Photosynthesis Research最新文献

Photoprotection mechanisms are ubiquitous among photosynthetic organisms. The photoprotection capacity of the green alga Chlamydomonas reinhardtii is correlated with protein levels of stress-related light-harvesting complex (LHCSR) proteins, which are strongly induced by high light (HL). However, the dynamic response of overall thylakoid structure during acclimation to growth in HL has not been fully understood. Here, we combined live-cell super-resolution microscopy and analytical membrane subfractionation to investigate macroscale structural changes of thylakoid membranes during HL acclimation in Chlamydomonas. Subdiffraction-resolution live-cell imaging revealed that the overall thylakoid structures became thinned and shrunken during HL acclimation. The stromal space around the pyrenoid also became enlarged. Analytical density-dependent membrane fractionation indicated that the structural changes were partly a consequence of membrane unstacking. The analysis of both an LHCSR loss-of-function mutant, npq4 lhcsr1, and a regulatory mutant that over-expresses LHCSR, spa1-1, showed that structural changes occurred independently of LHCSR protein levels, demonstrating that LHCSR was neither necessary nor sufficient to induce the thylakoid structural changes associated with HL acclimation. In contrast, stt7-9, a mutant lacking a kinase of major light-harvesting antenna proteins, had a slower thylakoid structural response to HL relative to all other lines tested but still showed membrane unstacking. These results indicate that neither LHCSR- nor antenna-phosphorylation-dependent HL acclimation are required for the observed macroscale structural changes of thylakoid membranes in HL conditions.

This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S₁ state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn₄O_x cluster (1) in the S_i (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T₀) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H₂O)_n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Y_z-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.

Far-red absorbing allophycocyanins (APC), identified in cyanobacteria capable of FRL photoacclimation (FaRLiP) and low-light photoacclimation (LoLiP), absorb far-red light, functioning in energy transfer as light-harvesting proteins. We report an optimized method to obtain high purity far-red absorbing allophycocyanin B, AP-B2, of Chroococcidiopsis thermalis sp. PCC7203 by synthesis in Escherichia coli and an improved purification protocol. The crystal structure of the trimer, (PCB-ApcD5/PCB-ApcB2)₃, has been resolved to 2.8 Å. The main difference to conventional APCs absorbing in the 650-670 nm range is a largely flat chromophore with the co-planarity extending, in particular, from rings BCD to ring A. This effectively extends the conjugation system of PCB and contributes to the super-red-shifted absorption of the α-subunit (λ_max = 697 nm). On complexation with the β-subunit, it is even further red-shifted (λ_{max, absorption} = 707 nm, λ_{max, emission} = 721 nm). The relevance of ring A for this shift is supported by mutagenesis data. A variant of the α-subunit, I123M, has been generated that shows an intense FR-band already in the absence of the β-subunit, a possible model is discussed. Two additional mechanisms are known to red-shift the chromophore spectrum: lactam-lactim tautomerism and deprotonation of the chromophore that both mechanisms appear inconsistent with our data, leaving this question unresolved.

The influence of poly(ethylene glycol) (PEG) polymers H-(O-CH₂-CH₂)_p-OH with different average molecular sizes $p$ on the micelle formation of n-alkyl-β-D-maltoside detergents with the number of carbon atoms in the alkyl chain ranging from $10$ to $12$ is investigated with the aim to learn more about the detergent behavior under conditions suitable for the crystallization of the photosynthetic pigment-protein complex photosystem II. PEG is shown to increase the critical micelle concentration (CMC) of all three detergents in the crystallization buffer in a way that the free energy of micelle formation increases linearly with the concentration of oxyethylene units (O-CH₂-CH₂) irrespective of the actual molecular weight of the polymer. The CMC shift is modeled by assuming for simplicity that it is dominated by the interaction between PEG and detergent monomers and is interpreted in terms of an increase of the transfer free energy of a methylene group of the alkyl chain by 0.2 kJ mol^-1 per 1 mol L^-1 increase of the concentration of oxyethylene units at 298 K. Implications of this effect for the solubilization and crystallization of protein-detergent complexes as well as detergent extraction from crystals are discussed.

Chlorophylls and bacteriochlorophylls are the primary pigments used by photosynthetic organisms for light harvesting, energy transfer, and electron transfer. Many molecular structures of (bacterio)chlorophyll-containing protein complexes are available, some of which contain mixtures of different (bacterio)chlorophyll types. Differentiating these, which sometimes are structurally similar, is challenging but is required for leveraging structural data to gain functional insight. The reaction center complex from Chloroacidobacterium thermophilum has a hybrid (bacterio)chlorophyll antenna system containing both chlorophyll a and bacteriochlorophyll a molecules. The recent availability of its cryogenic electron microscopy (cryo-EM) structure provides an opportunity for a quantitative analysis of their identities and chemical environments. Here, we describe a theoretical basis for differentiating chlorophyll a and bacteriochlorophyll a in a cryo-EM map, and apply the approach to the experimental cryo-EM maps of the (bacterio)chlorophyll sites of the chloroacidobacterial reaction center. The comparison reveals that at ~ 2.2-Å resolution, chlorophyll a and bacteriochlorophyll a are easily distinguishable, but the orientation of the bacteriochlorophyll a acetyl moiety is not; however, the latter can confidently be assigned by identifying a hydrogen bond donor from the protein environment. This study reveals the opportunities and challenges in assigning (bacterio)chlorophyll types in structural biology, the accuracy of which is vital for downstream investigations.

Photosynthetic light-dependent reactions occur in thylakoid membranes where embedded proteins capture light energy and convert it to chemical energy in the form of ATP and NADPH for use in carbon fixation. One of these integral membrane proteins is Photosystem I (PSI). PSI catalyzes light-driven transmembrane electron transfer from plastocyanin (Pc) to oxidized ferredoxin (Fd). Electrons from reduced Fd are used by the enzyme ferredoxin-NADP⁺ reductase (FNR) for the reduction of NADP⁺ to NADPH. Fd and Pc are both small soluble proteins whereas the larger FNR enzyme is associated with the membrane. To investigate electron shuttling between these diffusible and embedded proteins, thylakoid photoreduction of NADP⁺ was studied. As isolated, both spinach and cyanobacterial thylakoids generate NADPH upon illumination without extraneous addition of Fd. These findings indicate that isolated thylakoids either (i) retain a "pool" of Fd which diffuses between PSI and membrane bound FNR or (ii) that a fraction of PSI is associated with Fd, with the membrane environment facilitating PSI-Fd-FNR interactions which enable multiple turnovers of the complex with a single Fd. To explore the functional association of Fd with PSI in thylakoids, electron paramagnetic resonance (EPR) spectroscopic methodologies were developed to distinguish the signals for the reduced Fe-S clusters of PSI and Fd. Temperature-dependent EPR studies show that the EPR signals of the terminal [4Fe-4S] cluster of PSI can be distinguished from the [2Fe-2S] cluster of Fd at > 30 K. At 50 K, the cw X-band EPR spectra of cyanobacterial and spinach thylakoids reduced with dithionite exhibit EPR signals of a [2Fe-2S] cluster with g-values g_x = 2.05, g_y = 1.96, and g_z = 1.89, confirming that Fd is present in thylakoid preparations capable of NADP⁺ photoreduction. Quantitation of the EPR signals of P₇₀₀⁺ and dithionite reduced Fd reveal that Fd is present at a ratio of ~ 1 Fd per PSI monomer in both spinach and cyanobacterial thylakoids. Light-driven electron transfer from PSI to Fd in thylakoids confirms Fd is functionally associated (< 0.4 Fd/PSI) with the acceptor end of PSI in isolated cyanobacterial thylakoids. These EPR experiments provide a benchmark for future spectroscopic characterization of Fd interactions involved in multistep relay of electrons following PSI charge separation in the context of photosynthetic thylakoid microenvironments.

Flash-induced absorption changes in the Soret region arising from the [P_D1P_D2]⁺ state, the chlorophyll cation radical formed upon light excitation of Photosystem II (PSII), were measured in Mn-depleted PSII cores at pH 8.6. Under these conditions, Tyr_D is i) reduced before the first flash, and ii) oxidized before subsequent flashes. In wild-type PSII, when Tyr_D^● is present, an additional signal in the [P_D1P_D2]⁺-minus-[P_D1P_D2] difference spectrum was observed when compared to the first flash when Tyr_D is not oxidized. The additional feature was "W-shaped" with troughs at 434 nm and 446 nm. This feature was absent when Tyr_D was reduced, but was present (i) when Tyr_D was physically absent (and replaced by phenylalanine) or (ii) when its H-bonding histidine (D2-His189) was physically absent (replaced by a Leucine). Thus, the simple difference spectrum without the double trough feature at 434 nm and 446 nm, seemed to require the native structural environment around the reduced Tyr_D and its H bonding partners to be present. We found no evidence of involvement of P_D1, Chl_D1, Phe_D1, Phe_D2, Tyr_Z, and the Cytb₅₅₉ heme in the W-shaped difference spectrum. However, the use of a mutant of the P_D2 axial His ligand, the D2-His197Ala, shows that the P_D2 environment seems involved in the formation of "W-shaped" signal.

Water oxidation by photosystem II (PSII) sustains most life on Earth, but the molecular mechanism of this unique process remains controversial. The ongoing identification of the binding sites and modes of the two water-derived substrate oxygens ('substrate waters') in the various intermediates (S_i states, i = 0, 1, 2, 3, 4) that the water-splitting tetra-manganese calcium penta-oxygen (Mn₄CaO₅) cluster attains during the reaction cycle provides central information towards resolving the unique chemistry of biological water oxidation. Mass spectrometric measurements of single- and double-labeled dioxygen species after various incubation times of PSII with H₂¹⁸O provide insight into the substrate binding modes and sites via determination of exchange rates. Such experiments have revealed that the two substrate waters exchange with different rates that vary independently with the S_i state and are hence referred to as the fast (W_f) and the slow (W_S) substrate waters. New insight for the molecular interpretation of these rates arises from our recent finding that in the S₂ state, under special experimental conditions, two different rates of W_S exchange are observed that appear to correlate with the high spin and low spin conformations of the Mn₄CaO₅ cluster. Here, we reexamine and unite various proposed methods for extracting and assigning rate constants from this recent data set. The analysis results in a molecular model for substrate-water binding and exchange that reconciles the expected non-exchangeability of the central oxo bridge O5 when located between two Mn(IV) ions with the experimental and theoretical assignment of O5 as W_S in all S states. The analysis also excludes other published proposals for explaining the water exchange kinetics.

Calcium and chloride are activators of oxygen evolution in photosystem II (PSII), the light-absorbing water oxidase of higher plants, algae, and cyanobacteria. Calcium is an essential part of the catalytic Mn₄CaO₅ cluster that carries out water oxidation and chloride has two nearby binding sites, one of which is associated with a major water channel. The co-activation of oxygen evolution by the two ions is examined in higher plant PSII lacking the extrinsic PsbP and PsbQ subunits using a bisubstrate enzyme kinetics approach. Analysis of three different preparations at pH 6.3 indicates that the Michaelis constant, K_M, for each ion is less than the dissociation constant, K_S, and that the affinity of PSII for Ca²⁺ is about ten-fold greater than for Cl^-, in agreement with previous studies. Results are consistent with a sequential binding model in which either ion can bind first and each promotes the activation by the second ion. At pH 5.5, similar results are found, except with a higher affinity for Cl^- and lower affinity for Ca²⁺. Observation of the slow-decaying Tyr Z radical, Y_Z•, at 77 K and the coupled S₂Y_Z• radical at 10 K, which are both associated with Ca²⁺ depletion, shows that Cl^- is necessary for their observation. Given the order of electron and proton transfer events, this indicates that chloride is required to reach the S₃ state preceding Ca²⁺ loss and possibly for stabilization of Y_Z• after it forms. Interdependence through hydrogen bonding is considered in the context of the water environment that intervenes between Cl^- at the Cl-1 site and the Ca²⁺/Tyr Z region.

Kenneth (Ken) Sauer was a mainstay of research in photosynthesis at the University of California, Berkeley and the Lawrence Berkeley National Laboratory (LBNL) for more than 50 years. Ken will be remembered by his colleagues, and other workers in the field of photosynthesis as well, for his pioneering work that introduced the physical techniques whose application have enriched our understanding of the basic reactions of oxygenic photosynthesis. His laboratory was a training ground for many students and postdocs who went on to success in the field of photosynthesis and many others. Trained as a physical chemist, he always brought that quantitative approach to research questions and used several spectroscopic methods in his research. His broad scientific interests concerned the role of manganese in oxygen evolution, electronic properties of chlorophylls, energy transport in antenna complexes, and electron transport reactions. He was also an enthusiastic teacher, an enormously successful mentor who leaves behind a legion of scientists as his abiding legacy, a lover of music and the outdoors with many interests beyond science, and a dedicated family man with a great sense of humility. In this tribute, we summarize some aspects of Ken Sauer's life and career, illustrated with selected research achievements, and describe his approach to research and life as we perceived it, which is complemented by reminiscences of several current researchers in photosynthesis and other fields. The supporting material includes Ken Sauers's CV and publication list, as well as a list of the graduate students and postdocs he trained and of researchers that spent a sabbatical in his lab.