Photosystem II proteins PsbL and PsbJ regulate electron flow to the plastoquinone pool

Obscurity of chlorophyll tails - Is chlorophyll with farnesyl tail incorporated into PSII complexes?

Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.

Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll d-containing cyanobacterium

Acaryochloris marina is a unique cyanobacterium using chlorophyll d (Chl d) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from A. marina at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.

Modulation of antioxidant defense and PSII components by exogenously applied acetate mitigates salinity stress in Avena sativa

Salinity stress has detrimental effects on various aspects of plant development. However, our understanding of strategies to mitigate these effects in crop plants remains limited. Recent research has shed light on the potential of sodium acetate as a mitigating component against salinity stress in several plant species. Here, we show the role of acetate sodium in counteracting the adverse effects on oat (Avena sativa) plants subjected to NaCl-induced salinity stress, including its impact on plant morphology, photosynthetic parameters, and gene expression related to photosynthesis and antioxidant capacity, ultimately leading to osmoprotection. The five-week experiment involved subjecting oat plants to four different conditions: water, salt (NaCl), sodium acetate, and a combination of salt and sodium acetate. The presence of NaCl significantly inhibited plant growth and root elongation, disrupted chlorophylls and carotenoids content, impaired chlorophyll fluorescence, and down-regulated genes associated with the plant antioxidant defense system. Furthermore, our findings reveal that when stressed plants were treated with sodium acetate, it partially reversed these adverse effects across all analyzed parameters. This reversal was particularly evident in the increased content of proline, thereby ensuring osmoprotection for oat plants, even under stressful conditions. These results provide compelling evidence regarding the positive impact of sodium acetate on various plant development parameters, with a particular focus on the enhancement of photosynthetic activity.

Adaptation mechanisms of microalgal-bacterial granular sludge to outdoor light-limited conditions

Microalgal-bacterial granular sludge (MBGS) has attached attention for sustainable wastewater treatment, but it remains elusive whether it can adapt to outdoor light-limited conditions. This paper investigated the biological adaptation mechanisms of MBGS to outdoor light-limited diel conditions using real municipal wastewater. The results indicated that MBGS still had excellent pollutants removal performance, and that both the extracellular polymeric substances and glycogen content of MBGS increased significantly. The main functional microalgae and bacteria were revealed to be Leptolyngbyaceae and Rhodanobacteria, respectively. Further analyses indicated that the abundance of genes encoding PsbA, PsbD, PsbE, PsbJ, PsbP, Psb27, Psb28-2, PsaC, PsaE, PsaL, PsbX, PetB, PetA, and PetE increased in photosystem. Meanwhile, the abundance of gene encoding Rubisco decreased but the gene abundance regarding to crassulacean acid metabolism cycle increased. These suggested that MBGS could adjust the photosynthetic pathway to ensure the completion of photosynthesis. This study is anticipated to add fundamental insights for the MBGS process operated under outdoor light-limited conditions.

Binding and functions of the two chloride ions in the oxygen-evolving center of photosystem II

Light-driven water oxidation in photosynthesis occurs at the oxygen-evolving center (OEC) of photosystem II (PSII). Chloride ions (Cl^-) are essential for oxygen evolution by PSII, and two Cl^- ions have been found to specifically bind near the Mn₄CaO₅ cluster in the OEC. The retention of these Cl^- ions within the OEC is critically supported by some of the membrane-extrinsic subunits of PSII. The functions of these two Cl^- ions and the mechanisms of their retention both remain to be fully elucidated. However, intensive studies performed recently have advanced our understanding of the functions of these Cl^- ions, and PSII structures from various species have been reported, aiding the interpretation of previous findings regarding Cl^- retention by extrinsic subunits. In this review, we summarize the findings to date on the roles of the two Cl^- ions bound within the OEC. Additionally, together with a short summary of the functions of PSII membrane-extrinsic subunits, we discuss the mechanisms of Cl^- retention by these extrinsic subunits.

Properties of Photosystem II lacking the PsbJ subunit

Photosystem II (PSII), the oxygen-evolving enzyme, consists of 17 trans-membrane and 3 extrinsic membrane proteins. Other subunits bind to PSII during assembly, like Psb27, Psb28, and Tsl0063. The presence of Psb27 has been proposed (Zabret et al. in Nat Plants 7:524-538, 2021; Huang et al. Proc Natl Acad Sci USA 118:e2018053118, 2021; Xiao et al. in Nat Plants 7:1132-1142, 2021) to prevent the binding of PsbJ, a single transmembrane α-helix close to the quinone Q_B binding site. Consequently, a PSII rid of Psb27, Psb28, and Tsl0034 prior to the binding of PsbJ would logically correspond to an assembly intermediate. The present work describes experiments aiming at further characterizing such a ∆PsbJ-PSII, purified from the thermophilic Thermosynechococcus elongatus, by means of MALDI-TOF spectroscopy, thermoluminescence, EPR spectroscopy, and UV-visible time-resolved spectroscopy. In the purified ∆PsbJ-PSII, an active Mn₄CaO₅ cluster is present in 60-70% of the centers. In these centers, although the forward electron transfer seems not affected, the Em of the Q_B/Q_B^- couple increases by ≥ 120 mV , thus disfavoring the electron coming back on Q_A. The increase of the energy gap between Q_A/Q_A^- and Q_B/Q_B^- could contribute in a protection against the charge recombination between the donor side and Q_B^-, identified at the origin of photoinhibition under low light (Keren et al. in Proc Natl Acad Sci USA 94:1579-1584, 1997), and possibly during the slow photoactivation process.

Advances in the Understanding of the Lifecycle of Photosystem II

Photosystem II is a light-driven water-plastoquinone oxidoreductase present in cyanobacteria, algae and plants. It produces molecular oxygen and protons to drive ATP synthesis, fueling life on Earth. As a multi-subunit membrane-protein-pigment complex, Photosystem II undergoes a dynamic cycle of synthesis, damage, and repair known as the Photosystem II lifecycle, to maintain a high level of photosynthetic activity at the cellular level. Cyanobacteria, oxygenic photosynthetic bacteria, are frequently used as model organisms to study oxygenic photosynthetic processes due to their ease of growth and genetic manipulation. The cyanobacterial PSII structure and function have been well-characterized, but its lifecycle is under active investigation. In this review, advances in studying the lifecycle of Photosystem II in cyanobacteria will be discussed, with a particular emphasis on new structural findings enabled by cryo-electron microscopy. These structural findings complement a rich and growing body of biochemical and molecular biology research into Photosystem II assembly and repair.

Bridging the gap between Kok-type and kinetic models of photosynthetic electron transport within Photosystem II

Historically, two modeling approaches have been developed independently to describe photosynthetic electron transport (PET) from water to plastoquinone within Photosystem II (PSII): Markov models account for losses from finite redox transition probabilities but predict no reaction kinetics, and ordinary differential equation (ODE) models account for kinetics but not for redox inefficiencies. We have developed an ODE mathematical framework to calculate Markov inefficiencies of transition probabilities as defined in Joliot-Kok-type catalytic cycles. We adapted a previously published ODE model for PET within PSII that accounts for 238 individual steps to enable calculation of the four photochemical inefficiency parameters (miss, double hit, inactivation, backward transition) and the four redox accumulation states (S-states) that are predicted by the most advanced of the Joliot-Kok-type models (VZAD). Using only reaction kinetic parameters without other assumptions, the RODE-calculated time-averaged (e.g., equilibrium) inefficiency parameters and equilibrium S-state populations agree with those calculated by time-independent Joliot-Kok models. RODE also predicts their time-dependent values during transient photochemical steps for all 96 microstates involving PSII redox cofactors. We illustrate applications to two cyanobacteria, Arthrospira maxima and Synechococcus sp. 7002, where experimental data exists for the inefficiency parameters and the S-state populations, and historical data for plant chloroplasts as benchmarks. Significant findings: RODE predicts the microstates responsible for period-4 and period-2 oscillations of O₂ and fluorescence yields and the four inefficiency parameters; the latter parameters are not constant for each S state nor in time, in contrast to predictions from Joliot-Kok models; some of the recombination pathways that contribute to the backward transition parameter are identified and found to contribute when their rates exceed the oxidation rate of the terminal acceptor pool (PQH₂); prior reports based on the assumptions of Joliot-Kok parameters may require reinterpretation.

Tandem gene amplification restores photosystem II accumulation in cytochrome b559 mutants of cyanobacteria

Cytochrome (Cyt) b₅₅₉ is a key component of the photosystem II complex (PSII) that is essential for its proper functioning and assembly. Site-directed mutants of the model cyanobacterium Synechocystis sp. PCC6803 with mutated heme axial ligands of Cyt b₅₅₉ have little PSII and are therefore unable to grow photoautotrophically. Here we describe two types of Synechocystis autotrophic transformants that retained the same mutations in Cyt b₅₅₉ but are able to accumulate PSII and grow photoautotrophically. Whole-genome sequencing revealed that all of these autotrophic transformants carried a variable number of tandem repeats (from 5 to 15) of chromosomal segments containing the psbEFLJ operon. RNA-seq analysis showed greatly increased transcript levels of the psbEFLJ operon in these autotrophic transformants. Multiple copies of the psbEFLJ operon in these transformants were only maintained during autotrophic growth, while its copy numbers gradually decreased under photoheterotrophic conditions. Two-dimensional PAGE analysis of membrane proteins revealed a strong deficiency in PSII complexes in the Cyt b₅₅₉ mutants that was reversed in the autotrophic transformants. These results illustrate how tandem gene amplification restores PSII accumulation and photoautotrophic growth in Cyt b₅₅₉ mutants of cyanobacteria, and may serve as an important adaptive mechanism for cyanobacterial survival.

The availability of neither D2 nor CP43 limits the biogenesis of photosystem II in tobacco

The pathway of photosystem II (PSII) assembly is well understood, and multiple auxiliary proteins supporting it have been identified, but little is known about rate-limiting steps controlling PSII biogenesis. In the cyanobacterium Synechocystis PCC6803 and the green alga Chlamydomonas reinhardtii, indications exist that the biosynthesis of the chloroplast-encoded D2 reaction center subunit (PsbD) limits PSII accumulation. To determine the importance of D2 synthesis for PSII accumulation in vascular plants and elucidate the contributions of transcriptional and translational regulation, we modified the 5'-untranslated region of psbD via chloroplast transformation in tobacco (Nicotiana tabacum). A drastic reduction in psbD mRNA abundance resulted in a strong decrease in PSII content, impaired photosynthetic electron transport, and retarded growth under autotrophic conditions. Overexpression of the psbD mRNA also increased transcript abundance of psbC (the CP43 inner antenna protein), which is co-transcribed with psbD. Because translation efficiency remained unaltered, translation output of pbsD and psbC increased with mRNA abundance. However, this did not result in increased PSII accumulation. The introduction of point mutations into the Shine-Dalgarno-like sequence or start codon of psbD decreased translation efficiency without causing pronounced effects on PSII accumulation and function. These data show that neither transcription nor translation of psbD and psbC are rate-limiting for PSII biogenesis in vascular plants and that PSII assembly and accumulation in tobacco are controlled by different mechanisms than in cyanobacteria or in C. reinhardtii.

Jasmonic acid and methyl jasmonate modulate growth, photosynthetic activity and expression of photosystem II subunit genes in Brassica oleracea L

The effects of jasmonic acid (JA) and methyl jasmonate (Me-JA) on photosynthetic efficiency and expression of some photosystem (PSII) related in different cultivars of Brassica oleracea L. (var. italica, capitata, and botrytis) were investigated. Plants raised from seeds subjected to a pre-sowing soaking treatment of varying concentrations of JA and Me-JA showed enhanced photosynthetic efficiency in terms of qP and chlorophyll fluorescence. Maximum quantum efficiency of PSII (Fv/Fm) was increased over that in the control seedlings. This enhancement was more pronounced in the Me-JA-treated seedlings compared to that in JA-treated ones. The expression of PSII genes was differentially regulated among the three varieties of B. oleracea. The gene PsbI up-upregulated in var. botrytis after treatment of JA and Me-JA, whereas PsbL up-regulated in capitata and botrytis after supplementation of JA. The gene PsbM showed many fold enhancements in these expressions in italica and botrytis after treatment with JA. However, the expression of the gene PsbM increased by both JA and Me-JA treatments. PsbTc(p) and PsbTc(n) were also found to be differentially expressed which revealed specificity with the variety chosen as well as JA or Me-JA treatments. The RuBP carboxylase activity remained unaffected by either JA or Me-JA supplementation in all three varieties of B. oleracea L. The data suggest that exogenous application of JA and Me-JA to seeds before germination could influence the assembly, stability, and repair of PS II in the three varieties of B. oleracea examined. Furthermore, this improvement in the PS II machinery enhanced the photosynthetic efficiency of the system and improved the photosynthetic productivity in terms of saccharides accumulation.

Stabilization of Photosystem II by the PsbT protein impacts photodamage, repair and biogenesis

Photosystem II (PS II) catalyzes the light-driven process of water splitting in oxygenic photosynthesis. Four core membrane-spanning proteins, including D1 that binds the majority of the redox-active co-factors, are surrounded by 13 low-molecular-weight (LMW) proteins. We previously observed that deletion of the LMW PsbT protein in the cyanobacterium Synechocystis sp. PCC 6803 slowed electron transfer between the primary and secondary plastoquinone electron acceptors Q_A and Q_B and increased the susceptibility of PS II to photodamage. Here we show that photodamaged ∆PsbT cells exhibit unimpaired rates of oxygen evolution if electron transport is supported by HCO₃^- even though the cells exhibit negligible variable fluorescence. We find that the protein environment in the vicinity of Q_A and Q_B is altered upon removal of PsbT resulting in inhibition of Q_A^- oxidation in the presence of 2,5-dimethyl-1,4-benzoquinone, an artificial PS II-specific electron acceptor. Thermoluminescence measurements revealed an increase in charge recombination between the S₂ oxidation state of the water-oxidizing complex and Q_A^- by the indirect radiative pathway in ∆PsbT cells and this is accompanied by increased ¹O₂ production. At the protein level, both D1 removal and replacement, as well as PS II biogenesis, were accelerated in the ∆PsbT strain. Our results demonstrate that PsbT plays a key role in optimizing the electron acceptor complex of the acceptor side of PS II and support the view that repair and biogenesis of PS II share an assembly pathway that incorporates both de novo synthesis and recycling of the assembly modules associated with the core membrane-spanning proteins.

Effects of Stripe Rust Infection on the Levels of Redox Balance and Photosynthetic Capacities in Wheat

Wheat stripe rust (Puccinia striiformis f. sp. tritici, Pst) is the most destructive wheat disease and a major problem for the productivity of wheat in the world. To obtain a better understanding about different effects of redox homeostasis and photosystem (PS) to Pst infection in wheat, we investigated the differences in photosynthesis and the antioxidant defense system in wheat cultivar Chuanmai42 (CM42) in response to two Chinese Pst races known as CYR32 and V26. The results showed that V26-infected wheat accumulated a higher reactive oxygen species (ROS), cell death, and energy dissipation than CYR32-infected wheat when compared with the control. Furthermore, we found that the activities of three antioxidant enzymes (APX, GR, and GPX) and four resistance-related enzymes in CYR32-infected wheat were significantly higher than that in V26-infected wheat. In addition, quantitative RT-PCR indicated that the expression levels of two genes associated with resistant stripe rust in CYR32-infected wheat were clearly higher than that in V26-infected wheat. Compared with CYR32-infected wheat, lower photochemical efficiencies were observed in V26-infected wheat at the adult stage. Meanwhile, only a marked decline in D1 protein was observed in V26-infected wheat. We therefore deduced that wheat with stripe rust resistance could maintain high resistance and photosynthetic capacity by regulating the antioxidant system, disease-resistant related enzymes and genes, and the levels of PSII reaction center proteins.

The roles of Arabidopsis proteins of Lhcb4, Lhcb5 and Lhcb6 in oxidative stress under natural light conditions

Under light conditions, highly reactive oxygen species (ROS) can be generated in the antenna systems and the reaction center of photosystems (PS). The protective roles of Lhcb4 (CP29), Lhcb5 (CP26) and Lhcb6 (CP24), three minor chlorophyll binding antenna proteins during photoinhibition have been well studied. However, their regulatory mechanisms against oxidative damages under natural light conditions remain unknown. Here we investigated their specific roles in oxidative stress responses and photosynthetic adaptation by using the Arabidopsis thaliana knockout lines grown in the field condition. All three mutant lines exhibited decreased energy-transfer efficiency from the LHCII (light-harvesting complex II) to the PSII reaction center. Oxygen evolution capacity decreased slightly in the plants lacking Lhcb4 (koLHCB4) and Lhcb6 (koLHCB6). Photosynthetic rates and fitness for the plants lacking Lhcb5 (koLHCB5) or koLHCB6 grown in the field were affected, but not in the plants lacking Lhcb4. Antioxidant analysis indicated the lowest antioxidant enzyme activities and the lowest levels of non-enzymatic antioxidants in koLHCB6 plants. In addition, koLHCB6 plants accumulated much higher levels of superoxide and hydrogen, and suffered more severe oxidative-damages in the field. Our results clearly demonstrate that Lhcb6 may be involved in alleviating oxidative stress and photoprotection under natural conditions.

Gene essentiality, conservation index and co-evolution of genes in cyanobacteria

Cyanobacteria, a group of photosynthetic prokaryotes, dominate the earth with ~ 1015 g wet biomass. Despite diversity in habitats and an ancient origin, cyanobacterial phylum has retained a significant core genome. Cyanobacteria are being explored for direct conversion of solar energy and carbon dioxide into biofuels. For this, efficient cyanobacterial strains will need to be designed via metabolic engineering. This will require identification of target knockouts to channelize the flow of carbon toward the product of interest while minimizing deletions of essential genes. We propose "Gene Conservation Index" (GCI) as a quick measure to predict gene essentiality in cyanobacteria. GCI is based on phylogenetic profile of a gene constructed with a reduced dataset of cyanobacterial genomes. GCI is the percentage of organism clusters in which the query gene is present in the reduced dataset. Of the 750 genes deemed to be essential in the experimental study on S. elongatus PCC 7942, we found 494 to be conserved across the phylum which largely comprise of the essential metabolic pathways. On the contrary, the conserved but non-essential genes broadly comprise of genes required under stress conditions. Exceptions to this rule include genes such as the glycogen synthesis and degradation enzymes, deoxyribose-phosphate aldolase (DERA), glucose-6-phosphate 1-dehydrogenase (zwf) and fructose-1,6-bisphosphatase class1, which are conserved but non-essential. While the essential genes are to be avoided during gene knockout studies as potentially lethal deletions, the non-essential but conserved set of genes could be interesting targets for metabolic engineering. Further, we identify clusters of co-evolving genes (CCG), which provide insights that may be useful in annotation. Principal component analysis (PCA) plots of the CCGs are demonstrated as data visualization tools that are complementary to the conventional heatmaps. Our dataset consists of phylogenetic profiles for 23,643 non-redundant cyanobacterial genes. We believe that the data and the analysis presented here will be a great resource to the scientific community interested in cyanobacteria.

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b₆f complex. To understand how PLQ enters and leaves PSII, here we show results of coarse grained molecular dynamics simulations of PSII embedded in the thylakoid membrane, covering a total simulation time of more than 0.5 ms. The long time scale allows the observation of many spontaneous entries of PLQ into PSII, and the unbinding of plastoquinol (PLQol) from the complex. In addition to the two known channels, we observe a third channel for PLQ/PLQol diffusion between the thylakoid membrane and the PLQ binding sites. Our simulations point to a promiscuous diffusion mechanism in which all three channels function as entry and exit channels. The exchange cavity serves as a PLQ reservoir. Our simulations provide a direct view on the exchange of electron carriers, a key step of the photosynthesis machinery.

Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane

Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 μs molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid membrane model that reflects its native lipid composition. We describe in detail the setup of the protein complex and the many natural cofactors and characterize their mobility. Overall we find that the protein subunits and cofactors are more flexible toward the periphery of the complex as well as near the PLQ exchange cavity and at the dimer interface. Of all cofactors, β-carotenes show the highest mobility. Some of the β-carotenes diffuse in and out of the protein complex via the thylakoid membrane. In contrast with the PSII dimer, the monomeric form adopts a tilted conformation in the membrane, with strong interactions between the soluble PsbO subunit and the glycolipid headgroups. Interestingly, the tilted conformation causes buckling of the membrane. Together, our results provide an unprecedented view of PSII dynamics on a microsecond time scale. Our data may be used as basis for the interpretation of experimental data as well as for theoretical models describing exciton energy transfer.

Functional Update of the Auxiliary Proteins PsbW, PsbY, HCF136, PsbN, TerC and ALB3 in Maintenance and Assembly of PSII

Assembly of Photosystem (PS) II in plants has turned out to be a highly complex process which, at least in part, occurs in a sequential order and requires many more auxiliary proteins than subunits present in the complex. Owing to the high evolutionary conservation of the subunit composition and the three-dimensional structure of the PSII complex, most plant factors involved in the biogenesis of PSII originated from cyanobacteria and only rarely evolved de novo. Furthermore, in chloroplasts the initial assembly steps occur in the non-appressed stroma lamellae, whereas the final assembly including the attachment of the major LHCII antenna proteins takes place in the grana regions. The stroma lamellae are also the place where part of PSII repair occurs, which very likely also involves assembly factors. In cyanobacteria initial PSII assembly also occurs in the thylakoid membrane, in so-called thylakoid centers, which are in contact with the plasma membrane. Here, we provide an update on the structures, localisations, topologies, functions, expression and interactions of the low molecular mass PSII subunits PsbY, PsbW and the auxiliary factors HCF136, PsbN, TerC and ALB3, assisting in PSII complex assembly and protein insertion into the thylakoid membrane.

The importance of the hydrophilic region of PsbL for the plastoquinone electron acceptor complex of Photosystem II

The PsbL protein is a 4.5kDa subunit at the monomer-monomer interface of Photosystem II (PS II) consisting of a single membrane-spanning domain and a hydrophilic stretch of ~15 residues facing the cytosolic (or stromal) side of the photosystem. Deletion of conserved residues in the N-terminal region has been used to investigate the importance of this hydrophilic extension. Using Synechocystis sp. PCC 6803, three deletion strains: ∆(N6-N8), ∆(P11-V12) and ∆(E13-N15), have been created. The ∆(N6-N8) and ∆(P11-V12) strains remained photoautotrophic but were more susceptible to photodamage than the wild type; however, the ∆(E13-N15) cells had the most severe phenotype. The Δ(E13-N15) mutant showed decreased photoautotrophic growth, a reduced number of PS II centers, impaired oxygen evolution in the presence of PS II-specific electron acceptors, and was highly susceptible to photodamage. The decay kinetics of chlorophyll a variable fluorescence after a single turnover saturating flash and the sensitivity to low concentrations of PS II-directed herbicides in the Δ(E13-N15) strain indicate that the binding of plastoquinone to the QB-binding site had been altered such that the affinity of QB is reduced. In addition, the PS II-specific electron acceptor 2,5-dimethyl-p-benzoquinone was found to inhibit electron transfer through the quinone-acceptor complex of the ∆(E13-N15) strain. The PsbL Y20A mutant was also investigated and it exhibited increased susceptibility to photodamage and increased herbicide sensitivity. Our data suggest that the N-terminal hydrophilic region of PsbL influences forward electron transfer from QA through indirect interactions with the D-E loop of the D1 reaction center protein. Our results further indicate that disruption of interactions between the N-terminal region of PsbL and other PS II subunits or lipids destabilizes PS II dimer formation. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.

Structural, functional and auxiliary proteins of photosystem II

Photosystem II (PSII) is the water-splitting enzyme complex of photosynthesis and consists of a large number of protein subunits. Most of these proteins have been structurally and functionally characterized, although there are differences between PSII of plants, algae and cyanobacteria. Here we catalogue all known PSII proteins giving a brief description, where possible of their genetic origin, physical properties, structural relationships and functions. We have also included details of auxiliary proteins known at present to be involved in the in vivo assembly, maintenance and turnover of PSII and which transiently bind to the reaction centre core complex. Finally, we briefly give details of the proteins which form the outer light-harvesting systems of PSII in different types of organisms.

KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome

BACKGROUND

Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics.

DESCRIPTION

Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics.

CONCLUSIONS

We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.

A unique regulation of the expression of the psbA, psbD, and psbE genes, encoding the 01, 02 and cytochrome b559 subunits of the Photosystem II complex in the chlorophyll d containing cyanobacterium Acaryochloris marina

Photosynthetic electron transport, chromatic photoacclirnation and expression of the genes encoding the 01, 02, and cytochrome b559 subunits of the Photosystem II complex were studied in the chlorophyll d containing cyanobacterium Acaryochloris marina MBIC11017 under various environmental conditions. During oxygen deprivation and inhibition of photosynthetic electron transport by dibromothymoquinone the psbA1 gene encoding a 01' isoform was induced. All of the three psbA and one of the three psbD (psbD2) genes, encoding two different isoforms of the 01 and the abundant isoform of the 02 proteins, respectively were induced under exposure to UV-B radiation and high intensity visible light. Under far red light the amount of Photosystem II complexes increased, and expression of the psbE2 gene encoding the alpha-subunit of cytochrome b559 was enhanced. However, the psbF and psbE1 genes encoding the beta- and another isoform of alpha-cytochrome b559, respectively remained lowly expressed under all conditions. Far red light also induced the psbD3 gene encoding a 02' isoform whose primary structure is different from the abundant 02 isoform. psbD3 was also induced under low intensity visible light, when chromatic photoacclimation was indicated by a red-shifted absorption of chlorophyll d. Our results show that differential expression of multigene families encoding different isoforms of 01 and 02 plays an important role in the acclimation of A. marina to contrasting environmental conditions. Moreover, the disproportionate quantity of transcripts of the alpha and beta subunits of cytochrome b559 implies the existence of an alpha-alpha homodimer organization of cytochrome b559 in Photosystem II complexes.

Spectroscopic and functional characterization of cyanobacterium Synechocystis PCC 6803 mutants on the cytoplasmic-side of cytochrome b559 in photosystem II

We performed spectroscopic and functional characterization on cyanobacterium Synechocystis PCC6803 with mutations of charged residues of the cytoplasmic side of cytochrome (Cyt) b559 in photosystem II (PSII). All of the mutant cells grew photoautotrophically and assembled stable PSII. However, R7Eα, R17Eα and R17Lβ mutant cells grew significantly slower and were more susceptible to photoinhibition than wild-type cells. The adverse effects of the arginine mutations on the activity and the stability of PSII were in the following order (R17Lβ>R7Eα>R17Eα and R17Aα). All these arginine mutants exhibited normal period-four oscillation in oxygen yield. Thermoluminescence characteristics indicated a slight decrease in the stability of the S3QB(-)/S2QB(-) charge pairs in the R7Eα and R17Lβ mutant cells. R7Eα and R17Lβ PSII core complexes contained predominantly the low potential form of Cyt b559. EPR results indicated the displacement of one of the two axial ligands to the heme of Cyt b559 in R7Eα and R17Lβ mutant reaction centers. Our results demonstrate that the electrostatic interactions between these arginine residues and the heme propionates of Cyt b559 are important to the structure and redox properties of Cyt b559. In addition, the blue light-induced nonphotochemical quenching was significantly attenuated and its recovery was accelerated in the R7Lα and R17Lβ mutant cells. Furthermore, ultra performance liquid chromatography-mass spectrometry results showed that the PQ pool was more reduced in the R7Eα and R17Lβ mutant cells than wild-type cells in the dark. Our data support a functional role of Cyt b559 in protection of PSII under photoinhibition conditions in vivo.

Deletion of psbJ leads to accumulation of Psb27-Psb28 photosystem II complexes in Thermosynechococcus elongatus

The life cycle of Photosystem II (PSII) is embedded in a network of proteins that guides the complex through biogenesis, damage and repair. Some of these proteins, such as Psb27 and Psb28, are involved in cofactor assembly for which they are only transiently bound to the preassembled complex. In this work we isolated and analyzed PSII from a ΔpsbJ mutant of the thermophilic cyanobacterium Thermosynechococcus elongatus. From the four different PSII complexes that could be separated the most prominent one revealed a monomeric Psb27-Psb28 PSII complex with greatly diminished oxygen-evolving activity. The MALDI-ToF mass spectrometry analysis of intact low molecular weight subunits (<10kDa) depicted wild type PSII with the absence of PsbJ. Relative quantification of the PsbA1/PsbA3 ratio by LC-ESI mass spectrometry using (15)N labeled PsbA3-specific peptides indicated the complete replacement of PsbA1 by the stress copy PsbA3 in the mutant, even under standard growth conditions (50μmol photons m(-2) s(-1)). This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.

Effect of moderate and high light on photosystem II function in Arabidopsis thaliana depleted in digalactosyl-diacylglycerol

The response of the heat-sensitive dgd1-2 and dgd1-3 Arabidopsis mutants depleted in the galactolipid DGDG to photoinhibition of chloroplasts photosystem II was studied to verify if there is a relationship between heat stress vulnerability due to depletion in DGDG and the susceptibility to photoinhibitory damage. Non-photochemical quenching (NPQ) is known to dissipate excessive absorbed light energy as heat to protect plants against photodamage. The main component of NPQ is dependent of the transthylakoid pH gradient and is modulated by zeaxanthin (Zx) synthesis. These processes together with chlorophyll fluorescence induction were used to characterize the response of the genotypes. The mutants were more sensitive to photoinhibition to a small extent but this was more severe for dgd1-3 especially at high light intensity. It was deduced that DGDG was not a main factor to influence photoinhibition but other lipid components could affect PSII sensitivity towards photoinhibition in relation to the physical properties of the thylakoid membrane. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.

Photosystem II, a growing complex: updates on newly discovered components and low molecular mass proteins

Photosystem II is a unique complex capable of absorbing light and splitting water. The complex has been thoroughly studied and to date there are more than 40 proteins identified, which bind to the complex either stably or transiently. Another special feature of this complex is the unusually high content of low molecular mass proteins that represent more than half of the proteins. In this review we summarize the recent findings on the low molecular mass proteins (<15kDa) and present an overview of the newly identified components as well. We have also performed co-expression analysis of the genes encoding PSII proteins to see if the low molecular mass proteins form a specific sub-group within the Photosystem II complex. Interestingly we found that the chloroplast-localized genes encoding PSII proteins display a different response to environmental and stress conditions compared to the nuclear localized genes. This article is part of a Special Issue entitled: Photosystem II.

Photoinactivation of photosystem II: is there more than one way to skin a cat?

We briefly review the main mechanisms proposed for photodamage to photosystem II (PSII), at the donor and acceptor sides, and then discuss the mechanism whereby filamentous cyanobacteria inhabiting biological sand crusts such as Microcoleus sp. are able to avoid serious damage to their photosynthetic machinery. We show that the decline in fluorescence following exposure to excess light does not reflect a reduction in PSII activity but rather the activation of a non-radiative charge recombination in PSII. Furthermore, we show that the difference in the thermoluminescent peak temperature intensities in these organisms, in the presence and absence of inhibitors such as dichlorophenyl-dimethylurea (DCMU), is smaller than observed in model organisms suggesting that the redox gap between Q(A)⁻ and P₆₈₀+ is smaller. On the basis of these data, we propose that this could enable an alternative, pheophytin-independent recombination, thereby minimizing the damaging ¹O₂ production associated with radiative recombination.

Molecular functions of PsbP and PsbQ proteins in the photosystem II supercomplex

The PsbP and PsbQ proteins are extrinsic subunits of the photosystem II (PSII) supercomplex, which are found in green plants including higher plants and green algae. These proteins are thought to have evolved from their cyanobacterial homologs; cyanoP and cyanoQ respectively. It has been suggested that the functions of PsbP and PsbQ have largely changed from those of cyanoP and cyanoQ. In addition, multiple isoforms and homologs of PsbP and PsbQ were found in green plants, indicating that the acquisition of PsbP and PsbQ in PSII is not a direct path but a result of intensive functional divergence during evolution from cyanobacterial endosymbiont to chloroplast. In this review, we highlight newly introduced topics related to the functions and structures of both PsbP and PsbQ proteins. The present data suggest that PsbP together with PsbQ have specific and important roles in coordinating the activity of the donor and acceptor sides of PSII and stabilizing the active form of the PSII-light-harvesting complex II (LHCII) supercomplex.

Spectroscopic and functional characterizations of cyanobacterium Synechocystis PCC 6803 mutants on and near the heme axial ligand of cytochrome b559 in photosystem II

The functional role of cytochrome (cyt) b(559) in photosystem II (PSII) was investigated in H22K alpha and Y18S alpha cyt b(559) mutants of the cyanobacterium Synechocystis sp. PCC6803. H22K alpha and Y18S alpha cyt b(559) mutant carries one amino acid substitution on and near one of heme axial ligands of cyt b(559) in PSII, respectively. Both mutants grew photoautotrophically, assembled stable PSII, and exhibited the normal period-four oscillation in oxygen yield. However, both mutants showed several distinct chlorophyll a fluorescence properties and were more susceptible to photoinhibition than wild type. EPR results indicated the displacement of one of the two axial ligands to the heme of cyt b(559) in H22K alpha mutant reaction centers, at least in isolated reaction centers. The maximum absorption of cyt b(559) in Y18S alpha mutant PSII core complexes was shifted to 561 nm. Y18S alpha and H22K alpha mutant PSII core complexes contained predominately the low potential form of cyt b(559). The findings lend support to the concept that the redox properties of cyt b(559) are strongly influenced by the hydrophobicity and ligation environment of the heme. When the cyt b(559) mutations placed in a D1-D170A genetic background that prevents assembly of the manganese cluster, accumulation of PSII is almost completely abolished. Overall, our data support a functional role of cyt b(559) in protection of PSII under photoinhibition conditions in vivo.

Impact of PsbTc on forward and back electron flow, assembly, and phosphorylation patterns of photosystem II in tobacco

Photosystem II (PSII) of oxygen-evolving cyanobacteria, algae, and land plants mediates electron transfer from the Mn(4)Ca cluster to the plastoquinone pool. It is a dimeric supramolecular complex comprising more than 30 subunits per monomer, of which 16 are bitopic or peripheral, low-molecular-weight components. Directed inactivation of the plastid gene encoding the low-molecular-weight peptide PsbTc in tobacco (Nicotiana tabacum) does not prevent photoautotrophic growth. Mutant plants appear normal green, and levels of PSII proteins are not affected. Yet, PSII-dependent electron transport, stability of PSII dimers, and assembly of PSII light-harvesting complexes (LHCII) are significantly impaired. PSII light sensitivity is moderately increased and recovery from photoinhibition is delayed, leading to faster D1 degradation in DeltapsbTc under high light. Thermoluminescence emission measurements revealed alterations of midpoint potentials of primary/secondary electron-accepting plastoquinone of PSII interaction. Only traces of CP43 and no D1/D2 proteins are phosphorylated, presumably due to structural changes of PSII in DeltapsbTc. In striking contrast to the wild type, LHCII in the mutant is phosphorylated in darkness, consistent with its association with PSI, indicating an increased pool of reduced plastoquinone in the dark. Finally, our data suggest that the secondary electron-accepting plastoquinone of PSII site, the properties of which are altered in DeltapsbTc, is required for oxidation of reduced plastoquinone in darkness in an oxygen-dependent manner. These data present novel aspects of plastoquinone redox regulation, chlororespiration, and redox control of LHCII phosphorylation.

Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting

MOTIVATION

It is a question of whether the supramolecular organization of the protein complex has an impact on its function, or not. In the case of the photosystem II (PSII), water splitting might be influenced by cooperation of the PSIIs. Since PSII is the source of the atmospheric oxygen and because better understanding of the water splitting may contribute to the effective use of water as an alternative energy source, possible cooperation should be analyzed and discussed.

RESULTS

We suggest that the dimeric organization of the PSII induces cooperation in the water splitting. We show that the model of monomeric PSII is unable to produce the oxygen after the second short flash (associated with the double turnover of the PSII), in contrast to the experimental data and model of dimeric PSII with considered cooperation. On the basis of this fact and partially from the support from other studies, we concluded that the double turnover of the PSII induced by short flashes might be caused by the cooperation in the water splitting. We further discuss a possibility that the known pathway of the electron transport through the PSII might be incomplete and besides D1-Y161, other cofactor which is able to oxidize the special chlorophyll pair (P680) must be considered in the monomeric PSII to explain the oxygen production after the second short flash.

AVAILABILITY

Commented SBML codes (.XML files) of the monomeric and dimeric PSII models will be available (at the time of publication) in the BioModels database (www.ebi.ac.uk/biomodels).

Structure of Photosystems I and II

Photosynthesis is the major process that converts solar energy into chemical energy on Earth. Two and a half billion years ago, the ancestors of cyanobacteria were able to use water as electron source for the photosynthetic process, thereby evolving oxygen and changing the atmosphere of our planet Earth. Two large membrane protein complexes, Photosystems I and II, catalyze the primary step in this energy conversion, the light-induced charge separation across the photosynthetic membrane. This chapter describes and compares the structure of two Photosystems and discusses their function in respect to the mechanism of light harvesting, electron transfer and water splitting.

Crystal structure of cyanobacterial photosystem II at 3.0 A resolution: a closer look at the antenna system and the small membrane-intrinsic subunits

Photosystem II (PSII) is a homodimeric protein-cofactor complex embedded in the thylakoid membrane that catalyses light-driven charge separation accompanied by the water splitting reaction during oxygenic photosynthesis. In the first part of this review, we describe the current state of the crystal structure at 3.0 A resolution of cyanobacterial PSII from Thermosynechococcus elongatus [B. Loll et al., Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II, Nature 438 (2005) 1040-1044] with emphasis on the core antenna subunits CP43 and CP47 and the small membrane-intrinsic subunits. The second part describes first the general theory of optical spectra and excitation energy transfer and how the parameters of the theory can be obtained from the structural data. Next, structure-function relationships are discussed that were identified from stationary and time-resolved experiments and simulations of optical spectra and energy transfer processes.

Spermine and spermidine inhibition of photosystem II: Disassembly of the oxygen evolving complex and consequent perturbation in electron donation from TyrZ to P680+ and the quinone acceptors QA− to QB

Polyamines are implicated in plant growth and stress response. However, the polyamines spermine and spermidine were shown to elicit strong inhibitory effects in photosystem II (PSII) submembrane fractions. We have studied the mechanism of this inhibitory action in detail. The inhibition of electron transport in PSII submembrane fractions treated with millimolar concentrations of spermine or spermidine led to the decline of plastoquinone reduction, which was reversed by the artificial electron donor diphenylcarbazide. The above inhibition was due to the loss of the extrinsic polypeptides associated with the oxygen evolving complex. Thermoluminescence measurements revealed that charge recombination between the quinone acceptors of PSII, QA and QB, and the S2 state of the Mn-cluster was abolished. Also, the dark decay of chlorophyll fluorescence after a single turn-over white flash was greatly retarded indicating a slower rate of QA- reoxidation.

Deletion of PsbM in tobacco alters the QB site properties and the electron flow within photosystem II

Photosystem II, the oxygen-evolving complex of photosynthetic organisms, includes an intriguingly large number of low molecular weight polypeptides, including PsbM. Here we describe the first knock-out of psbM using a transplastomic, reverse genetics approach in a higher plant. Homoplastomic Delta psbM plants exhibit photoautotrophic growth. Biochemical, biophysical, and immunological analyses demonstrate that PsbM is not required for biogenesis of higher order photosystem II complexes. However, photosystem II is highly light-sensitive, and its activity is significantly decreased in Delta psbM, whereas kinetics of plastid protein synthesis, reassembly of photosystem II, and recovery of its activity are comparable with the wild type. Unlike wild type, phosphorylation of the reaction center proteins D1 and D2 is severely reduced, whereas the redox-controlled phosphorylation of photosystem II light-harvesting complex is reversely regulated in Delta psbM plants because of accumulation of reduced plastoquinone in the dark and a limited photosystem II-mediated electron transport in the light. Charge recombination in Delta psbM measured by thermoluminescence oscillations significantly differs from the 2/6 patterns in the wild type. A simulation program of thermoluminescence oscillations indicates a higher Q(B)/Q(-)(B) ratio in dark-adapted mutant thylakoids relative to the wild type. The interaction of the Q(A)/Q(B) sites estimated by shifts in the maximal thermoluminescence emission temperature of the Q band, induced by binding of different herbicides to the Q(B) site, is changed indicating alteration of the activation energy for back electron flow. We conclude that PsbM is primarily involved in the interaction of the redox components important for the electron flow within, outward, and backward to photosystem II.

Lipids in photosystem II: interactions with protein and cofactors

Photosystem II (PSII) is a homodimeric protein-cofactor complex embedded in the thylakoid membrane that catalyses light-driven charge separation accompanied by the oxidation of water during oxygenic photosynthesis. Biochemical analysis of the lipid content of PSII indicates a number of integral lipids, their composition being similar to the average lipid composition of the thylakoid membrane. The crystal structure of PSII at 3.0 A resolution allowed for the first time the assignment of 14 integral lipids within the protein scaffold, all of them being located at the interface of different protein subunits. The reaction centre subunits D1 and D2 are encircled by a belt of 11 lipids providing a flexible environment for the exchange of D1. Three lipids are located in the dimerization interface and mediate interactions between the PSII monomers. Several lipids are located close to the binding pocket of the mobile plastoquinone Q(B), forming part of a postulated diffusion pathway for plastoquinone. Furthermore two lipids were found, each ligating one antenna chlorophyll a. A detailed analysis of lipid-protein and lipid-cofactor interactions allows to derive some general principles of lipid binding pockets in PSII and to suggest possible functional properties of the various identified lipid molecules.

PsbI affects the stability, function, and phosphorylation patterns of photosystem II assemblies in tobacco

Photosystem II (PSII) core complexes consist of CP47, CP43, D1, D2 proteins and of several low molecular weight integral membrane polypeptides, such as the chloroplast-encoded PsbE, PsbF, and PsbI proteins. To elucidate the function of PsbI in the photosynthetic process as well as in the biogenesis of PSII in higher plants, we generated homoplastomic knock-out plants by replacing most of the tobacco psbI gene with a spectinomycin resistance cartridge. Mutant plants are photoautotrophically viable under green house conditions but sensitive to high light irradiation. Antenna proteins of PSII accumulate to normal amounts, but levels of the PSII core complex are reduced by 50%. Bioenergetic and fluorescence studies uncovered that PsbI is required for the stability but not for the assembly of dimeric PSII and supercomplexes consisting of PSII and the outer antenna (PSII-LHCII). Thermoluminescence emission bands indicate that the presence of PsbI is required for assembly of a fully functional Q(A) binding site. We show that phosphorylation of the reaction center proteins D1 and D2 is light and redox-regulated in the wild type, but phosphorylation is abolished in the mutant, presumably due to structural alterations of PSII when PsbI is deficient. Unlike wild type, phosphorylation of LHCII is strongly increased in the dark due to accumulation of reduced plastoquinone, whereas even upon state II light phosphorylation is decreased in delta psbI. These data attest that phosphorylation of D1/D2, CP43, and LHCII is regulated differently.

Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II

Oxygenic photosynthesis in plants, algae and cyanobacteria is initiated at photosystem II, a homodimeric multisubunit protein-cofactor complex embedded in the thylakoid membrane. Photosystem II captures sunlight and powers the unique photo-induced oxidation of water to atmospheric oxygen. Crystallographic investigations of cyanobacterial photosystem II have provided several medium-resolution structures (3.8 to 3.2 A) that explain the general arrangement of the protein matrix and cofactors, but do not give a full picture of the complex. Here we describe the most complete cyanobacterial photosystem II structure obtained so far, showing locations of and interactions between 20 protein subunits and 77 cofactors per monomer. Assignment of 11 beta-carotenes yields insights into electron and energy transfer and photo-protection mechanisms in the reaction centre and antenna subunits. The high number of 14 integrally bound lipids reflects the structural and functional importance of these molecules for flexibility within and assembly of photosystem II. A lipophilic pathway is proposed for the diffusion of secondary plastoquinone that transfers redox equivalents from photosystem II to the photosynthetic chain. The structure provides information about the Mn4Ca cluster, where oxidation of water takes place. Our study uncovers near-atomic details necessary to understand the processes that convert light to chemical energy.