EXAFS structural study of FX, the low-potential Fe-S center in photosystem I

Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I

Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron-sulfur cluster FX, which is followed by two terminal iron-sulfur clusters FA and FB. Experiments have shown that FX has lower oxidation potential than FA and FB, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint Em potentials of the FX, FA and FB clusters. Our calculations show that FX has the lowest oxidation potential compared to FA and FB due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for FX compared to FA and FB. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for FX compared to both FA and FB. These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics.

Inactivation of iron-sulfur cluster biogenesis regulator SufR in Synechocystis sp. PCC 6803 induces unique iron-dependent protein-level responses

BACKGROUND

Iron-sulfur (Fe-S) clusters are protein-bound cofactors associated with cellular electron transport and redox sensing, with multiple specific functions in oxygen-evolving photosynthetic cyanobacteria. The aim here was to elucidate protein-level effects of the transcriptional repressor SufR involved in the regulation of Fe-S cluster biogenesis in the cyanobacterium Synechocystis sp. PCC 6803.

METHODS

The approach was to quantitate 94 pre-selected target proteins associated with various metabolic functions using SRM in Synechocystis. The evaluation was conducted in response to sufR deletion under different iron conditions, and complemented with EPR analysis on the functionality of the photosystems I and II as well as with RT-qPCR to verify the effects of SufR also on transcript level.

RESULTS

The results on both protein and transcript levels show that SufR acts not only as a repressor of the suf operon when iron is available but also has other direct and indirect functions in the cell, including maintenance of the expression of pyruvate:ferredoxin oxidoreductase NifJ and other Fe-S cluster proteins under iron sufficient conditions. Furthermore, the results imply that in the absence of iron the suf operon is repressed by some additional regulatory mechanism independent of SufR.

CONCLUSIONS

The study demonstrates that Fe-S cluster metabolism in Synechocystis is stringently regulated, and has complex interactions with multiple primary functions in the cell, including photosynthesis and central carbon metabolism.

GENERAL SIGNIFICANCE

The study provides new insight into the regulation of Fe-S cluster biogenesis via suf operon, and the associated wide-ranging protein-level changes in photosynthetic cyanobacteria.

Structure and function of photosystem I and its application in biomimetic solar-to-fuel systems

Photosystem I (PSI) is one of the most efficient biological macromolecular complexes that converts solar energy into condensed energy of chemical bonds. Despite high structural complexity, PSI operates with a quantum yield close to 1.0 and to date, no man-made synthetic system approached this remarkable efficiency. This review highlights recent developments in dissecting molecular structure and function of the prokaryotic and eukaryotic PSI. It also overviews progress in the application of this complex as a natural photocathode for production of hydrogen within the biomimetic solar-to-fuel nanodevices.

Structure and Function of Photosynthetic Reaction Centres

Extensive biochemical, biophysical, molecular biological and structural studies on a wide range of prokaryotic and eukaryotic photosynthetic organisms has revealed common features of their reaction centres where light induced charge separation and stabilization occurs. There is little doubt that all reaction centres have evolved from a common ancestor and have been optimized to maximum efficiency. As such they provide principles that can be used as a blueprint for developing artificial photo-electrochemical catalytic systems to generate solar fuels. This chapter summarises the common features of the organization of cofactors, electron transfer pathways and protein environments of reaction centres of anoxygenic and oxygenic phototrophs. In particular, the latest molecular details derived from X-ray crystallography are discussed in context of the specific catalytic functions of the Type I and Type II reaction centres.

Bidirectional electron transfer in the reaction centre of photosystem I

In the past decade light-induced electron transfer reactions in photosystem I have been the subject of intensive investigations that have led to the elucidation of some unique characteristics, the most striking of which is the existence of two parallel, functional, redox active cofactors chains. This process is generally referred to as bidirectional electron transfer. Here we present a review of the principal evidences that have led to the uncovering of bidirectionality in the reaction centre of photosystem I. A special focus is dedicated to the results obtained combining time-resolved spectroscopic techniques, either difference absorption or electron paramagnetic resonance, with molecular genetics, which allows, through modification of the binding of redox active cofactors with the reaction centre subunits, an effect on their physical-chemical properties.

The structure of genetically modified iron-sulfur cluster F(x) in photosystem I as determined by X-ray absorption spectroscopy

Photosystem I (PS I) mediates light-induced electron transfer from P700 through a chlorophyll a, a quinone and a [4Fe-4S] iron-sulfur cluster F(X), located on the core subunits PsaA/B to iron-sulfur clusters F(A/B) on subunit PsaC. Structure function relations in the native and in the mutant (psaB-C565S/D566E) of the cysteine ligand of F(X) cluster were studied by X-ray absorption spectroscopy (EXAFS) and transient spectroscopy. The structure of F(X) was determined in PS I lacking clusters F(A/B) by interruption of the psaC2 gene of PS I in the cyanobacterium Synechocystis sp PCC 6803. PsaC-deficient mutant cells assembled the core subunits of PS I which mediated electron transfer mostly to the phylloquinone. EXAFS analysis of the iron resolved a [4Fe-4S] cluster in the native PsaC-deficient PS I. Each iron had 4 sulfur and 3 iron atoms in the first and second shells with average Fe-S and Fe-Fe distances of 2.27 A and 2.69 A, respectively. In the C565S/D566E serine mutant, one of the irons of the cluster was ligated to three oxygen atoms with Fe-O distance of 1.81 A. The possibility that the structural changes induced an increase in the reorganization energy that consequently decreased the rate of electron transfer from the phylloquinone to F(X) is discussed.

Structural analysis of Arabidopsis CnfU protein: an iron-sulfur cluster biosynthetic scaffold in chloroplasts

CnfU, a key iron-sulfur (Fe-S) cluster biosynthetic scaffold that is required for biogenesis of ferredoxin and photosystem I in chloroplasts, consists of two tandemly repeated domains in which only the N-terminal domain contains a conserved CXXC motif. We have determined the crystal structure of the metal-free dimer of AtCnfU-V from Arabidopsis thaliana at 1.35 A resolution. The N-terminal domains of the two monomers are linked together through two intermolecular disulfide bonds between the CXXC motifs. At the dimer interface, a total of four cysteine sulfur atoms provide a Fe-S cluster assembly site surrounded by uncharged but hydrophilic structurally mobile segments. The C-terminal domain of one monomer interacts with the N-terminal domain of the opposing monomer and thereby stabilizes dimer formation. Furthermore, Fe K-edge X-ray absorption spectroscopic analysis of the holo-CnfU dimer in solution suggests the presence of a typical [2Fe-2S]-type cluster coordinated by four thiolate ligands. Based on these data, a plausible model of the holo-AtCnfU-V dimer containing a surface-exposed [2Fe-2S] cluster assembled in the dimer interface was deduced. We propose that such a structural framework is important for CnfU to function as a Fe-S cluster biosynthetic scaffold.

Modelling of the electron transfer reactions in Photosystem I by electron tunnelling theory: The phylloquinones bound to the PsaA and the PsaB reaction centre subunits of PS I are almost isoenergetic to the iron–sulfur cluster FX

Photosystem I is a large macromolecular complex located in the thylakoid membranes of chloroplasts and in cyanobacteria that catalyses the light driven reduction of ferredoxin and oxidation of plastocyanin. Due to the very negative redox potential of the primary electron transfer cofactors accepting electrons, direct estimation by redox titration of the energetics of the system is hampered. However, the rates of electron transfer reactions are related to the thermodynamic properties of the system. Hence, several spectroscopic and biochemical techniques have been employed, in combination with the classical Marcus theory for electron transfer tunnelling, in order to access these parameters. Nevertheless, the values which have been presented are very variable. In particular, for the case of the tightly bound phylloquinone molecule A(1), the values of the redox potentials reported in the literature vary over a range of about 350 mV. Previous models of Photosystem I have assumed a unidirectional electron transfer model. In the present study, experimental evidence obtained by means of time resolved absorption, photovoltage, and electron paramagnetic resonance measurements are reviewed and analysed in terms of a bi-directional kinetic model for electron transfer reactions. This model takes into consideration the thermodynamic equilibrium between the iron-sulfur centre F(X) and the phylloquinone bound to either the PsaA (A(1A)) or the PsaB (A(1B)) subunit of the reaction centre and the equilibrium between the iron-sulfur centres F(A) and F(B). The experimentally determined decay lifetimes in the range of sub-picosecond to the microsecond time domains can be satisfactorily simulated, taking into consideration the edge-to-edge distances between redox cofactors and driving forces reported in the literature. The only exception to this general behaviour is the case of phylloquinone (A(1)) reoxidation. In order to describe the reported rates of the biphasic decay, of about 20 and 200 ns, associated with this electron transfer step, the redox potentials of the quinones are estimated to be almost isoenergetic with that of the iron sulfur centre F(X). A driving force in the range of 5 to 15 meV is estimated for these reactions, being slightly exergonic in the case of the A(1B) quinone and slightly endergonic, in the case of the A(1A) quinone. The simulation presented in this analysis not only describes the kinetic data obtained for the wild type samples at room temperature and is consistent with estimates of activation energy by the analysis of temperature dependence, but can also explain the effect of the mutations around the PsaB quinone binding pocket. A model of the overall energetics of the system is derived, which suggests that the only substantially irreversible electron transfer reactions are the reoxidation of A(0) on both electron transfer branches and the reduction of F(A) by F(X).

Reduction of unusual iron-sulfur clusters in the H2-sensing regulatory Ni-Fe hydrogenase from Ralstonia eutropha H16

The regulatory Ni-Fe hydrogenase (RH) from Ralstonia eutropha functions as a hydrogen sensor. The RH consists of the large subunit HoxC housing the Ni-Fe active site and the small subunit HoxB containing Fe-S clusters. The heterolytic cleavage of H(2) at the Ni-Fe active site leads to the EPR-detectable Ni-C state of the protein. For the first time, the simultaneous but EPR-invisible reduction of Fe-S clusters during Ni-C state formation was demonstrated by changes in the UV-visible absorption spectrum as well as by shifts of the iron K-edge from x-ray absorption spectroscopy in the wild-type double dimeric RH(WT) [HoxBC](2) and in a monodimeric derivative designated RH(stop) lacking the C-terminal 55 amino acids of HoxB. According to the analysis of iron EXAFS spectra, the Fe-S clusters of HoxB pronouncedly differ from the three Fe-S clusters in the small subunits of crystallized standard Ni-Fe hydrogenases. Each HoxBC unit of RH(WT) seems to harbor two [2Fe-2S] clusters in addition to a 4Fe species, which may be a [4Fe-3S-3O] cluster. The additional 4Fe-cluster was absent in RH(stop). Reduction of Fe-S clusters in the hydrogen sensor RH may be a first step in the signal transduction chain, which involves complex formation between [HoxBC](2) and tetrameric HoxJ protein, leading to the expression of the energy converting Ni-Fe hydrogenases in R. eutropha.

HYSCORE Spectroscopy in the Cytochrome b559 of the Photosystem II Reaction Center

A HYSCORE investigation of the heme center in the cytochrome b(559) is presented. To assign the observed signals to specific nuclei, bis-imidazol coordinated heme compounds that model the iron environment in cytochrome b(559) are also studied. In the model compounds selective isotopic substitution of nitrogen atoms has been performed. The HYSCORE spectra allow us to obtain the hyperfine and quadrupolar coupling tensors of heme and imidazol bonding nitrogen atoms. The results can be interpreted in terms of the structure and the electronic distribution of the active center. The hyperfine tensors indicate that the unpaired electron is confined in a nonbonding iron orbital with a negligible nitrogen p orbital contribution. Quadrupolar coupling tensors suggest that the orientation of the semioccupied orbital is driven by the orientation of the two parallel imidazol rings of the axial histidine side chains. The results are discussed in terms of the structure-function relationship of cytochromes.

The binding of cofactors to photosystem I analyzed by spectroscopic and mutagenic methods

This review focuses on cofactor-ligand and protein-protein interactions within the photosystem I reaction center. The topics include a description of the electron transfer cofactors, the mode of binding of the cofactors to protein-bound ligands, and a description of intraprotein contacts that ultimately allow photosystem I to be assembled (in cyanobacteria) from 96 chlorophylls, 22 carotenoids, 2 phylloquinones, 3 [4Fe-4S] clusters, and 12 polypeptides. During the 15 years that have elapsed from the first report of crystals to the atomic-resolution X-ray crystal structure, cofactor-ligand interactions and protein-protein interactions were systematically being explored by spectroscopic and genetic methods. This article charts the interplay between these disciplines and assesses how good the early insights were in light of the current structure of photosystem I.

Absence of Mn-centered oxidation in the S(2) --> S(3) transition: implications for the mechanism of photosynthetic water oxidation

A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen-evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S(3) --> [S(4)] --> S(0) transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn Kbeta X-ray emission spectroscopy (Kbeta XES) to this problem for the first time. The Kbeta XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electron paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S(2) --> S(3) transition, in contrast to the S(0) --> S(1) and S(1) --> S(2) transitions, does not involve a Mn-centered oxidation. On the basis of new structural data from the S(3)-state, manganese mu-oxo bridge radical formation is proposed for the S(2) --> S(3) transition, and three possible mechanisms for the O-O bond formation are presented.

Absence of Mn-centered oxidation in the S(2) --> S(3) transition: implications for the mechanism of photosynthetic water oxidation

A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen-evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S(3) --> [S(4)] --> S(0) transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn Kbeta X-ray emission spectroscopy (Kbeta XES) to this problem for the first time. The Kbeta XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electron paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S(2) --> S(3) transition, in contrast to the S(0) --> S(1) and S(1) --> S(2) transitions, does not involve a Mn-centered oxidation. On the basis of new structural data from the S(3)-state, manganese mu-oxo bridge radical formation is proposed for the S(2) --> S(3) transition, and three possible mechanisms for the O-O bond formation are presented.

Structure-function studies on the interaction of PsaC with the Photosystem 1 heterodimer : The site directed change R561E in PsaB destabilizes the subunit interaction in Synechocystis sp. PCC 6803

The interaction of PsaC with the core heterodimer of Photosystem 1 was studied in wild type Synechocystis sp. PCC 6803 and the site-directed mutant R561E of PsaB. The mutant reaction center was much less stable in urea and the functional reconstitution of the mutant core using PsaC was impaired. However, the extent of reconstitution increased in the presence of divalent cations whereas that of the wild type was inhibited. We conclude that the reaction center in the mutant is unstable, most likely due to the introduction of an unfavorable electrostatic interaction between surface-exposed residues on PsaC and the binding site for the subunit on the core heterodimer in support of the model proposed previously (Rodday et al. (1993) Photosynth Res 36: 1-9).

Interaction of the FAF B-containing subunit with the Photosystem 1 core heterodimer

The structure of the predicted amino acid sequence in the FX domain of Photosystem 1 was studied by molecular modeling and a working hypothesis was developed for the functional interaction of PsaC with the core heterodimer. We propose that the intervening sequences between homologous cysteines in the FX cluster form two flexible loops and participate in the binding of PsaC, and that the arginine residues in the two surface-exposed loops may promote the interaction between the P700-FX core and the subunit. The model was tested experimentally; chemical modification of arginine residues in the P700-FX core using phenylglyoxal prevented reconstitution of the core with PsaC and PsaD after insertion of FeS clusters in vitro. Treatment of the P700-FX core with trypsin also prevented reconstitution of terminal electron transfer to FAFB, although neither treatments affected the electron transfer to FX as judged by flash kinetic spectrophotometry. Electron transfer in the P700-FAFB complex was not impaired by either phenylglyoxal or trypsin treatment indicating that the small subunit(s) protect the arginine residues that become chemically modified or cleaved. The data are consistent with the working model and point to additional experiments designed to identify the specific residues involved in the interaction between the P700-FX core and PsaC.

Charge recombination between P700+ and A1- occurs directly to the ground state of P700 in a photosystem I core devoid of FX, FB, and FA

The charge recombination between P700+ and electron acceptor A1- was studied by flash kinetic spectroscopy in a photosystem I core devoid of iron-sulfur centers FX, FB, and FA. We showed previously that the majority of the flash-induced absorption change at 820 nm decayed with a 10-microseconds half-time, which we assigned to the disappearance of the P700 triplet formed from the backreaction of P700+ with A1- [Warren, P.V., Parrett, K.G., Warden, J.T., & Golbeck, J.H. (1990) Biochemistry 29, 6545-6550]. We have reinvestigated this assignment in the near-UV, blue, and near-IR wavelength regions. The difference spectrum from 380 to 480 nm and from 720 to 910 nm shows that the P700+ A1- charge recombination is dominated by the P700 cation rather than the P700 triplet. Accordingly, the 10-microseconds kinetic transient represents the direct backreaction of P700+ with A1-, which repopulates the ground state of P700. This is unlike a P700-FA/FB complex where, in the presence of reduced FX-, FB-, and FA-, the P700+ A1- charge recombination populates the P700 triplet state [Sétif, P., & Bottin, H. (1989) Biochemistry 28, 2689-2697]. The A1 acceptor is highly susceptible to disruption by detergents in the absence of iron-sulfur center FX. The addition of 0.1% Triton X-100 to the P700-A1 core leads to a approximately 2.5-fold increase in the magnitude of the flash-induced absorption change at 780 nm; thereafter, 85% of the absorption change decays with a 25-ns half-time and 15% decays with a 3-microseconds half-time.(ABSTRACT TRUNCATED AT 250 WORDS)