-Nbp35)
AG Adrian (Proteomics).
Complex Iron-Sulfur Cluster Assembly for Biological Nitrogen Fixation
Oliver Einsle
Albert-Ludwigs-Universität Freiburg
The [Mo:7Fe:9S:C]:homocitrate cluster known as FeMo cofactor is the catalytic center of nitrogenase and thus the active principle of biological nitrogen fixation. It is synthesized ex situ, in parallel with the maturation of the protein component NifDK, requiring the interplay of a large number of maturation factors that assemble the unique and intricate structure of the cluster from simple [2Fe:2S] fragments. The biogenesis of nitrogenase largely does not rely on the constitutive enzymes of [Fe:S] assembly, but employs a dedicated system consisting of the cysteine desulfurase NifS, the scaffold protein NifU and the radical/SAM enzyme NifB that assembles the cluster core while inserting an unusual, interstitial carbide ion into its center. In order to better understand the molecular basis of FeMo cofactor biogenesis, this project focuses on the recombinant production and analysis of the proteins NifS, NifU and NifB from a variety of organisms, aiming at a crystallographic analysis as well as a spectroscopic and functional characterization within the Priority Programme 1927.
We will furthermore investigate the recently presented complex of FeMo cofactor with the inhibitor carbon monoxide. From this, we on one hand expect important insights into the general reaction mechanism of nitrogenase, and on the other hand a deeper analysis of the reduction of CO itself. While CO acts primarily as an inhibitor of Mo-dependent nitrogenase, the alternative, V-dependent enzyme can break the triple bond of the molecule, reducing the carbon portion to a spectrum of short-chain and partially unsaturated hydrocarbons. The mechanistic implications of these activities are only partly understood and will be addressed by a concerted study employing a broad range of methodologies.
A further part of the project aims at the application and development of the SpReAD method that allows for a spatially-resolved analysis of the X-ray absorption properties of individual atoms within a crystalline sample. This provides information on the individual oxidation states of atoms and thereby on the properties and reactivities of entire metal enters. The method is established and will be used in a series of collaborations within priority program 2917, including systems such as nitrogenase, hydrogenase and CO dehydrogenase.
Collaborations
Thorsten Friedrich Gunhild Layer/Jürgen Moser
Serena DeBeer / Frank Neese Oliver Lenz
Ingo Zebger Matthias Ullmann
Holger Dobbek Antonio Pierik
Volker Schünemann Matthias Boll
Franc Meyer
Assembly of Iron-Sulfur Clusters in the NADH:Ubiquinone Oxidoreductase
Thorsten Friedrich
University Freiburg
Energy-converting NADH:ubiquinone oxidoreductase, complex I, couples the transfer of two electrons from NADH to ubiquinone with the translocation of four protons across the membrane. The Escherichia coli complex consists of 13 different subunits and one flavin mononucleotide and nine different iron-sulfur (Fe/S) clusters as cofactors for electron transfer. The assembly of the Fe/S clusters in bacterial complex I has not been investigated so far. Their biogenesis is assumed to be catalyzed by the ISC and SUF systems, but this has never been challenged experimentally. One aim of the project is to identify whether one or both maturation systems are involved in the biogenesis of the Fe/S clusters of complex I, taking into account different growth conditions. Other assembly factors possibly involved in their biogenesis such as GrxD, BolA, NfuA and others have not yet been identified. Especially, it is not known whether the biogenesis of individual clusters of the complex depend on individual assembly factors. In the project we will characterize factors needed for the assembly of the individual clusters under normal and stress conditions such as the presence of reactive oxygen species (ROS). A special focus is put on the role of the inducible lysine decarboxylase, known to be involved in bacterial acid stress response, for the assembly of the Fe/S cluster called N2 that is coordinated by a unique arrangement of cysteine residues. The possible involvement of a putative triad complex comprising the inducible lysine decarboxylase, the AAA+ enzyme RavA and ViaA containing a von-Willebrandt factor in the assembly of cluster N2 is the main focus of this project. The complicated assembly of N2 might be due to its proposed function in energy-conservation. Consequently, we will investigate whether cluster N2 is directly involved in proton translocation.
Planned cooperations:
Adrian: Complex I in Dehalococcoides McCartyi
Berndt/Lillig: Role of GrxD in the assembly of complex I iron-sulfur clusters
Einsle: SpReAD of complex I and variants
Leimkühler: Comparative analysis with nitrate/DMSO reductases
Lill: Comparative analysis of the role GrxD, BolA and NfuA
Mendel: Metal binding to LdcI (CadA)
Ullmann: Protonation of Fe/S cluster
Zebger: Resonance Raman spectroscopy of complex I iron-sulfur clusters
Analysis of the properties and the assembly of the intramembranous FeS cluster of the Na+ -NQR and the RNF complex
Günter Fritz Julia Fritz-Steuber
Uniklinik Freiburg University of Hohenheim
Respiratory complexes may contain FeS clusters that are involved in electron transfer coupled to ion translocation. The so-called “Rhodobacter nitrogen fixation” (Rnf) respiratory complex was identified as an essential part of the nitrogen fixation machinery. Deletion of the rnf genes causes a defect in FeS cluster assembly characterized by an accumulation of inactive and iron deficient NifH protein. The Rnf complex consists of six subunits and catalyzes the oxidation of ferredoxin using NAD+ as an electron acceptor to drive transport of Na+ across the membrane. Rnf complex is closely related to another Na+-pumping respiratory enzyme, the Na+-translocating NADH:quinone oxido-reductase (Na+-NQR). Both membrane protein complexes share the same basic architecture and mechanism of redox-driven ion translocation. The X-ray structure of Na+-NQR revealed an unusual and hitherto unknown FeS center in the midst of the membrane that is part of a transmembrane electron transfer pathway. The FeS binding site is strictly conserved in the corresponding subunits RnfA and RnfE of the Rnf complex. This FeS center is so far unique with respect to its unprecedented localization, its coordination and its unusual spectroscopic properties. The localization in the membrane raises the question how this FeS is inserted into these integral membrane proteins, and we will study its maturation by genetic and biochemical approaches. We will characterize the intramembranous FeS cluster by Mössbauer, EXAFS and quantum chemical calculations in collaboration with S. deBeer and F. Neese to resolve the electronic structure of the cluster. We want to explore whether the Fe-Fe distances change during electron transfer. Such redox-dependent changes might influence the structure of the redox-driven pump. The redox properties of the FeS cluster will be addressed using EPR spectroscopy in collaboration with O. Einsle.
Collaborations
With S. DeBeer and F. Neese:
Mössbauer, EXAFS and quantum chemical calculations to resolve the electronic structure of the intramembranous FeS cluster of the NQR
With O. Einsle:
EPR spectroscopy to determine the redox potential of the intramembranous FeS cluster at varying Na+ concentrations
Deciphering the stepwise cellular assembly and integration of the [FeFe]-hydrogenase H-cluster
Thomas Happe
Ruhr-Universität Bochum
The maturation of complex FeS-clusters in living cells usually requires a comparatively large number of helper proteins (maturases) that enable cofactor assembly in a sequential and well-coordinated manner. In case of the cofactor of [FeFe]-hydrogenases (H-cluster) the dedicated maturation system of the unique [2Fe2S]-subcluster (2FeH) consists of only three enzymes. The radical SAM proteins HydE and HydG provide the basic subparts (synthons), including the unusual ligand sphere of the Fe ions. The GTPase and scaffold protein HydF offers the proper environment for the assembly of a cofactor precursor (p2FeH) and determines the succession of assembly steps by specific consecutive interactions with HydE and HydG. While numerous aspects of synthon synthesis via HydG have been clarified, the steps of 2FeH assembly on HydF and the final steps of H-cluster integration into the non-maturated [FeFe]-hydrogenase protein are still not characterized in sufficient detail, leaving open several questions regarding the entire process.
To understand the sequence of events required to assemble p2FeH on HydF, we will characterize intermediates of the structurally characterized HydF of Thermosipho melanesiensis and directed protein variants spectroscopically. Interestingly, the maturation system of green algal [FeFe]-hydrogenases is even more compact than what is known from bacteria, as the number of maturases is reduced to only two proteins, HydG and HydEF, the latter being a fusion protein between HydE and HydF. We plan to heterologously express and crystallize HydEF to understand the specifics of the fusion protein. Additionally, the characteristics of 2FeH precursor assembly on the HydF domain will be compared to those of T. melanesiensis HydF. Identified commonalities and differences will help us to fill the gaps in understanding the in vivo maturation process.
Collaborations
- Oliver Einsle
- Ute Krämer
- Oliver Lenz/ Ingo Zebger
- Franc Meyer
- Antonio Pierik
- Gary Sawers
- Michael Schroda
- Volker Schünemann
- Seigo Shima
Characterization and reaction mechanism of the nitrogenase-like reductase NflH/NflD involved in cofactor F430 biosynthesis
Gunhild Layer
Universität Freiburg
The complex metallo-enzyme nitrogenase and several simpler, iron-sulfur cluster containing nitrogenase-like enzyme systems are involved in three key metabolic processes necessary to sustain life on earth, namely nitrogen fixation, photosynthesis and biological methane formation. Whereas nitrogenase catalyzes the reduction of dinitrogen to ammonia, the nitrogenase-like enzymes dark operative protochlorophyllide oxidoreductase (DPOR) and chlorophyllide oxidoreductase (COR) catalyze specific C-C double bond reduction reactions during the biosynthesis of chlorophylls and bacteriochlorophylls, respectively. The third nitrogenase-like enzyme system is termed Nfl (nitrogen fixation like), is found in all methanogenic archaea and catalyzes several C-C double bond reduction reactions during the biosynthesis of the nickel-containing tetrapyrrole cofactor F430. The Nfl system is only scarcely characterized. Therefore, the aim of this project is the characterization and reaction mechanism of this nitrogenase-like reductase.
As is the case for nitrogenase, DPOR and COR, the Nfl system consists of two components: a reductase termed CfbC and a catalytic component named CfbD. However, the Nfl system seems to exhibit a simpler architecture than nitrogenase, DPOR and COR. Based on our preliminary work, CfbC and CfbD are homodimeric proteins containing an intersubunit [4Fe-4S] cluster each. CfbC is proposed to transfer electrons to CfbD where the reduction of the actual substrate takes place. In this project within the SPP 1927 we plan to characterize the iron-sulfur clusters of CfbC and CfbD in detail by different spectroscopic techniques and identify the cluster ligands. The potential ATP-induced conformational changes within CfbC and the interaction between the two proteins will be studied. The substrate specificity of CfbC/CfbD will be investigated in order to obtain insights into the NflD active site architecture and plasticity. We will study the possibility that the reductase components of nitrogenase, DPOR and COR might be exchangeable with the reductase of the Nfl system. Another aim will be the identification of potential interaction partners of CfbC/CfbD in vivo and in vitro. Finally, we will try to crystallize CfbC and CfbD in order to obtain the crystal structures of these proteins.
Cooperations
Lorenz Adrian (UFZ Leipzig) – Mass-spectrometry
Oliver Einsle (Universität Freiburg) – Small artificial substrates, X-ray crystallography
Jürgen Moser (TU Braunschweig) – Artificial tetrapyrrole substrates, Anaerobic protein crystallization
Antonio Pierik (TU Kaiserslautern) – EPR spectroscopy, Dye-mediated redox titration
Volker Schünemann (TU Kaiserslautern) – Mössbauer spectroscopy
Ingo Zebger (TU Berlin) – Resonance Raman spectroscopy, Conformational changes in NflH and NflD,
FT-IR difference spectroscopy
Iron-sulphur cofactors involved in metal centre assembly and catalysis of hydrogenase
Oliver Lenz, Ingo Zebger
Technische Universität Berlin
In the second funding period of the Priority Program (PP) 1927, our joint project will focus, first, on the elucidation of the unusual active site properties of an O2-tolerant, thermostable NAD+-reducing [NiFe]-hydrogenase and their impact on the catalytic properties of this complex FeS cluster enzyme. The molecular and mechanistic details will be investigated in a collaborative approach, which will involve electron paramagnetic resonance (EPR), infrared (IR), and resonance Raman (RR) spectroscopy to identify and characterize catalytically relevant redox states both in vitro and in vivo. Comparative studies will be performed on a related F420-reducing [NiFe]-hydrogenase. In this context, we will apply a recently established experimental setup, which allows (cryogenic) IR and RR measurements on the same protein crystal under controlled gas atmospheres. In combination with X-ray crystallography and theoretical methods, these experiments will provide detailed structural and electronic information on individual catalytic intermediates. This interdisciplinary approach will be extended to analyze [Fe] hydrogenase and nitrogenase. In the second part of our joint project, we seek to improve the understanding of the multistep biosynthesis process of the NiFe(CN)2(CO) cofactor of [NiFe] hydrogenase. We will investigate the reaction mechanism by which HypX converts formyl-tetrahydrofolate via formyl-CoA into the active site CO ligand of [NiFe] hydrogenases under oxic conditions. Experiments are planned to unveil the composition of the FeS cluster-containing HypCD maturation complex competent in receiving the (HypX-generated) CO molecule to eventually form the Fe(CN)2(CO) synthon. Based on a recently developed strategy, we are now able to purify isolated large subunits of [NiFe]-hydrogenases in different maturation stages of the catalytic center. This unique situation allows us to unravel the sequence of events of NiFe(CN)2(CO) cofactor assembly. Vibrational spectroscopic techniques will be used to investigate the role and interplay of FeS centers and other metals in the maturation and catalysis of hydrogenase, nitrogenase(-like) enzymes and Complex I. In close collaboration with members of the PP consortium and external partners, we will exploit our results to gain a detailed picture of the overarching principles of FeS-based maturation and catalysis.
Cooperations
- Sawers: Function of the accessory HypD protein involved in [NiFe]-hydrogenase active site assembly, biosynthesis of the active site ligands under anaerobic conditions.
- Shima: IR-spectroscopic characterisation of early reaction intermediates in the catalytic cycle of [Fe]-hydrogenase together with S. Stripp, V. Schünemann, A. Pierik, S. DeBeer.
- Einsle: Spectroscopic characterisation of the P-cluster and its maturation intermediates as well as of the active site in nitrogenases.
- DeBeer / F. Neese/ R. Björnsen: Analysis of metal-ligand interactions by X-ray absorption/emission spectroscopy and QM/MM calculations on metal cofactors.
- Layer: IR spectroscopic characterization of substrate interaction, and conformational changes in nitrogenase-like enzymes.
- Lill: Role of conserved histidines within the GLRX5-BOLA1 complex for [2Fe2S] cluster ligation
- Friedrich: Analysis of protonation events in the vicinity of the N2 FeS cluster of Complex I.
- Dobbek: Spectroscopic analysis of the double-cubane protein and the F420-reducing [NiFe]-hydrogenase, crystallization of hydrogenase maturation intermediates
- Schulzke: Spectroscopic characterisation of Moco model compounds.
- Schünemann: Mößbauer-related techniques on specific states of thermophilic [NiFe]-hydrogenase and nitrogenases
- Ullmann: QM/MM calculations on the active site in [NiFe]-hydrogenases
Cooperative function of Iron-Sulfur clusters and metal homeostasis on the biosynthesis of molybdoenzymes
Silke Leimkühler
Universität Potsdam
Recently, a link between the biosynthesis of the molybdenum cofactor (Moco) and FeS cluster biosynthesis has been discovered. The biosynthesis of Moco is a highly conserved and complex pathway, in which the MoaA protein presents a conserved protein which catalyzes the first and essential step in Moco biosynthesis in bacteria. MoaA belongs to the class of radical/SAM enzymes which contain the SAM-binding [4Fe4S] cluster at their N-terminus and, in addition, the MoaA proteins contain a [4Fe4S] cluster at its C-terminus, which binds the substrate GTP. The further steps of Moco biosynthesis involve the IscS protein as a major player. IscS was initially described as a housekeeping L-cysteine desulfurase which mobilizes the sulfur for FeS cluster biosynthesis. IscS was shown to be additionally involved in the mobilization of sulfur for the synthesis of the dithiolene group of MPT. Recently it was shown that IscS is also required for the formation of the terminal sulfido ligand present at the molybdenum active site of molybdoenzymes like formate dehydrogenases and the periplasmic aldehyde oxidoreductase in Escherichia coli. In addition, many molybdoenzymes coordinate FeS clusters and, thus, directly depend on FeS cluster synthesis and their insertion to produce active holo-enzymes.
Our goal is to study the crosstalk of FeS cluster biosynthesis and Moco biosynthesis in E. coli. A special link is presented between both pathways on the level of availability of the L-cysteine desulfurase IscS, and the so far unidentified FeS cluster inserting proteins. We will study the biosynthesis and insertion of FeS clusters into MoaA and molybdoenzymes like nitrate reductase, DMSO reductase and the periplasmic aldehyde oxidoreductase. Total metal homoeostasis (here the availability of Fe, Mo and Zn) will be analyzed on its effect on Moco biosynthesis, the synthesis of cPMP, the conversion of cPMP to MPT and the insertion of Moco and FeS clusters into molybdoenzymes. In total, our analyses will shed light into the complex FeS cluster network for molybdoenzyme maturation in E. coli.
Collaborations
Lorenz Adrian (UFZ Leipzig): blue native 2D nLC MS/MS
Matthias Boll (Universität Freiburg): Wco insertion and biosynthesis
Thorsten Friedrich (Universität Freiburg): comparative studies of the FeS cluster insertion
Johann Heider (Universität Marburg): Moco and Wco biosynthesis
Ute Krämer (Ruhr-Universität Bochum): RNAseq
Roland Lill (Universität Marburg): FeS clusters insertion
Ralf Mendel (TU Braunschweig): FeS cluster insertion into Nit7
Antonio Pierik (Universität Kaiserslautern): identification of common motifs for FeS clusters
Constanze Pinske (Universität Halle): studies on the assembly of formate:hydrogen lyase
Gary Sawers (Universität Halle): influence on hydrogenase activity in E. coli k.o. strains
Volker Schünemann (Universität Kaiserslautern): Mössbauer spectroscopy on whole cells,
Carola Schulzke (Universität Greifswald): Moco model compounds
Günter Schwarz (Universität Köln): comparative studies of FeS insertion into MoaA/MOCS1A
Hans Richnow (UFZ Leipzig): NanoSIMS on Fe and Mo distribution in bacterial cells
Role of the mitochondrial Bol1 and Bol3 proteins in iron-sulfur cluster delivery to diverse recipient proteins
Roland Lill
Phillips-Universität Marburg
The biogenesis of mitochondrial iron-sulfur (Fe/S) proteins is catalyzed by the conserved ISC assembly machinery and can be dissected into three major steps (see Lill, R. (2020) Annu. Rev. Biochem.). First, a [2Fe-2S] cluster is synthesized de novo on the scaffold protein Isu1 by the sulfur donor complex Nfs1-Isd11-Acp1 and four other ISC factors. Second, the Fe/S cluster is released from Isu1 by a dedicated Hsp70 chaperone system, and transferred via the monothiol glutaredoxin Grx5 to [2Fe-2S] target proteins. Third, the transiently Grx5-bound [2Fe-2S] cluster is converted by the Isa1-Isa2-Iba57 proteins to a [4Fe-4S] cluster, a reaction requiring electron input from the ferredoxin Yah1. The newly made [4Fe-4S] cluster, after intermediate binding to the ISC targeting factors Nfu1 or Ind1, finally becomes inserted into recipient [4Fe-4S] proteins. Work within the “Fe/S for Life” priority program has identified the two yeast mitochondrial proteins Bol1 and Bol3 as additional ISC targeting factors. They cooperatively facilitate specific maturation of lipoyl synthase and respiratory complex II. Patient analysis and recent biochemical work shows that human BOLA3 (Bol3 homolog) but not human BOLA1 performs a similar targeting function. We have described an interaction of the two Bol proteins with [2Fe-2S] cluster-containing Grx5, but the physiological meaning of this complex is unclear. In the current funding period, we aim to reach a physiologically meaningful mechanistic understanding of holo-Grx5-Bol3 function that explains its involvement in [4Fe-4S] protein maturation. To this end, we will reconstitute lipoyl synthase (Lip5) maturation in vitro. We will perform cell biological and biochemical studies to elucidate whether the Bol-Grx5 complexes act before or after the Isa-Iba57 proteins. By examining the function and interaction partners of the Bol proteins we will be able to deduce whether these ISC factors exhibit an increased importance under oxidative stress conditions. A comprehensive mechanistic understanding of Bol protein function will be important for a molecular view of the BOLA3-associated mitochondrial disease MMDS2.
Collaborations
Thorsten Friedrich: Function of the bacterial glutaredoxin GrxD, BolA and NfuA proteins in respiratory complex I assembly.
Carsten Berndt / Christopher H. Lillig: Vertebrate glutaredoxins in regulatory processes.
Antonio J. Pierik: Function of the conserved tryptophan in cytosolic-nuclear Fe/S proteins. EPR spectroscopy
Silke Leimkühler: ISC protein function during the assembly of MoCo in bacteria.
Ralf R. Mendel: Role of the mitochondrial Fe/S protein Nit-7A in fungal Moco biosynthesis.
Günter Schwarz: Maturation of mitochondrial MOCS1A and MOCS1AB proteins.
Holger Dobbek: Function of metal-dependent MinD-type ATPases.
Franc Meyer: Chemistry of Fe/S cluster coordination, model compounds mimicking Fe/S cluster coordination.
Sandra DeBeer: X-ray spectroscopy on Grx-Bol model systems.
Seigo Shima – Hans Heider: Local technical collaboration in the use of equeipment.
Lorenz Adrian – Hans H. Richnow: Use of NanoSIMS and ToFSIMS.
Molybdenum cofactor-biosynthesis and crosstalk to FeS metabolism in Neurospora crassa
Ralf R. Mendel
TU Braunschweig
Molybdenum cofactor (Moco) is the catalytically active prosthetic group in Mo-containing enyzmes. In all eukaryotes studied so far, the first step of Moco biosynthesis resides in the mitochondria while all subsequent steps proceed in the cytosol. This step is catalyzed by two proteins where the first one (Nit-7A) harbors two FeS clusters of the [4Fe-4S] type. But GTP as starting compound is also available in the cytosol. And the cytosol harbors also a FeS cluster synthesis machinery. So the question arises why Moco biosynthesis step 1 is located in the mitochondria. Using the filamentous fungus Neurospora crassa as yeast-like model system we wish to analyse the crosstalk between Moco-biosynthesis and FeS metabolism. In yeast (S. cerevisiae) all principles of eukaryotic FeS cluster biogenesis have been successfully worked out, but yeast has no Mo metabolism. In a first project line, we plan to express the N. crassa nit-7 gene in yeast thus establishing Moco biosynthesis step 1 in yeast. A successful expression of nit-7 in yeast would open up a whole new perspective because the complete arsenal of yeast FeS biogenesis research tools would be at our hands. Clearly, this attempt would also allow to uncover whether the yeast mitochondrial exporter Atm1p which facilitates the export of FeS cluster equivalents, would be able to export also the product of Moco biosynthesis step 1, which we have postulated for its plant homolog ATM3. For a second project line, in preliminary experiments we have already expressed Nit-7A ectopically and stably in the cytosol of N. crassa in a nit-7 knock out-background. We plan to characterize this strain (i) phenotypically (growth on nitrate-media creates a strong demand for Moco and thus also for FeS), (ii) biochemically (re-isolation of ectopically expressed Nit-7A and Nit-7AB and analysis of FeS-clusters), and (iii) via transcriptome analysis (nitrate-induced transcriptional changes in FeS cluster assembly and Moco biosynthesis) in order to address the following questions: What is the donor of FeS clusters for ectopically expressed Nit-7A in the cytosol? Is this process co-regulated with Moco- and FeS-biosynthesis? Are there differences between fungal and human step 1 Moco biosynthsis?
Collaborations:
- Roland Lill
- Günter Schwarz
- Silke Leimkühler
- Antonio Pierik
- Carola Schulzke
Deciphering the function of Fe/S cofactors with alternative cluster ligands: model studies using synthetic analogues
Franc Meyer
Georg-August-Universität Göttingen
Building upon our recent work on the development of high fidelity functional models for the {Cys2His2} ligated Rieske center and the isolation of [2Fe-2S] clusters in unusual oxidation states, this projects aims at deciphering the function of Fe/S cofactors with alternative cluster ligands in a synthetic analogue approach. Specific objectives are: (A) Elucidating intrinsic trends for the thermodynamic and kinetic parameters of proton coupled electron transfer (PCET) reactions at Fe/S clusters, mainly [2Fe-2S] clusters with His-like terminal ligands, to demonstrate a potential PCET role of His-ligation beyond the Rieske centers. (B) Understanding intrinsic ligand rearrangement and exchange processes at specifically designed [2Fe-2S] clusters, which is relevant for understanding ligand exchange during biological Fe/S cluster maturation and transfer. (C) Characterizing the species that form upon reaction of mixed S/N ligated [2Fe-2S] clusters with nitric oxide in order to unravel the effect of cluster oxidation state and His protonation state on NO reactivity pathways, and on potential H2S generation. (D) Emulating radical reactivity at auxiliary Fe/S cofactors in radical SAM enzymes and elucidating factors that control sulfur donation from the Fe/S cluster to a substrate, as seen in biotin synthase (BioB) or lipoyl synthase (LipA). (E) Providing suitable chemically synthesized Fe/S model systems for various other groups in the SPP network; these models either will serve as benchmark systems for new spectroscopic or analytical methods, or will be used for reconstituting Fe/S proteins via integration into the apoforms. In addition, some exploratory attempts will be made at synthesizing a first Fe/S cluster that contains a carbide (C) or carbyne unit (CR) within the cluster core.
Collaborations
- Serena DeBeer/Frank Neese: we provide model systems that are crucial for benchmarking X-ray spectroscopy signatures of Fe/S clusters. On the other hand, the X-ray spectroscopy and theory results will provide important electronic structure information that may help to rationalize Fe/S cluster reactivity patterns observed in this project. Furthermore, DFT support from the Neese group will help to establish the thermodynamics of the radical reactions.
- Volker Schünemann: NRVS studies of intermediates and products of the reaction of synthetic [2Fe-2S] complexes to identify characteristic NO-iron-sulfur modes may provide valuable reference data for the NO-mediated Grx iron-sulfur disassembly that the Schünemann groups studies in cooperation with Carsten Berndt (HHU Düsseldorf) and Christopher H. Lillig (U Greifswald). Furthermore, magnetic field Mössbauer measurements on our synthetic Fe/S models will be performed in the Schünemann lab.
- Carola Schulzke: we will perform magnetic measurements (SQUID) for the molybdenum dithiolene complexes prepared in the Schulzke lab as a contribution to deciphering electronic structures, oxidation and spin states of those molybdopterin model systems. On the other hand, we plan to perform temperature dependent electrochemical measurements in collaboration with the Schulzke group to assess the thermodynamics (entropy and enthalpy) of the redox processes relevant for the PCET studies in our group.
- Matthias Ullmann: we will provide data for redox potentials and pKa values of model complexes that are needed for his simulations of the coupling of catalysis and electron transfer along chains of Fe/S clusters
- Oliver Einsle: a series of [2Fe-2S] (and perhaps also [4Fe-4S]) clusters in varied oxidation states will be made available to the Einsle group to collect reference and benchmarking data for their SpReAD analysis (see section 2.3.E).
- Ingo Zegber/ Peter Hildebrandt: it was envisaged to provide model complexes as reference compounds for their resonance Raman measurements.
Molecular determinants for cytosolic iron-sulfur cluster insertion
Antonio J. Pierik
University of Kaiserslautern
Cytosolic and nuclear iron-sulfur (FeS) proteins act in a broad range of cellular processes in eukaryotes. These proteins are of crucial importance for tRNA modification, ribosomal maturation, DNA replication and repair, and are therefore found in all eukaryotes, including man. The so-called cytosolic iron-sulfur protein assembly (CIA) machinery composed of 11 proteins takes care of FeS protein biogenesis in this cell compartment. In contrast to the rapid increase of knowledge on this machinery, determinants for recognition of the more than forty FeS proteins among the thousands of cytosolic proteins have remained completely obscure. A path driven by FeS cluster transfer to a thermodynamically favoured binding site at the target is tacitly assumed. However, our bioinformatic analysis and preliminary data suggest that a C-terminal tryptophan residue is one of the determinants for the recognition of FeS apoproteins by the Cia1-Cia2-Mms19 targeting complex of the CIA machinery.
In this project we will identify the role and extent of interaction of the C-terminal tryptophan-containing peptides and potential other amino acid sequence determinants with the targeting complex. Mutagenesis experiments, yeast two-hybrid screens, EPR spectroscopy and bioinformatic analysis is used to define surfaces of interaction important for cluster insertion. By training and cooperation the findings will be extended with 3D-structural characterization and compared with assembly in complex FeS-containing enzymes. The interdisciplinary project will yield insight into the molecular determinants for FeS cluster insertion into eukaryotic cytosolic and nuclear proteins. Moreover, this knowledge can be applied to more efficiently assemble complex FeS proteins in the biotechnologically favourable organism yeast.
Training
55Fe-incorporation in the laboratory of Lill.
Peptide binding studies in the laboratory of Leimkühler.
NMR-titration at the CERM in Florence.
Cocrystallization trials in the laboratory of Dobbek.
Training of a PhD student of the Dobbek group (together with Schünemann group).
Training of a PhD student of the Layer group (EPR-based redoxtitration).
Collaborations
EPR (and Mössbauer) spectroscopy (Berndt/Lillig, Heider, Shima, Lill).
EPR spectroscopy of molybdenum (V) in model compounds (Schulzke).
Spectroscopic characterization of maturation factors (Sawers, Schwarz).
Towards a mechanistic understanding of the role of the iron-sulphur cluster-containing HypD protein in diatomic ligand biosynthesis of NiFe-hydrogenases
Gary Sawers
Martin-Luther Universität Halle
[NiFe]-hydrogenases have an unusual active-site cofactor whereby the iron atom carries a carbon monoxide and two cyanides as diatomic ligands. Six conserved Hyp proteins are required to synthesize this NiFe(CN)2CO cofactor. The Fe(CN)2CO portion of the cofactor is synthesized on a scaffold comprising HypCDEF. It is inserted into the apo-catalytic subunit and then nickel is added by the HypA, HypB and SlyD. The synthesis of the Fe(CN)2CO group is not fully understood but it is known that the HypE2F2 heterotetramer generates the cyanide ligands from the precursor carbamoylphosphate. HypD is an iron-sulphur enzyme that, in complex with the small ‘chaperone-like’ protein HypC, has a key function in Fe(CN)2CO synthesis. We have strong circumstantial evidence that the CO ligand is generated from endogenous CO2 bound to an iron atom by HypCD. The HypCD complex functions as a scaffold with which the other Hyp proteins interact. Moreover, HypD is the only Hyp protein with a redox function. We will focus primarily on elucidating the biochemical function of HypD and how it generates the Fe(CN)2CO moiety. HypC and HypD form a tight complex and HypC is responsible for recognition of the apo-catalytic subunit of the hydrogenase by the complex. However, HypC also binds iron with CO2 attached to it, but so far, it has not been possible to isolate HypC with a bound Fe(CN)2CO moiety. Therefore, our current working hypothesis is that HypC delivers the iron bound by CO2 to HypD where reduction to an Fe(I)-CO intermediate occurs. Subsequently, the cyanide groups are transferred from the HypEF complex to the Fe(I)-CO. We have recently demonstrated that HypD undergoes disulphide-thiol redox chemistry, explaining how CO2 reduction might proceed. Therefore, the aims of this project are: to determine the mechanism by which HypD catalyzes reduction of CO2; to analyze whether ATP is involved in CO2 reduction; to show how the HypCD complex transfers the Fe(CN)2CO group into the active site of the hydrogenase; and to identify the physiological electron donor to HypD.
Collaborations
Lorenz Adrian, Leipzig
Antonio Pierik, Kaiserslautern
Constanze Pinske, Halle
Seigo Shima, Marburg
Ingo Zebger and Oliver Lenz, Berlin
Functional analysis of the Fe-S cluster containing chloroplast J-domain proteins CDJ3-5
Michael Schroda
TU Kaiserslautern
Hsp70 chaperone systems are highly conserved and exist in the cytosol, the ER, mitochondria, and chloroplasts of eukaryotic cells. The chloroplast Hsp70 system is derived from bacteria and consists of an Hsp70, a GrpE-type nucleotide exchange factor, and so-called J-domain proteins. The latter bind specific substrate proteins and hand them over to Hsp70 for further processing. CDJ3-5 are three out of six J-domain proteins in the chloroplast of the unicellular green alga Chlamydomonas reinhardtii. In addition to the J domain and a domain of unknown function, they harbor a bacterial ferredoxin domain, which binds redox-active 4Fe-4S clusters in CDJ3 and CDJ4. Members of the CDJ3-5 proteins exist in the chloroplasts of all Viridiplantae (plants and algae) as well as in the Thaumarchaeota, who have acquired it via horizontal gene transfer. CDJ3 and CDJ4 interact ATP-dependently with chloroplast Hsp70 and stimulate its ATPase activity. However, they do not support the folding of denatured proteins and therefore play no role in protein homeostasis. The CDJ3 gene is inducible by light and CDJ3 forms a complex with RNA in the stroma. CDJ3-5 all accumulate at very low levels.
The goal of this project is to shed light onto the functions of CDJ3-5 in Chlamydomonas reinhardtii. We will overexpress CDJ3-5 wild-type and mutant forms lacking the conserved HPD motif in the J domain and the cysteines required for Fe-S cluster binding. These variants will be expressed also with C-terminal extensions allowing us to i) identify stably interacting proteins via affinity purification and LC-MS/MS; ii) identify transient interaction partners via proximity labeling; iii) identify bound RNA species via RIP-Chip and CLIP; iv) determine the suborganellar localization of CDJ3-5 in the chloroplast. Further, CRISPR/Cpf1 will be used to generate cdj3-5 knock-out mutants. These and the overexpressor lines will then be subjected to quantitative shotgun proteomics based on the 15N stable isotope to identify differentially expressed proteins. Finally, the FeS cluster in CDJ5 will be analyzed by Mössbauer spectroscopy.
Collaborations
- Antonio Pierik: proximity labeling and ESR spectroscopy
- Thorsten Friedrich: redox titration
- Volker Schünemann: Mössbauer spectroscopy
- Thomas Happe: Chlamydomonas Synthetic Biology
Mössbauer spectroscopic methods to study iron-sulfur assembly, disassembly and catalysis
Volker Schünemann
University of Kaiserslautern
The aim of this project is to contribute to the understanding of the assembly, the biosynthesis and the catalysis of iron-sulfur centers with experimental methods based on the Mössbauer effect. Thereby we want to get more insight into functional electronic, vibrational and structural properties of the iron sites in mononuclear and polynuclear iron-sulfur centers.
Using laboratory based Mössbauer spectroscopy in high fields up to 5 T we will identify ligand binding sites in a variety of iron-sulfur enzymes provided by collaboration partners within the SPP1927. These proteins have mononuclear, 2Fe-2S, 4Fe-4S centers but also more complex iron-sulfur centers like those in nitrogenase.
In addition, we will study the Fe-S cluster assembly by performing Mössbauer experiments on whole cells. Here we envisage temperature and field dependent Mössbauer spectroscopy in order to identify the iron-sulfur centers within the cells and quantify the corresponding iron-sulfur contribution in different cell lines.
Also the interaction of iron-sulfur centers with small signaling molecules like NO and CO will be investigated and synchrotron based nuclear resonance vibrational spectroscopy (NRVS) experiments will be performed in order to identify iron ligand vibrations.
Collaborations
- Pierik, TU Kaiserslautern: EPR-investigations of Fe-S centers
- DeBeer, MPI for Chemical Energy Conversion, Mülheim: FeMoCo
- Boll, U. Freiburg: Mössbauer Spectroscopy on class II Benzoyl CoA reductase
- Berndt, U Düsseldorf: Mössbauer spectroscopy and NRVS of human Grx2
- Dobbek, HU Berlin: ACS maturation
- Einsle, U Freiburg: Mössbauer spectroscopy and NRVS on CO nitrogenase
- Layer, U Leipzig: Nitrogenase-like enzyme system NflH/NflD
- Lill, U Marburg: 4Fe-4S insertion into mitochondrial apoproteins
- Lillig, U Greifswald: Mössbauer spectroscopy and NRVS of human Grx2
- Leimkühler, U Potsdam: Fe-S assembly in E. coli cells
- Meyer, U Göttingen: NO-iron-sulfur model compounds
- Neese, MPI for Chemical Energy Conversion, Mülheim: Theoretical studies on FeMoCo
- Schwarz, U Köln: Iron-sulfur binding in MOCS1A and MOCS1AB
- Shima, MPI for Terrestrial Microbiology, Marburg: Hydrogenases
- Soboh, FU Berlin: Mössbauer spectroscopy for the study of Fe-containing maturation proteins
- Schroda, TU Kaiserslautern: chloroplast-targeted DnaJ-like proteins
Sulfido dithiolene complexes modeling molybdenum and tungsten-dependent oxidoreductases
Carola Schulzke
Ernst-Moritz-Arndt Universität Greifswald
Iron-sulfur cluster are very important for the maturation/biosynthesis and the function of essential oxidoreductases. We aim to investigate several aspects of the FeS dependent biosynthesis and catalytic activity of molybdenum and tungsten cofactors and their respective enzymes by means of synthesizing, characterizing and evaluating model compounds regarding catalytic activity, kinetic properties and interactions with proteins (chaperones, apoenzymes). Important questions to be addressed include particularly the role of the sulfido-ligand (inserted by IscS in vivo) at the active site of molybdenum and tungsten enzymes. It is planned to understand at the chemical level the mode of action of sulfide insertion and sulfido function for the reactivity of enzymes in detail, to elucidate the catalytic reaction mechanisms and to help distinguishing between actual and artifactual presence of sulfur in the active sites. The possibility to specifically label distinct atoms of the model complexes with isotopes will significantly expedite the respective investigations regarding the latter. The findings are envisioned to support the understanding of cellular processes and eventually medical aspects for the treatment of MoCo (molybdenum cofactor) related diseases. Known mono-oxo bis-dithiolene complexes of molybdenum and tungsten with dithiolene ligands mimicking aspects of the natural ligand system molybdopterin (MPT) will be tested for binding an additional sulfide ligand giving MOS species and for changing the MO moiety to an MS moiety. In a second approach metal precursors will be used in procedures adapted from methods for oxo complexes, which already carry the sulfide ligand as well as those with readily replaceable ligands as halides or CO. In addition the development of new metal precursors and new ligand systems facilitating binding tom proteins is planned. Besides a thorough characterization by various methods, the synthetic complexes will be tested for their catalytic potential, kinetic properties and biological activity (specific binding with proteins involved in the maturation of molybdenum and tungsten cofactors and the respective apoenzymes; catalytic activity of the semi-synthetic enzymes).
Collaborations
- Silke Leimkühler: protein binding, incorporation experiments, catalytic assays, determining oxo versus sulfido coordination in the active sites; outgoing lab rotations
- Matthias Boll: catalytic transformations of aromatic substrates with models and enzymes, identifying the sixth ligand in W‐dependent benzoylcoenzyme A reductase
- Matthias Ullmann: providing electrochemical and pKa data of model compounds to be used for optimizing calculations of the active site properties of the enzymes
- Johann Heider: investigating the oxidation state requirements for an incubation of the mature cofactor into the apo‐enzymes, specifically aimed at tungsten‐dependent AOR
- Serena DeBeer/Frank Neese: X‐ray absorption and emission spectroscopy on our model compounds and combined enzyme‐model species, theoretical evaluation of the data; producing MoFe3‐clusters following procedures developed by the Holm group
- Ingo Zebger/Oliver Lenz: Resonance Raman spectroscopy of model complexes to complement IR studies)
- Ralf Mendel: interactions of our models with fungal proteins to determine their protein binding properties/potential
- Antonio J. Pierik: EPR of our model compounds in oxidation state +5 and comparison with protein data
- Franc Meyer: magnetic measurements (SQUID) of our complexes for deciphering electronic structures, oxidation and spin states; temperature dependent electrochemical measurements to assess the thermodynamics (entropy and enthalpy) of the redox processes relevant for the studies
Biogenesis, mitochondrial assembly and function of human FeS-dependent molybdenum cofactor synthesis MOCS1 proteins
Günter Schwarz
Universität Köln
The molybdenum cofactor (Moco) is synthesized in a highly conserved multi-step pathway which is strictly dependent on the biosynthesis of [4Fe-4S] clusters. Human MOCS1 proteins are expressed by alternative splicing yielding two active proteins, MOCS1A and MOCS1AB. MOCS1A harbours two [4Fe-4S] clusters and is suggested to catalyse the radical SAM-dependent conversion of GTP into 3´,8-cylo-dihydro-GTP based on findings in E. coli. MOCS1AB represents a fusion protein of the MOCS1A and MOCS1B domains with only the MOCS1B domain exhibiting activity. Even though the overall biosynthesis of Moco is highly conserved, the fusion of MOCS1A and MOCS1B can only be found in animals and fungi. Whether this fusion has any effect on protein function or maturation has yet to be answered.
After having identified both MOCS1A and MOCS1AB as mitochondrial proteins it remains to be elucidated, what functions are retained within the MOCS1A domain, how are the [4Fe-4S] clusters incorporated, how does this domain interact with the MOCS1A protein and how does the overall machinery function and assemble within mitochondria. Additionally functional aspects of the reaction mechanism and parameters of MOCS1 proteins are yet to be determined. This is of particular interest in order to understand Moco deficiencies (MoCD) caused by single amino acid exchanges resulting in severe neurodegeneration.
Furthermore the interplay of [FeS] cluster biogenesis and MOCS1 activity still remains unclear. Therefore we are interested in investigating the influence of diseases linked to [4Fe-4S] cluster biosynthesis to MoCD, since diseases linked to FeS protein assembly often also manifest with sever neurodegeneration. In this context we are interested in the [4Fe-4S] cluster maturation and insertion in MOCS1A proteins within the mitochondrial matrix.
Collaborations
Roland Lill (Marburg): Determination of the influence of different FeS protein maturation defects on Moco synthesis by investigating the function of MOCS1A. We will focus on SiRNA based depletion of either core ISC components, ABCB7, or ISCA-IBA57 proteins to analyse where MOCS1A receives its [4Fe-4S] cluster. Furthermore, patient fibroblast and body fluids will be provided to determine Mo enzyme activities and Mo enzyme biomarkers.
Silke Leimkühler (Potsdam): Bacterial Moco synthesis and comparison of our MOCS1 data to MoaA and MoaC. Determination of Fe content by ICP-MS.
Ralf R. Mendel (Braunschweig): The Mendel lab aims to relocate the step 1 in Moco synthesis from mitochondria into the cytosol. Comparison of our results with the Nit7A/AB proteins.
Antonio J. Pierik (Kaiserslautern): EPR spectroscopy of MOCS1A and MOCS1AB proteins.
Volker Schünemann (Kaiserslautern): Mössbauer spectroscopy of MOCS1A and MOCS1AB proteins.
Carsten Berndt (Düsseldorf): Investigation of the potential molecular link between glutaredoxins (Grxs), Moco biosynthesis, and activities of Moco enzymes. We will measure activity of Moco proteins in cell lines with modulated expression of Grx2 (redox regulation), Grx3 (iron trafficking) or Grx5 (FeS cluster biosynthesis). We will also investigate sulfite oxidase related biomarker status in Grx deficient mice.
Johann Heider (Marburg) and Matthias Boll (Freiburg): Support in the in vitro insertion of tungsten cofactor (Wco) via Wco synthesizing proteins (MoaB and MoeA1/A2) that convert metal-binding pterin (MPT) into Wco.
[Fe]-hydrogenase: Role of Iron-sulfur bonding in holoenzyme assembly and in FeGP-cofactor biosynthesis
Seigo Shima
Max Planck Institute for Terrestrial Microbiology, Marburg
[Fe]-hydrogenase catalyzes the reversible transfer of a hydride from H2 to methenyl-tetrahydromethanopterin, which is an intermediary step in methanogenesis from H2 and CO2. The enzyme contains one iron per active site. The iron is associated with a unique iron-guanylylpyridinol (FeGP) cofactor, in which a low spin Fe(II) is complexed with two CO, one pyridinol-nitrogen, one acyl-carbon and, when the cofactor is bound to the holoenzyme, one thiolate from Cys176. The iron-sulfur bond is essential for hydrogenase activity. Apparently, iron-sulfur bonding is involved in assembly and catalysis of [Fe]-hydrogenase and the biosynthesis of its FeGP cofactor. In the proposed project, we want to study the biosynthesis of the FeGP cofactor. In many methanogens, the [Fe]-hydrogenase structural gene (hmd) is clustered with hmd-co-occurring genes (hcgA-G), which have been shown to be involved in FeGP cofactor biosynthesis. In previous studies, we have identified the function of five of the hcg gene-products (HcgB, HcgC, HcgD, HcgE and HcgF) using structure to function strategies and biochemical assays. HcgB catalyzed guanylyl-transfer from GTP to the 4-hydroxypyridinol. HcgC is a SAM-dependent methyltransferase; HcgD is a putative iron chaperone. HcgE catalyzes the adenylylation of the carboxy group of a 6-carboxymethyl-guanylylpyridinol precursor. Subsequently the product of HcgE reacts with Cys9 of HcgF yielding a thioester and AMP. Hypothesis is, based on chemical precedents that the thioester now reacts with an iron species forming the acyl and thiolate ligands. In the next three years, we would like to prove or disprove this hypothesis and identify the function of the two remaining Hcg proteins (HcgA and HcgG), both of which are predicted to be iron-sulfur proteins. For this purpose, we will – as before – employ structure to function strategies, in vitro biosynthesis and metabolite analysis of hcg knock-out mutants.
The collaborations we plan within the SPP
– Peter Hildebrandt and Ingo Zebger, Technische Universität Berlin, Institut für Chemie; Resonance Raman spectroscopic analysis of the biosynthetic intermediates.
– Antonio J. Pierik and Volker Schünemann, Technische Universität Kaiserslautern, Fachbereich Chemie; Electron paramagnetic resonance and Mössbauer spectroscopic analysis of the biosynthetic intermediate.
– Lucia Banci, Centro Risonanze Magnetiche, University of Florence; NMR analysis of the biosynthetic intermediates.
– Serena DeBeer, Max-Planck-Institute für chemische Energiekonversion, X-ray absorption spectroscopic analysis of the biosynthetic precursors.
– Holger Dobbek, Humboldt Universität Berlin and Lorenz Adrian, The Helmholtz Centre for Environmental Research Physiology, protein analysis of methanogenic archaea.
– Roland Lill, Marburg University; heterologous production of Hcg proteins in yeast and circular dichroism spectroscopy.
– Gary Sawers, University Halle-Wittenberg; Johann Heider, Marburg University and Constanze Pinske, University Halle-Wittenberg, crystallization of hydrogenases and other iron-sulfur proteins.
An in vitro system for the study of [NiFe]-hydrogenase maturation
Basem Soboh
Freie Universität Berlin
Our research focuses on the in vitro biosynthesis of complex Fe-S cofactors. We currently employ hydrogenases that make or oxidize hydrogen gas. [NiFe]-hydrogenase has a complicated catalytic active site that contains nickel and iron bound to the protein in addition to unique non-protein ligands.
The biosynthesis of hydrogenases is a multi-step process that requires the coordinated activity of several accessory proteins. Our interest lies in determining how this complex cofactor is assembled and incorporated into these enzymes.
Our strategy concept of an in vitro system is based on isolation of an active maturation machinery, followed by “watching” the stepwise synthesis and assembly of cofactor over time. This concept involves a broad range of methodologies ranging from microbiology, molecular biology and protein biochemistry to biophysical methods including X-ray crystallography, FT-IR, EPR, Raman and EXAFS spectroscopy.
Recently we could demonstrate the in vitro synthesis of active [NiFe]-hydrogenase using only purified components. This finding allows us to exert much greater control over the hydrogenase maturation machinery. It provides the possibility to study each of maturation steps individually at molecular level. This study includes determination of the temporal sequence of events and analysis of the compositions of functional complexes at each maturation step along the path of cofactor biosynthesis. A more thorough spectroscopic and structural investigation of an all-pure-component-based in vitro system is required to conclusively trace the intermediates of the assembly process of [NiFe]-hydrogenase.
Collaborations:
AG DeBeer/Neese: EXAFS analysis of intermediates of [NiFe]-hydrogenases
AG Shima: Anaerobic crystallization of functional protein complexes and intermediates
AG Pinske: Generation of chromosomal mutants and variants
AG Einsle: Crystallization, FeMo-co biogenesis and catalysis
AG Schünemann: Mössbauer spectroscopy for the study f Fe-containing maturation proteins
AG Lill: 55Fe-labeling to identify the source, route and incorporation of iron into hydrogenase
AG Pierik: EPR spectroscopy of maturation proteins and intermediates
AG Adrian: Identification of protein/cofactor modifications and analysis of the compositions of functional protein complexes by Mass-spectrometry.
AG Schaffrath: characterization of electron transfer reactions
Bioinorganic Vibrational Spectroscopy
Sven Stripp
Freie Universität Berlin
Understanding the catalysis of gas-processing iron-sulphur enzymes, tailor-made spectroscopic solutions are necessary. At the example of [FeFe]- and [NiFe]-hydrogenase, I developed an in situ approach to observe catalytic changes and proton transfer as a function of educt/product titrations via the gas phase, electrochemistry, or visible light irradiation. For this, I focus on infrared difference spectroscopy under “physiological” conditions. In the context of priority program 1927, I aim to expand my spectroscopic toolbox towards iron-sulphur protein and enzymes, e.g. hydrogenase, nitrogenase, CO dehydrogenase, or formate dehydrogenase. I have an interdisciplinary background including molecular biology, physical chemistry, and biophysics to facilitate this.
Collaborations
- Oliver Einsle – Nitrogenase
- Thomas Happe – [FeFe]-hydrogenase
- Antonio Pierik – EPR spectroscopy
- Volker Schünemann – Mössbauer Spectroscopy
- Seigo Shima – [Fe]-hydrogenase
- Basem Soboh – [NiFe]-hydrogenase
Simulating the Coupling of Catalysis and Electron Transfer along Chains of FeS-Clusters in Molybdo- and Tungsto-Pterin Enzymes
Matthias Ullmann
Universität Bayreuth
Iron-sulfur (FeS) clusters play a role in enzyme catalysis and electron transfer. In many enzymes, iron sulfur clusters align to enable electron transfer over large distances and often connect two catalytic centers of enzymes. Examples are molybdo- and tungsto-pterin enzymes. While the catalytic action of some of these enzymes has been investigated in detail, its connection to the electron transfer reactions has not been studied to the same level. The goal of this project is to lie the foundations for simulating the coupling of the chemical reactions and the electron transfer between the catalytic sites. For this purpose, we plan to extend our method to simulate the electron transfer dynamics using a master equation to enzyme catalysis. The enzyme is modeled as a system of sites (redox active site, protonatable sites, the catalytic centers). In each microstates, the protonation, redox state, and conformation of all sites are exactly defined. The energy of each microstate is obtained as a sum of site energies and the interactions between the sites. The site energies and the interactions are calculated from electrostatic calculations using the Poisson-Boltzmann equation. Rate constant for going from one microstate to the other are obtained from Marcus theory for charge transfer reactions and form QM/MM calculation for more complex chemical reactions in the active site. From these simulations, we will be able to deduce enzymatic mechanism of even very complex enzymes with several active sites. This method has so far only been applied to simple electron transfer reaction. In this project, we plan to applied it to molybdo- and tungsto-pterin enzymes that connect to active sites by a chain FeS clusters. In order to be able to do such calculations, we need to obtain reliable “model redox potentials”, i.e., redox potential data the FeS clusters would have in aqueous solutions. These values will be calculated on the basis of experimental redox potential of small proteins and synthetic model compounds of the active sites of enzymes. The simulation method will be applied to analyze the coupling of the chemical catalysis in Xanthine Dehydrogenase to the electron transfer to NAD+ via a chain of [2Fe2S] clusters and a FAD. This simulation will be a first test case our method. Moreover, we want to apply the method to study the mechanism of BamBC, an enzyme involved in the degradation of aromatic compounds. In the second funding period, we envision that the developed methodology can be applied to even more complex enzymes such as the whole Bam B-I complex. Also the study interplay of Nitrate Reductase and Formate Dehydrogenase in the bioenergetics of E. coli is an potential goal for the second funding period of the priority program.
Collaborations
Oliver Einsle: Structure of Various Small FeS Proteins
Thorsten Friedrich: Redox Potential Determination
Matthias Boll: Structural and Functional Studies of the Bam Complex
Franc Meyer: Model Compounds of FeS Complexes
Carola Schulzke: Model Compounds of Molybdo- and Tungstopterin Complexes
Silke Leimkühler: Functional Studies on Molybdo- and Tungstopterin Enzymes
Fueling CO2-fixation by detoxifying CO, what are the secrets behind the electron-confurcating hydrogenase/formate dehydrogenase complex of homoacetogens?
Tristan Wagner
MPI for Marine Microbiology Bremen
Reduction of CO2 into formate answers to two main challenges of our society: (1) trapping the greenhouse gas; (2) safely storing the energy generated through renewable sources (e.g. wind, solar…) by using stable formate as an energy-carrier. We aim to decipher the chemical tricks behind the biological CO2-fixation catalyzed by formate dehydrogenase (Fdh), addressing the key question: how can enzymes reduce the inert CO2? We use the model bacterium Clostridium autoethanogenum and related species that use CO2-fixation for both carbon assimilation and energy acquisition. These acetogens has a high-impact in biotechnology by their ability to turn waste gases (e.g. syngas) into biofuels (acetate and ethanol). As such gases contain high concentration of carbon monoxide (CO), inhibitor of both Fdh and hydrogenases, an efficient CO2-fixation should be impossible. However, C. autoethanogenum and related species developed a genuine seven-subunit electron-bifurcating hydrogenase/formate dehydrogenase complex (HytA-E/Fdh), intriguingly resistant to CO and able to use the conversion of this latter as a fuel for CO2-reduction. Indeed, the complex merges electrons obtained from oxidation of reduced ferredoxins, generated by CO-oxidation, and NADPH in an electron confurcation event, whom mechanism is unknown, to allow the CO2 reduction by tungstopterin-dependent Fdh. To avoid saturation of turnover capacities, the system uses an [FeFe]-hydrogenase (HytA) as an exhauster, evacuating extra electrons by proton reduction into H2. Under H2/CO2 growth, HytA feeds the system by H2 oxidation.
The project aims to elucidate the key points of the complex: which cofactor operates the electron confurcation/bifurcation event? If a new cofactor is involved, how its biosynthesis and incorporation is performed? How hydrogenase and Fdh cross-talk to synchronize electron repartition? And how does Fdh reduce CO2? Our workflow starts by the cultivation of different homoacetogens under CO, followed by native anaerobic purification and crystallization of HytA-E/Fdh. Structural investigations will provide insights about its global architecture, cofactors composition, electron pathways and the key catalytic residues involved in the reactions. To obtain the full image of the mechanistic of HytA-E/Fdh, integration and interaction with the other groups among the DFG-SPP 1927 is indispensable. Complementary analyses through physiology, biophysics, spectroscopy, electro-chemistry and structure-based calculation will confirm our structural hypotheses and expand our views on this revolutionary energy converter.
Collaborations
- Silke Leimkühler (Potsdam): Expertise in Tungstopterin/Molybdopterin cofactor enzyme mechanistics and ICP/MS.
- Antonio Pierik (Kaiserslautern): EPR / Mössbauer spectroscopy of Iron-Sulfur and Tungstopterin centers.
- Thorsten Friedrich (Freiburg): EPR spectroscopy of NADPH-oxidoreductase module.
- Ingo Zebger, (Berlin): In cristallo spectroscopy.
- Matthias Ullmann, (Bayreuth): Computational prediction.
- Serena DeBeer/Frank Neese (Mülheim): X-ray spectroscopy methods to decipher metallo-center composition.