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PubMed2002

Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex.

We have used several docking algorithms (GRAMM, FTDOCK, DOT, AUTODOCK) to examine protein-protein interactions between plastocyanin (Pc)/photosystem I (PSI) in the electron transfer reaction. Because of the large size and complexity of this system, it is faster and easier to use computer simulations than conduct x-ray crystallography or nuclear magnetic resonance experiments. The main criterion for complex selection was the distance between the copper ion of Pc and the P700 chlorophyll special pair. Additionally, the unique tyrosine residue (Tyr(12)) of the hydrophobic docking surface of Prochlorothrix hollandica Pc yields a specific interaction with the lumenal surface of PSI, thus providing the second constraint for the complex. The structure that corresponded best to our criteria was obtained by the GRAMM algorithm. In this structure, the solvent-exposed histidine that coordinates copper in Pc is at the van der Waals distance from the pair of stacked tryptophans that separate the chlorophylls from the solvent, yielding the shortest possible metal-to-metal distance. The unique tyrosine on the surface of the Prochlorothrix Pc hydrophobic patch also participates in a hydrogen bond with the conserved Asn(633) of the PSI PsaB polypeptide (numbering from the Synechococcus elongatus crystal structure). Free energy calculations for complex formation with wild-type Pc, as well as the hydrophobic patch Tyr(12)Gly and Pro(14)Leu Pc mutants, were carried out using a molecular mechanics Poisson-Boltzman, surface area approach (MM/PBSA). The results are in reasonable agreement with our experimental studies, suggesting that the obtained structure can serve as an adequate model for P. hollandica Pc-PSI complex that can be extended for the study of other cyanobacterial Pc/PSI reaction pairs.

Algorithms↗
PubMed2003

Bridging the gap between structural and lattice models: a parameterization of energy transfer and trapping in Photosystem I.

In the absence of an accurate structural model, the excited state dynamics of energy-transferring systems are often modeled using lattice models. To demonstrate the validity and other potential merits of such an approach we present the results of the modeling of the energy transfer and trapping in Photosystem I based upon the 2.5 A structural model, and show that these results can be reproduced in terms of a lattice model with only a few parameters. It has recently been shown that at room temperature the dynamics of a hypothetical Photosystem I particle, not containing any red chlorophylls (chls), are characterized by a longest (trapping) lifetime of 18 ps. The structure-based modeling of the dynamics of this particle yields an almost linear relationship between the possible values of the intrinsic charge-separation time at P700, 1/gamma, and the average single-site lifetime in the antenna, tauss. Lattice-based modeling, using the approach of a perturbed two-level model, reproduces this linear relation between tauss and 1/gamma. Moreover, this approach results in a value of the (modified) structure-function corresponding to a structure exhibiting a mixture of the characteristics of both a square and a cubic lattice, consistent with the structural model. These findings demonstrate that the lattice model describes the dynamics of the system appropriately. In the lattice model, the total trapping time is the sum of the delivery time to the reaction center and the time needed to quench the excitation after delivery. For the literature value of tauss=150 fs, both these times contribute almost equally to the total trapping time of 18 ps, indicating that the system is neither transfer- nor trap-limited. The value of approximately 9 ps for the delivery time is basically equal to the excitation-transfer time from the bulk chls to the red chls in Synechococcus elongatus, indicating that energy transfer from the bulk to the reaction center and to the red chls are competing processes. These results are consistent with low-temperature time-resolved and steady-state fluorescence measurements. We conclude that lattice models can be used to describe the global energy-transfer properties in complex chromophore networks, with the advantage that such models deal with only a few global, intuitive parameters rather than the many microscopic parameters obtained in structure-based modeling.

Biophysical Phenomena↗
PubMed2004

Insight into the structural role of carotenoids in the photosystem I: a quantum chemical analysis.

The structural stabilization role of carotenoids in the formation of photosynthetic pigment-protein complexes is investigated theoretically. The pi-pi stacking and CH-pi interactions between beta-carotenes and their surrounding chlorophylls (and/or aromatic residues) in Photosystem I (PS1) from the cyanobacterium Synechococcus elongatus were studied by means of the supermolecular approach at the level of the second-order Møller-Plesset perturbation method. PS1 features a core integral antenna system consisting of 22 beta-carotenes intertwined with 90 chlorophyll molecules. The binding environments of all 22 beta-carotenes were systematically analyzed. For 21 out of the 22 cases, one or more chlorophyll molecules exist within van der Waals' contacts of the beta-carotene molecule. The calculated strengths of pi-pi stacking interactions between the conjugated core of beta-carotene and the aromatic tetrapyrrole rings of chlorophyll are substantial, ranging from -3.54 kcal/mol for the perpendicular-positioned BCR4004...CHL1217 pair to -16.01 kcal/mol for the parallel-oriented BCR4007...CHL1122 pair. A strong dependence of the pi-pi stacking interaction energies on the intermolecular configurations of the two interacting pi-planes is observed. The parallel-oriented beta-carotene and chlorophyll pair is energetically much more stable than the perpendicular-positioned pair. The larger the extent of pi-pi overlapping, the stronger the interaction strength. In many cases, the beta-ring ends of beta-carotene molecules are found to interact with the tetrapyrrole rings of chlorophyll via CH-pi interactions. For the latter interactions, the calculated interaction strengths vary from -7.03 to -11.03 kcal/mol, depending on the intermolecular configuration. This work leads to the conclusion that pi-pi stacking and CH-pi interactions between beta-carotene and their surrounding chlorophylls and aromatic residues play an essential role in binding beta-carotenes in PS1 from S. elongatus. Consequently, the molecular basis of the structural stabilization function of carotenoids in formation of the photosynthetic pigment-protein complexes is established.

Biophysics↗
PubMed1994

Kinetic modeling of exciton migration in photosynthetic systems. 2. Simulations of excitation dynamics in two-dimensional photosystem I core antenna/reaction center complexes.

Kinetic modeling of the exciton migration in the cyanobacterial photosystem I core complex from Synechococcus sp. was performed by an exact solution of the Pauli master equation for exciton motion. A square two-dimensional 10 x 10 pigment lattice and a Förster dipole-dipole coupling between chromophores was assumed. We calculated decay-associated spectra and lifetimes and compared them to the corresponding experimental data from picosecond fluorescence and transient absorption obtained by global analysis. Seven spectral chlorophyll(Chl) forms, identical in shape but shifted in their absorption maximums, were used to describe the non-homogeneous broadening of the PS I-100 particle absorption spectrum. The optimized Chl lattice arrangement best reproducing the experimental decay-associated spectra as well as the steady-state fluorescence spectrum indicated the long-wavelength-absorbing Chls forming a cluster in the corner of the lattice with the reaction center (RC) placed apart at a distance of two lattice constants. The variable parameters, i.e., the charge separation rate in the RC and the lattice constant a, were found to be optimal at kRC = 2.3 ps-1 and a = 1.14 nm, respectively. The surprising conclusions of the simulations is that Chls with absorption maxima as long a 724 nm have to be taken into account to describe the time-resolved spectra of this PS I particle properly. The dependencies of the exciton decay in the model PS I particle on the excitation wavelength and on the temperature are discussed. We also show that the excited state decay of similar PS I particles that lack the long-wavelength absorbing Chls is nearly mono-exponential. Various critical factors that limit the general reliability of the conclusions of such simulations are discussed in detail.

Biophysical Phenomena↗
PubMed1998

PsaC subunit of photosystem I is oriented with iron-sulfur cluster F(B) as the immediate electron donor to ferredoxin and flavodoxin.

The PsaC subunit of photosystem I (PS I) binds two [4Fe-4S] clusters, F(A) and F(B), functioning as electron carriers between F(X) and soluble ferredoxin. To resolve the issue whether F(A) or F(B) is proximal to F(X), we used single-turnover flashes to promote step-by-step electron transfer between electron carriers in control (both F(A) and F(B) present) and HgCl2-treated (F(B)-less) PS I complexes from Synechococcus sp. PCC 6301 and analyzed the kinetics of P700+ reduction by monitoring the absorbance changes at 832 nm in the presence of a fast electron donor (phenazine methosulfate (PMS)). In control PS I complexes exogenously added ferredoxin, or flavodoxin could be photoreduced on each flash, thus allowing P700+ to be reduced from PMS. In F(B)-less complexes, both in the presence and in the absence of ferredoxin or flavodoxin, P700+ was reduced from PMS only on the first flash and was reduced from F(X)- on the following flashes, indicating lack of electron transfer to ferredoxin or flavodoxin. In the F(B)-less complexes, a normal level of P700 photooxidation was detected accompanied by a high yield of charge recombination between P700+ and F(A)- in the presence of a slow donor, 2,6-dichlorophenol-indophenol. This recombination remained the only pathway of F(A)- reoxidation in the presence of added ferredoxin, consistent with the lack of forward electron transfer. F(A)- could be reoxidized by methyl viologen in F(B)-less PS I complexes, although at a concentration two orders of magnitude higher than is required in wild-type PS I complexes, thus implying the presence of a diffusion barrier. The inhibition of electron transfer to ferredoxin and flavodoxin was completely reversed after reconstituting the F(B) cluster. Using rate versus distance estimates for electron transfer rates from F(X) to ferredoxin for two possible orientations of PsaC, we conclude that the kinetic data are best compatible with PsaC being oriented with F(A) as the cluster proximal to F(X) and F(B) as the distal cluster that donates electrons to ferredoxin.

Biophysical Phenomena↗
PubMed1998

Secondary pair charge recombination in photosystem I under strongly reducing conditions: temperature dependence and suggested mechanism.

Photoinduced electron transfer in photosystem I (PS I) proceeds from the excited primary electron donor P700 (a chlorophyll a dimer) via the primary acceptor A0 (chlorophyll a) and the secondary acceptor A1 (phylloquinone) to three [4Fe-4S] clusters, Fx, FA, and FB. Prereduction of the iron-sulfur clusters blocks electron transfer beyond A1. It has been shown previously that, under such conditions, the secondary pair P700+A1- decays by charge recombination with t1/2 approximately 250 ns at room temperature, forming the P700 triplet state (3P700) with a yield exceeding 85%. This reaction is unusual, as the secondary pair in other photosynthetic reaction centers recombines much slower and forms directly the singlet ground state rather than the triplet state of the primary donor. Here we studied the temperature dependence of secondary pair recombination in PS I from the cyanobacterium Synechococcus sp. PCC6803, which had been illuminated in the presence of dithionite at pH 10 to reduce all three iron-sulfur clusters. The reaction P700+A1- --> 3P700 was monitored by flash absorption spectroscopy. With decreasing temperature, the recombination slowed down and the yield of 3P700 decreased. In the range between 303 K and 240 K, the recombination rates could be described by the Arrhenius law with an activation energy of approximately 170 meV. Below 240 K, the temperature dependence became much weaker, and recombination to the singlet ground state became the dominating process. To explain the fast activated recombination to the P700 triplet state, we suggest a mechanism involving efficient singlet to triplet spin evolution in the secondary pair, thermally activated repopulation of the more closely spaced primary pair P700+A0- in a triplet spin configuration, and subsequent fast recombination (intrinsic rate on the order of 10(9) s(-1)) forming 3P700.

Chlorophyll↗
PubMed1999

Electronic spectra of PS I mutants: the peripheral subunits do not bind red chlorophylls in Synechocystis sp. PCC 6803.

Steady-state fluorescence and absorption spectra have been obtained in the Qy spectral region (690-780 nm and 600-750 nm, respectively) for several subunit-deficient photosystem I mutants from the cyanobacterium Synechocystis sp. PCC 6803. The 77 K fluorescence spectra of the wild-type and subunit-deficient mutant photosystem I particles are all very similar, peaking at approximately 720 nm with essentially the same excitation spectrum. Because emission from far-red chlorophylls absorbing near 708 nm dominates low-temperature fluorescence in Synechocystis sp., these pigments are not coordinated to any the subunits PsaF, Psa I, PsaJ, PsaK, PsaL, or psaM. The room temperature (wild-type-mutant) absorption difference spectra for trimeric mutants lacking the PsaF/J, PsaK, and PsaM subunits suggest that these mutants are deficient in core antenna chlorophylls (Chls) absorbing near 685, 670, 675, and 700 nm, respectively. The absorption difference spectrum for the PsaF/J/I/L-deficient photosystem I complexes at 5 K reveals considerably more structure than the room-temperature spectrum. The integrated absorbance difference spectra (when normalized to the total PS I Qy spectral area) are comparable to the fractions of Chls bound by the respective (groups of) subunits, according to the 4-A density map of PS I from Synechococcus elongatus. The spectrum of the monomeric PsaL-deficient mutant suggests that this subunit may bind pigments absorbing near 700 nm.

Chlorophyll↗
PubMed2000

Isopentenyl diphosphate isomerase deficiency in Synechocystis sp. strain PCC6803.

Isopentenyl diphosphate isomerase (IPP isomerase) in many organisms and in plastids is central to isoprenoid synthesis and involves the conversion between IPP and dimethylallyl diphosphate (DMAPP). It is shown that Synechocystis PCC6803 is deficient in IPP isomerase activity, consistent with the absence in its genome of an obvious homologue for the enzyme. Incorporation of [1-(14)C]IPP in cell extracts, primarily into C(20), occurs only upon priming with DMAPP in Synechocystis PCC6803 and in Synechococcus PCC7942. Isoprenoid synthesis in these cyanobacteria does not appear to involve interconversion of IPP and DMAPP, raising the possibility that they are not within the plastid evolutionary lineage.

Carbon-Carbon Double Bond Isomerases↗
PubMed2001

Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC.

kaiABC, a gene cluster, encodes KaiA, KaiB and KaiC proteins that are essential to circadian rhythms in the unicellular cyanobacterium Synechococcus sp. strain PCC 7942. Kai proteins can interact with each other in all possible combinations. This study identified two KaiA-binding domains (C(KABD1) and C(KABD2)) in KaiC at corresponding regions of its duplicated structure. Clock mutations on the two domains and kaiA altered the strength of C(KABD)-KaiA interactions assayed by the yeast two-hybrid system. Thus, interaction between KaiA and KaiC through C(KABD1) and C(KABD2) is likely important for circadian timing in the cyanobacterium.

Adenosine Triphosphate↗
PubMed2001

Subunit positioning and transmembrane helix organisation in the core dimer of photosystem II.

Recently 3D structural models of the photosystem II (PSII) core dimer complexes of higher plants (spinach) and cyanobacteria (Synechococcus elongatus) have been derived by electron [Rhee et al. (1998) Nature 396, 283-286; Hankamer et al. (2001) J. Struct. Biol., in press] and X-ray [Zouni et al. (2001) Nature 409, 739-743] crystallography respectively. The intermediate resolutions of these structures do not allow direct identification of side chains and therefore many of the individual subunits within the structure are unassigned. Here we review the structure of the higher plant PSII core dimer and provide evidence for the tentative assignment of the low molecular weight subunits. In so doing we highlight the similarities and differences between the higher plant and cyanobacterial structures.

Cell Membrane↗
PubMed2003

CO2 response for expression of ribulose-1,5-bisphosphate carboxylase/oxygenase genes is inhibited by AT-rich decoy in the cyanobacterium.

The CO(2)-regulatory function of the AT-rich element in the promoter for ribulose-1,5-bisphosphate carboxylase/oxygenase (rbc) genes in the cyanobacterium Synechococcus sp. PCC7002 was analyzed using the transcription factor decoy approach. Double-stranded phosphorothioate AT-rich oligonucleotides with high affinity for a sequence-specific DNA-binding protein were successfully introduced into cyanobacterial cells in culture without any transfection reagent. The AT-rich decoy oligonucleotides interfered with CO(2) regulation of rbc expression by blocking the binding of the sequence-specific DNA-binding protein, indicating that the AT-rich element plays a critical role in CO(2) regulation for rbc genes. The decoy oligonucleotide approach to cyanobacteria provides a simple and excellent tool for investigating transcriptional regulation in vivo.

AT Rich Sequence↗
PubMed2003

Prokaryotic origins for the mitochondrial alternative oxidase and plastid terminal oxidase nuclear genes.

The mitochondrial alternative oxidase is a diiron carboxylate quinol oxidase (Dox) found in plants and some fungi and protists, but not animals. The plastid terminal oxidase is distantly related to alternative oxidase and is most likely also a Dox protein. Database searches revealed that the alpha-proteobacterium Novosphingobium aromaticivorans and the cyanobacteria Nostoc sp. PCC7120, Synechococcus sp. WH8102 and Prochlorococcus marinus subsp. pastoris CCMP1378 each possess a Dox homolog. Each prokaryotic protein conforms to the current structural models of the Dox active site and phylogenetic analyses suggest that the eukaryotic Dox genes arose from an ancestral prokaryotic gene.

Alphaproteobacteria↗
PubMed1997

Biosynthesis of ketocarotenoids in transgenic cyanobacteria expressing the algal gene for beta-C-4-oxygenase, crtO.

The ketocarotenoid astaxanthin is produced by a number of marine bacteria and microalgae. It is synthesized from beta-carotene by the addition of two keto groups to carbons C4 and C4' and two hydroxyl groups to C3 and C3'. The gene, crtO, encoding beta-C-4-oxygenase which converts beta-carotene to canthaxanthin was cloned from the green alga Haematococcus plurialis. We transferred crtO to the cyanobacterium Synechococcus PCC7942, which contains a beta-carotene hydroxylase gene and normally accumulates beta-carotene and zeaxanthin. The genetically engineered cyanobacterium produced astaxanthin as well as other ketocarotenoids. The results confirm that crtO can function in cyanobacteria in conjunction with the intrinsic carotenoid enzymes to produce astaxanthin. Specifically, this finding indicates that beta-carotene hydroxylase, which normally converts beta-carotene to zeaxanthin, can also function in the biosynthesis of astaxanthin. These results provide the first evidence of genetic manipulation of a plant-type carotenoid biosynthesis pathway toward the production of novel carotenoids.

Bacterial Proteins↗
PubMed1998

Increased cellular resistance to oxidative stress by expression of cyanobacterium catalase-peroxidase in animal cells.

To exploit prokaryotic antioxidant enzymes for protection of animal cells from oxidative damage, we expressed catalase-peroxidase of cyanobacterium Synechococcus PCC 7942 in 104C1 cells. The gene for this enzyme was inserted into the mammalian expression vector pRc/CMV. The stable transfectants obtained had higher specific activities of catalase and as a result became more resistant to H2O2 or paraquat than the parental cells. Subcellular fractionation and immunoblot analysis revealed that the expressed catalase-peroxidase was confined to the cytosol; this localization may be the basis for the effective protection of the transfectants from the oxidative cell damage.

Animals↗
PubMed1998

Purification and characterization of alkaline phosphatase containing phosphotyrosyl phosphatase activity from the bacterium Prevotella intermedia.

A novel alkaline phosphatase, designated PiALP, has been purified and characterized from Prevotella intermedia ATCC 25611, an anaerobe implicated in progressive periodontal disease. The enzyme was a homodimer of apparently identical subunits of Mr 54 kDa. Thiol-reducing agents completely inhibited the purified enzyme. The enzyme was highly stable even at 80 degrees C. It exhibited substantial activity against tyrosine-phosphate-containing Raytide. The phosphatase activity was sensitive to orthovanadate and Zn2+ but highly resistant to okadaic acid. The amino acid sequence of peptides derived from PiALP showed a high degree of identity (65%) with alkaline phosphatases from Zymomonas mobilis and Synechococcus. The present results imply that PiALP might represent a new family of alkaline phosphotyrosyl phosphatases which has not been described previously.

Alkaline Phosphatase↗
PubMed1998

Electrogenicity accompanies photoreduction of the iron-sulfur clusters F(A) and F(B) in photosystem I.

Photovoltage responses accompanying electron transfer on the acceptor side of photosystem I (PS I) were investigated in proteoliposomes containing PS I complexes from the cyanobacterium Synechococcus sp. PCC 6301 using a direct electrometrical technique. The relative contributions of the F(X) --> F(B) and the F(X) --> F(A) electron transfer reactions to the overall electrogenicity were elucidated by comparing the sodium dithionite-induced decrease in the magnitude of the total photoelectric responses in control and in F(B)-less (HgCl2-treated) PS I complexes. The results obtained suggest that the electrogenesis on the acceptor side of PS I is related to electron transfers between both F(X) and F(A) and F(A) and F(B). Based on the electrogenic nature of the latter reaction in PS I complexes, we conclude that F(A) rather than F(B) is the acceptor proximal to F(X).

Cyanobacteria↗
PubMed1999

Inorganic Fe2+ formation upon Fe-S protein thermodestruction in the membranes of thermophilic cyanobacteria: Mössbauer spectroscopy study.

A model description of the Mössbauer spectrum (80 K) of native membranes of the thermophilic cyanobacterium Synechococcus elongatus is suggested on the basis of the known values of quadrupole splitting (deltaE(Q)) and isomer shift (deltaFe) for the iron-containing components of the photosynthetic apparatus. Using this approach, we found that heating the membranes at 70-80 K results in a decrease of doublet amplitudes belonging to F(X), F(A), F(B) and ferredoxin and simultaneous formation of a new doublet with deltaE(Q) = 3.10 mm/s and delta-Fe = 1.28 mm/s, typical of inorganic hydrated forms of Fe2+. The inhibition of electron transfer via photosystem I to oxygen, catalyzed by ferredoxin, occurs within the same range of temperatures. The data demonstrate that the processes of thermoinduced Fe2+ formation and distortions in the photosystem I electron transport in the membranes are interrelated and caused mainly by the degradation of ferredoxin. The possible role of Fe2+ formation in the damage of the photosynthetic apparatus resulting from heating and the action of other extreme factors is discussed.

Bacterial Proteins↗
PubMed1999

HtpG is essential for the thermal stress management in cyanobacteria.

The heat shock protein (Hsp) HtpG is a member of the Hsp90 protein family. We cloned a single-copy gene encoding a homologue of HtpG from the unicellular cyanobacterium Synechococcus sp. PCC 7942. Sequence alignment with HtpGs from other prokaryotes revealed unique features in the cyanobacterial HtpG primary sequence. A monocistronic mRNA of the htpG gene increased transiently in response to heat shock. In order to elucidate the role of HtpG in vivo, we inactivated the htpG gene by targeted mutagenesis. Although the mutation did not affect the photoautotrophic growth at 30 and 42 degrees C, the mutant cells were unable to grow at 45 degrees C. They lost both basal and acquired thermotolerances. These results indicate that HtpG plays an essential role for the thermal stress management in cyanobacteria, the first such an example for either a photosynthetic or a prokaryotic organism.

Amino Acid Sequence↗