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

Engineered hypermutation adapts cyanobacterial photosynthesis to combined high light and high temperature stress

Photosynthesis can be impaired by combined high light and high temperature (HLHT) stress. Obtaining HLHT tolerant photoautotrophs is laborious and time-consuming, and in most cases the underlying molecular mechanisms remain unclear. Here, we increase the mutation rates of cyanobacterium Synechococcus elongatus PCC 7942 by three orders of magnitude through combinatory perturbations of the genetic fidelity machinery and cultivation environment. Utilizing the hypermutation system, we isolate Synechococcus mutants with improved HLHT tolerance and identify genome mutations contributing to the adaptation process. A specific mutation located in the upstream non-coding region of the gene encoding a shikimate kinase results in enhanced expression of this gene. Overexpression of the shikimate kinase encoding gene in both Synechococcus and Synechocystis leads to improved HLHT tolerance. Transcriptome analysis indicates that the mutation remodels the photosynthetic chain and metabolism network in Synechococcus. Thus, mutations identified by the hypermutation system are useful for engineering cyanobacteria with improved HLHT tolerance.

Transcriptome analysis of Citrus limon infected with Citrus yellow vein clearing virus

BACKGROUND

Citrus yellow vein clearing virus (CYVCV) is the causative agent of citrus yellow vein clearing disease, and poses a serious threat to the lemon industry in Asia. The common symptoms of CYVCV-infected lemon plants are leaf crinkling, leaf chlorotic mottling, and yellow vein clearing. However, the molecular mechanisms underlying CYVCV-citrus interaction that responsible for symptom occurrence is still unclarified. In this study, RNA-seq was performed to analyze the gene expression patterns of 'Eureka' lemon (Citrus limon Burm. f.) plants in response to CYVCV infection.

RESULTS

There were 3691 differentially expressed genes (DEGs) identified by comparison between mock and CYVCV-infected lemon plants through RNA-seq. Bioinformatics analyses revealed that these DEGs were components of different pathways involved in phenylpropanoid biosynthesis, brassinosteroid biosynthesis, flavonoid biosynthesis and photosynthesis. Among these, the DEGs related to phytohormone metabolism and photosynthesis pathways were further enriched and analyzed. This study showed that different phytohormone-related genes had different responses toward CYVCV infection, however almost all of the photosynthesis-related DEGs were down-regulated in the CYVCV-infected lemon plants. The obtained RNA-seq data were validated by RT-qPCR using 12 randomly chosen genes, and the results of mRNA expression analysis were consistent with those of RNA-seq.

CONCLUSIONS

The phytohormone biosynthesis, signaling and photosynthesis-related genes of lemon plants were probably involved in systemic infection and symptom occurrence of CYVCV. Notably, CYVCV infection had regulatory effects on the biosynthesis and signaling of phytohormone, which likely improve systemic infection of CYVCV. Additionally, CYVCV infection could cause structural changes in chloroplast and inhibition of photosynthesis pathway, which probably contribute to the appearance of leaf chlorotic mottling and yellow vein clearing in CYVCV-infected lemon plants. This study illustrates the dynamic nature of the citrus-CYVCV interaction at the transcriptome level and provides new insights into the molecular mechanism underlying the pathogenesis of CYVCV in lemon plants.

Plant protease as regulator and signaling molecule for enhancing environmental stress-tolerance

Proteases are ubiquitous in prokaryotes and eukaryotes. Plant proteases are key regulators of various physiological processes, including protein homeostasis, organelle development, senescence, seed germination, protein processing, environmental stress response, and programmed cell death. Proteases are involved in the breakdown of peptide bonds resulting in irreversible posttranslational modification of the protein. Proteases act as signaling molecules that specifically regulate cellular function by cleaving and triggering receptor molecules. Peptides derived from proteolysis regulate ROS signaling under oxidative stress in the plant. It degrades misfolded and abnormal proteins into amino acids to repair the cell damage and regulates the biological process in response to environmental stress. Proteases modulate the biogenesis of phytohormones which control plant growth, development, and environmental stresses. Protein homeostasis, the overall balance between protein synthesis and proteolysis, is required for plant growth and development. Abiotic and biotic stresses are major factors that negatively impact cellular survivability, biomass production, and reduced crop yield potentials. Therefore, the identification of various stress-responsive proteases and their molecular functions may elucidate valuable information for the development of stress-resilient crops with higher yield potentials. However, the understanding of molecular mechanisms of plant protease remains unexplored. This review provides an overview of proteases related to development, signaling, and growth regulation to acclimatize environmental stress in plants.

Effects and possible mechanisms of sanguinarine on the competition between Raphidiopsis raciborskii (Cyanophyta) and Scenedesmus obliquus (Chlorophyta): A comparative toxicological study

The phytogenic algicide sanguinarine shows strong inhibitory effects on some bloom-forming cyanobacteria and exhibits great potential in cyanobacterial bloom mitigation. To evaluate the possible ecological effects of sanguinarine on microalgae, the effects and possible mechanisms of sanguinarine on the competition between bloom-forming cyanobacterium Raphidiopsis raciborskii (formerly named Cylindrospermopsis raciborskii) and green alga Scenedesmus obliquus were investigated through co-culture competition test and comparative toxicological study including growth characteristics, chlorophyll fluorescence transients, activities of antioxidant enzymes, and lipid peroxidation. The results of Raphidiopsis-Scenedesmus co-culture competition test showed that sanguinarine decreased the competition ability of R. raciborskii, which benefitted S. obliquus in winning the competition. Toxicological studies have shown that sanguinarine exhibited high inhibitory effects on the growth and photosynthesis of R. raciborskii but no obvious toxicity on S. obliquus at concentrations of no more than 80 μg L^-1. Oxidative damage partially contributed but was not the primary mechanism for the toxicity of sanguinarine on R. raciborskii. The results presented in this study indicate that sanguinarine may be a good algicidal candidate in mitigation of Raphidiopsis-based water bloom.

Mutation of YL Results in a Yellow Leaf with Chloroplast RNA Editing Defect in Soybean

RNA editing plays a key role in organelle gene expression. Little is known about how RNA editing factors influence soybean plant development. Here, we report the isolation and characterization of a soybean yl (yellow leaf) mutant. The yl plants showed decreased chlorophyll accumulation, lower PS II activity, an impaired net photosynthesis rate, and an altered chloroplast ultrastructure. Fine mapping of YL uncovered a point mutation in Glyma.20G187000, which encodes a chloroplast-localized protein homologous to Arabidopsis thaliana (Arabidopsis) ORRM1. YL is mainly expressed in trifoliate leaves, and its deficiency affects the editing of multiple chloroplast RNA sites, leading to inferior photosynthesis in soybean. Taken together, these results demonstrate the importance of the soybean YL protein in chloroplast RNA editing and photosynthesis.

A trigger mechanism of herbicides to phytoplankton blooms: From the standpoint of hormesis involving cytochrome b559, reactive oxygen species and nitric oxide

The cause of phytoplankton blooms has been extensively discussed and largely attributed to favorable external conditions such as nitrogen/phosphorus resources, pH and temperature. Here from the standpoint of hormesis response, we propose that phytoplankton blooms are initiated by stimulatory effects of low concentrations of herbicides as environmental contaminants spread over estuaries and lakes. The experimental results revealed general stimulations by herbicides on Microcystis aeruginosa and Selenastrum capricornutum, with the maximum stimulation in the 30-60% range, depending on the agent and experiment. In parallel with enhancing stimulation, the ratio of HP (high-potential) form to LP (low-potential) form of cytochrome b₅₅₉ (RHL) was observed decreasing, while intracellular reactive oxygen species (ROS) were observed increasing. We propose that the ROS originated from the thermodynamic transformation of cytochrome b₅₅₉, enhancing the stimulatory response. Furthermore, the results also proved that thermodynamic states of cytochrome b₅₅₉ could be modulated by nitric oxide, thus affecting cellular equilibrium of oxidative stress (OS) and correspondingly causing the inhibitory effect of higher concentrations of herbicides on phytoplankton. This suggests that hormesis substantially derives from equilibrium shifting of OS. Moreover, it is reasonable to infer that phytoplankton blooms would be motivated by herbicides or other environmental pollutants. This study provides a new thought into global phytoplankton blooms from a contaminant perspective.

Photosynthetic characterization of transgenic Synechocystis expressing a plant thiol/disulfide-modulating protein

A previous study showed that introducing an Arabidopsis thaliana thiol/disulfide-modulating protein, Low Quantum Yield of Photosystem II 1 (LQY1), into the cyanobacterium Synechocystis sp. PCC6803 increased the efficiency of Photosystem II (PSII) photochemistry. In the present study, the authors provided additional evidence for the role of AtLQY1 in improving PSII photochemical efficiency and cell growth. Light response curve analysis showed that AtLQY1-expressing Synechocystis grown at a moderate growth light intensity (50 µmol photons m^-2 s^-1) had higher minimal, maximal, and variable fluorescence than the empty-vector control, under a wide range of actinic light intensities. Light induction and dark recovery curves demonstrated that AtLQY1-expressing Synechocystis grown at the moderate growth light intensity had higher effective PSII quantum yield, higher photochemical quenching, lower regulated heat dissipation (non-photochemical quenching), low amounts of reduced plastoquinone, and higher amounts of oxidized plastoquinone than the empty-vector control. Furthermore, growth curve analysis indicated that AtLQY1-expressing Synechocystis grew faster than the empty-vector control at the moderate growth light intensity. These results suggest that transgenic expression of AtLQY1 in Synechocystis significantly improves PSII photochemical efficiency and overall cell growth.

Introducing an Arabidopsis thaliana Thylakoid Thiol/Disulfide-Modulating Protein Into Synechocystis Increases the Efficiency of Photosystem II Photochemistry

Photosynthetic species are subjected to a variety of environmental stresses, including suboptimal irradiance. In oxygenic photosynthetic organisms, a major effect of high light exposure is damage to the Photosystem II (PSII) reaction-center protein D1. This process even happens under low or moderate light. To cope with photodamage to D1, photosynthetic organisms evolved an intricate PSII repair and reassembly cycle, which requires the participation of different auxiliary proteins, including thiol/disulfide-modulating proteins. Most of these auxiliary proteins exist ubiquitously in oxygenic photosynthetic organisms. Due to differences in mobility and environmental conditions, land plants are subject to more extensive high light stress than algae and cyanobacteria. Therefore, land plants evolved additional thiol/disulfide-modulating proteins, such as Low Quantum Yield of PSII 1 (LQY1), to aid in the repair and reassembly cycle of PSII. In this study, we introduced an Arabidopsis thaliana homolog of LQY1 (AtLQY1) into the cyanobacterium Synechocystis sp. PCC6803 and performed a series of biochemical and physiological assays on AtLQY1-expressing Synechocystis. At a moderate growth light intensity (50 µmol photons m-2 s-1), AtLQY1-expressing Synechocystis was found to have significantly higher F v /F m , and lower nonphotochemical quenching and reactive oxygen species levels than the empty-vector control, which is opposite from the loss-of-function Atlqy1 mutant phenotype. Light response curve analysis of PSII operating efficiency and electron transport rate showed that AtLQY1-expressing Synechocystis also outperform the empty-vector control under higher light intensities. The increases in F v /F m , PSII operating efficiency, and PSII electron transport rate in AtLQY1-expressing Synechocystis under such growth conditions most likely come from an increased amount of PSII, because the level of D1 protein was found to be higher in AtLQY1-expressing Synechocystis. These results suggest that introducing AtLQY1 is beneficial to Synechocystis.

Time-Dependent Toxicities of Quorum Sensing Inhibitors to Aliivibrio fischeri and Bacillus subtilis

Quorum sensing inhibitors (QSIs) are being used widely as a promising alternative to antibiotics and drawing attention as potential pollutants. However, the assessment methods of the toxicities of QSIs, including model organism and affecting time, have not been established. To investigate how model organism and acting time impact the toxicities of QSIs, the effect of 4 QSIs to Aliivibrio fischeri and Bacillus subtilis were determined at different exposing time in the present study. The results showed that the toxic effects of QSIs to gram-negative bacteria (A fischeri) and gram-positive bacteria (B subtilis) were different and time dependent. As for A fischeri, QSI (furaneol acetate, FA) merely showed inhibition on the bioluminescence from hours 1 to 2. But from hours 3 to 6, low concentration FA exerted stimulation on the bioluminescence. Then, this stimulation disappeared from hours 7 to 14, and after hour 15 the stimulation appeared again. That is to say, QSIs showed intermittent hormesis effect on the bioluminescence of A fischeri. By contrast, only inhibition was observed in the toxicity test process of QSIs to B subtilis. As exposing time goes, the inhibition weakened gradually when FA was at low concentration regions. What is more, in the present, study toxic mechanisms were also discussed based on model organisms and exposing time. This study demonstrates appreciable impacts of model organism and exposing time on toxicities of QSIs and provides a theoretical basis for risk assessments after QSIs being widely used into the environment.

'Photosystem II: the water splitting enzyme of photosynthesis and the origin of oxygen in our atmosphere'

About 3 billion years ago an enzyme emerged which would dramatically change the chemical composition of our planet and set in motion an unprecedented explosion in biological activity. This enzyme used solar energy to power the thermodynamically and chemically demanding reaction of water splitting. In so doing it provided biology with an unlimited supply of reducing equivalents needed to convert carbon dioxide into the organic molecules of life while at the same time produced oxygen to transform our planetary atmosphere from an anaerobic to an aerobic state. The enzyme which facilitates this reaction and therefore underpins virtually all life on our planet is known as Photosystem II (PSII). It is a pigment-binding, multisubunit protein complex embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria. Today we have detailed understanding of the structure and functioning of this key and unique enzyme. The journey to this level of knowledge can be traced back to the discovery of oxygen itself in the 18th-century. Since then there has been a sequence of mile stone discoveries which makes a fascinating story, stretching over 200 years. But it is the last few years that have provided the level of detail necessary to reveal the chemistry of water oxidation and O-O bond formation. In particular, the crystal structure of the isolated PSII enzyme has been reported with ever increasing improvement in resolution. Thus the organisational and structural details of its many subunits and cofactors are now well understood. The water splitting site was revealed as a cluster of four Mn ions and a Ca ion surrounded by amino-acid side chains, of which seven provide direct ligands to the metals. The metal cluster is organised as a cubane structure composed of three Mn ions and a Ca2+ linked by oxo-bonds with the fourth Mn ion attached to the cubane. This structure has now been synthesised in a non-protein environment suggesting that it is a totally inorganic precursor for the evolution of the photosynthetic oxygen-evolving complex. In summary, the overall structure of the catalytic site has given a framework on which to build a mechanistic scheme for photosynthetic dioxygen generation and at the same time provide a blue-print and incentive to develop catalysts for artificial photo-electrochemical systems to split water and generate renewable solar fuels.

Roles of Lipids in Photosynthesis

Thylakoid membranes in cyanobacterial cells and chloroplasts of algae and higher plants are the sites of oxygenic photosynthesis. The lipid composition of the thylakoid membrane is unique and highly conserved among oxygenic photosynthetic organisms. Major lipids in thylakoid membranes are glycolipids, monogalactosyldiacylglycerol, digalactosyldiacylglycerol and sulfoquinovosyldiacylglycerol, and the phospholipid, phosphatidylglycerol. The identification of almost all genes involved in the biosynthesis of each lipid class over the past decade has allowed the generation and isolation of mutants of various photosynthetic organisms incapable of synthesizing specific lipids. Numerous studies using such mutants have revealed that these lipids play important roles not only in the formation of the lipid bilayers of thylakoid membranes but also in the folding and assembly of the protein subunits in photosynthetic complexes. In addition to the studies with the mutants, recent X-ray crystallography studies of photosynthetic complexes in thylakoid membranes have also provided critical information on the association of lipids with photosynthetic complexes and their activities. In this chapter, we summarize our current understanding about the structural and functional involvement of thylakoid lipids in oxygenic photosynthesis.

RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis Sp

The photosynthetic cyanobacterium, Synechocystis sp. strain 6803, is a potential platform for the production of various chemicals and biofuels. In this study, direct photosynthetic production of a biopolymer, polyhydroxyalkanoate (PHA), in genetically engineered Synechocystis sp. achieved as high as 14 wt%. This is the highest production reported in Synechocystis sp. under photoautotrophic cultivation conditions without the addition of a carbon source. The addition of acetate increased PHA accumulation to 41 wt%, and this value is comparable to the highest production obtained with cyanobacteria. Transcriptome analysis by RNA-seq coupled with real-time PCR was performed to understand the global changes in transcript levels of cells subjected to conditions suitable for photoautotrophic PHA biosynthesis. There was lower expression of most PHA synthesis-related genes in recombinant Synechocystis sp. with higher PHA accumulation suggesting that the concentration of these enzymes is not the limiting factor to achieving high PHA accumulation. In order to cope with the higher PHA production, cells may utilize enhanced photosynthesis to drive the product formation. Results from this study suggest that the total flux of carbon is the possible driving force for the biosynthesis of PHA and the polymerizing enzyme, PHA synthase, is not the only critical factor affecting PHA-synthesis. Knowledge of the regulation or control points of the biopolymer production pathways will facilitate the further use of cyanobacteria for biotechnological applications.

Functional prediction and physiological characterization of a novel short trans-membrane protein 1 as a subunit of mitochondrial respiratory complexes

Mitochondrial respiration is mediated by a set of multisubunit assemblies of proteins that are embedded in the mitochondrial inner membranes. Respiratory complexes do not only contain central catalytic subunits essential for the bioenergetic transformation, but also many short trans-membrane subunits (sTMs) that are implicated in the proper assembly of complexes. Defects in sTMs have been discovered in some human neurodegenerative diseases. Here we identify a new subunit that we named Stmp1 and have characterized its function using both computational and experimental approaches. Stmp1 is a short trans-membrane protein, and sequence/structure analysis revealed that it shares common features like the small size, presence of a single or two TM region, and a COOH-terminal charged region, as many typical sTMs of respiratory complexes. In situ hybridization and RT-PCR assays showed that the Stmp1 expression is ubiquitous throughout zebrafish embryogenesis. In adults, Stmp1 expression was highest in the brain compared with muscle and liver. In zebrafish larvae (3-5 days postfertilization), antisense morpholino oligonucleotide-mediated knockdown of the Stmp1 gene (Stmp1-MO) resulted in a series of mild morphological defects, including abnormal shape of head and jaw and cardiac edema. Larvae injected with the Stmp1-MO had negligible responses to touch stimuli. By ventilation frequency analysis we found that Stmp1-MO-injected zebrafish displayed a severe dysfunction of ventilatory activities when exposed to hypoxic conditions, suggesting a defective mitochondrial activity induced by the loss of Stmp1. Phylogenetic profiling of known respiratory sTMs compared with Stmp1 revealed that all defined sTMs from four respiratory complexes have restricted or variable phyletic distribution, indicating that they are products of evolutionary innovations to fulfill lineage-related functional requirements for respiratory complexes. Thus, being present in animals, filasterea, choanoflagellida, amoebozoa, and plants, Stmp1 may have evolved to confer a new or complementary regulation of respiratory activities.

Composition, architecture and dynamics of the photosynthetic apparatus in higher plants

The process of oxygenic photosynthesis enabled and still sustains aerobic life on Earth. The most elaborate form of the apparatus that carries out the primary steps of this vital process is the one present in higher plants. Here, we review the overall composition and supramolecular organization of this apparatus, as well as the complex architecture of the lamellar system within which it is harbored. Along the way, we refer to the genetic, biochemical, spectroscopic and, in particular, microscopic studies that have been employed to elucidate the structure and working of this remarkable molecular energy conversion device. As an example of the highly dynamic nature of the apparatus, we discuss the molecular and structural events that enable it to maintain high photosynthetic yields under fluctuating light conditions. We conclude the review with a summary of the hypotheses made over the years about the driving forces that underlie the partition of the lamellar system of higher plants and certain green algae into appressed and non-appressed membrane domains and the segregation of the photosynthetic protein complexes within these domains.

The Psb32 protein aids in repairing photodamaged photosystem II in the cyanobacterium Synechocystis 6803

Photosystem II (PSII), a membrane protein complex, catalyzes the photochemical oxidation of water to molecular oxygen. This enzyme complex consists of approximately 20 stoichiometric protein components. However, due to the highly energetic reactions it catalyzes as part of its normal activity, PSII is continuously damaged and repaired. With advances in protein detection technologies, an increasing number of sub-stoichiometric PSII proteins have been identified, many of which aid in the biogenesis and assembly of this protein complex. Psb32 (Sll1390) has previously been identified as a protein associated with highly active purified PSII preparations from the cyanobacterium Synechocystis sp. PCC 6803. To investigate its function, the subcellular localization of Psb32 and the impact of deletion of the psb32 gene on PSII were analyzed. Here, we show that Psb32 is an integral membrane protein, primarily located in the thylakoid membranes. Although not required for cell viability, Psb32 protects cells from oxidative stress and additionally confers a selective fitness advantage in mixed culture experiments. Specifically, Psb32 protects PSII from photodamage and accelerates its repair. Thus, the data suggest that Psb32 plays an important role in minimizing the effect of photoinhibition on PSII.

Supramolecular organization of photosystem II in green plants

Green plant photosystem II (PSII) is involved in the light reactions of photosynthesis, which take place in the thylakoid membrane of the chloroplast. PSII is organized into large supercomplexes with variable amounts of membrane-bound peripheral antenna complexes. These supercomplexes are dimeric and contain usually 2-4 copies of trimeric LHCII complexes and have a further tendency to associate into megacomplexes or into crystalline domains, of which several types have been characterized. This review focuses on the overall composition and structure of the PSII supercomplex of green plants and its organization and interactions within the photosynthetic membrane. Further, we present the current knowledge how the thylakoid membrane is three-dimensionally organized within the chloroplast. We also discuss how the supramolecular organization in the thylakoid membrane and the PSII flexibility may play roles in various short-term regulatory mechanisms of green plant photosynthesis. This article is part of a Special Issue entitled: Photosystem II.

Zwitterion modulation of O(2)-evolving activity of cyanobacterial photosystem II

Photosystem II (PSII) is the only enzyme in nature that can catalyze the challenging catalytic photooxidation of H(2)O into four protons, four electrons, and O(2). Slowing down turnover of the O(2)-evolving complex (OEC) is a plausible approach to gain mechanistic information on the reaction. However, modulating the kinetics of the reaction without perturbing the active site is a challenge. In this study, it is shown that the steady-state activity of cyanobacterial PSII is inhibited by small zwitterions, such as glycine betaine and β-alanine. We show that the binding of zwitterions is nondenaturing, is highly reversible, and results in the decrease of the rate of catalytic turnover by ∼50% in the presence of excess zwitterion. Control measurements of photoinduced electron transfer in O(2)-inactive PSII show that the inhibition by zwitterions is the result of a specific decrease in the rate of catalytic turnover of the OEC. Recovery of activity upon addition of an exogenous proton carrier (HCO(3)(-)) provides evidence that proton-transfer pathways, thought to be essential for the relay of protons from the OEC to the lumen, are affected. Interestingly, no inhibition is observed for spinach PSII, suggesting that zwitterions act specifically by binding to the extrinsic proteins on the lumenal side of PSII, which differ significantly between plants and cyanobacteria, to slow proton transfer on the electron donor side of PSII.

Protein translocation into and within cyanelles (Review)

The cyanelles of the glaucocystophyte alga Cyanophora paradoxa resemble endosymbiotic cyanobacteria in morphology, pigmentation and, especially, in the presence of a peptidoglycan wall situated between the inner and outer envelope membranes. However, it is now clear that cyanelles in fact are primitive plastids. Phylogenetic analyses of plastid, nuclear and mitochondrial genes support a single primary endosymbiotic event. In this scenario cyanelles and all other plastid types are derived from an ancestral photosynthetic organelle combining the high plastid gene content of the Porphyra purpurea rhodoplast and the peptidoglycan wall of glaucocystophyte cyanelles. This means that the import apparatus of all primary plastids should be homologous. Indeed, heterologous in vitro import can now be shown in both directions, provided a phenylalanine residue essential for cyanelle import is engineered into the N-terminal part of chloroplast transit peptides. The cyanelle and likely also the rhodoplast import apparatus can be envisaged as prototypes with a single receptor showing this requirement for N-terminal phenylalanine. In chloroplasts, multiple receptors with overlapping and less stringent specificities have evolved explaining the efficient heterologous import of native precursors from C. paradoxa. With respect to conservative sorting in cyanelles, both the Sec and Tat pathways could be demonstrated. Another cyanobacterial feature, the dual location of the Sec translocase in thylakoid and inner envelope membranes, is also unique to cyanelles. For the first time, protease protection of internalized lumenal proteins could be shown for cyanobacteria-like, phycobilisome-bearing thylakoid membranes after import into isolated cyanelles.

Mass spectrometric characterization of membrane integral low molecular weight proteins from photosystem II in barley etioplasts

In Photosystem II (PSII), a high number of plastid encoded and membrane integral low molecular weight proteins smaller than 10 kDa, the proteins PsbE, F, H, I, J, K, L, M, N, Tc, Z and the nuclear encoded PsbW, X, Y1, Y2 proteins have been described. Here we show that all low molecular weight proteins of PSII already accumulate in the etioplast membrane fraction in darkness, whereas PsaI and PsaJ of photosystem I (PSI) represent the only low molecular weight proteins that do not accumulate in darkness. We found by BN-PAGE separation of membrane protein complexes and selective MS that the accumulation of one-helix proteins from PSII is light independent and occurs in etioplasts. In contrast, in chloroplasts isolated from light-grown plants, low molecular weight proteins were found to specifically accumulate in PSI and II complexes. Our results demonstrate how plants grown in darkness prepare for the induction of chlorophyll dependent photosystem assembly upon light perception. We anticipate that our investigation will provide the essential means for the analysis of protein assembly in any membrane utilizing low molecular weight protein subunits.

Localization of 13 one-helix integral membrane proteins in photosystem II subcomplexes

Photosystem II is a multimeric protein complex of the thylakoid membrane in chloroplasts. Approximately half of the at least 26 different integral membrane protein subunits have molecular masses lower than 10 kDa. After one-dimensional (1D) or two-dimensional (2D) polyacrylamide gel electrophoresis (PAGE) separation, followed by enzymatic digestion of detected proteins, hardly any of these low-molecular-weight (LMW) subunits are detectable. Therefore, we developed a method for the analysis of highly hydrophobic LMW proteins. Intact proteins are extracted from acrylamide gels using a mixture of formic acid and organic solvent, precipitated with acetone, and analyzed by "top-down" mass spectrometry (MS). After offline nanoESI (electrospray ionization) MS, all LMW one-helix proteins from photosystem II were detected. In the four detected photosystem II supercomplexes of Nicotiana tabacum wild-type plants, 11 different one-helix proteins were identified as PsbE, -F, -H, -I, -K, -L, -M, -Tc, -W, and two isoforms of PsbX. The proteins PsbJ, -Y1, and -Y2 were localized in the buffer front after blue native (BN) PAGE, indicating their release during solubilization. Assembled PsbW is detected exclusively in supercomplexes, whereas it is absent in photosystem II core complexes, corroborating the protein's function for assembly of the light-harvesting complexes. This approach will substantiate gel-blot immunoanalysis for localization and identification of LMW protein subunits in any membrane protein complex.

The PsbP-like protein (sll1418) of Synechocystis sp. PCC 6803 stabilises the donor side of Photosystem II

The PsbP-like protein of the cyanobacterium Synechocystis sp. PCC 6803 is a peripheral component of Photosystem II, located at the lumenal side of the thylakoid membrane. Removal of this protein leads to decreased competitive potential of a PsbP-like deletion mutant when grown in a mixture with wild-type cells. Flash-induced oxygen evolution traces of the mutant show a higher probability of misses, correlated with increased amplitudes of the S-states decay in the dark. Thermoluminescence emission traces demonstrate a changed charge recombination pattern in the mutant, the S(3)Q(B)(-) couple becoming the major species instead of the S(2)Q(B)(-). Our data suggest a possible role of the PsbP-like protein in stabilisation of the charge separation in Photosystem II of cyanobacteria through interaction with the Mn cluster.

Dynamics of electron transfer in photosystem II

Photosystem II, being a constituent of light driven photosynthetic apparatus, is a highly organized pigment-protein-lipid complex. The arrangement of PSII active redox cofactors insures efficiency of electron transfer within it. Donation of electrons extracted from water by the oxygen evolving complex to plastoquinones requires an additional activation energy. In this paper we present theoretical discussion of the anharmonic fluctuations of the protein-lipid matrix of PSII and an experimental evidence showing that the fluctuations are responsible for coupling of its donor and acceptor side. We argue that the fast collective motions liberated at temperatures higher that 200 K are crucial for the two final steps of the water splitting cycle and that one can distinguish three different dynamic regimes of PSII action which are controlled by the timescales of forward electron transfer, which vary with temperature. The three regimes of the dynamical behavior are related to different spatial domains of PSII.

Photosystem II: an enzyme of global significance

Photosystem II (PSII) is a multisubunit enzyme embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria. Powered by light, this enzyme catalyses the chemically and thermodynamically demanding reaction of water splitting. In so doing, it releases dioxygen into the atmosphere and provides the reducing equivalents required for the conversion of CO2 into the organic molecules of life. Recently, a fully refined structure of a 700 kDa cyanobacterial dimeric PSII complex was elucidated by X-ray crystallography which gave organizational and structural details of the 19 subunits (16 intrinsic and three extrinsic) which make up each monomer and provided information about the position and protein environments of 57 different cofactors. The water-splitting site was revealed as a cluster of four Mn ions and a Ca2+ ion surrounded by amino acid side chains, of which six or seven form direct ligands to the metals. The metal cluster was modelled as a cubane-like structure composed of three Mn ions and the Ca2+ linked by oxo-bonds with the fourth Mn attached to the cubane via one of its oxygens. The overall structure of the catalytic site is providing a framework to develop a mechanistic scheme for the water-splitting process, knowledge which could have significant implications for mimicking the reaction in an artificial chemical system.

Photodamaged D1 protein is degraded inArabidopsismutants lacking the Deg2 protease

In plants exposed to high irradiances of visible light, the D1 protein in the reaction center of photosystem II is oxidatively damaged and rapidly degraded. Earlier work in our laboratory showed that the serine protease Deg2 performs the primary cleavage of photodamaged D1 protein in vitro. Here, we demonstrate that the rate of D1 protein degradation under light stress conditions in Arabidopsis mutants lacking the Deg2 protease is similar to those in wild-type plants. Therefore, we propose that several redundant D1 protein degradation pathways might exist in vivo.

Mapping the proteome of thylakoid membranes byde novo sequencing of intermembrane peptide domains

The proteome of a membrane compartment has been investigated by de novo sequence analysis after tryptic in gel digestion. Protein complexes and corresponding protein subunits were separated by a 2-D Blue Native (BN)/SDS-PAGE system. The transmembrane proteins of thylakoid membranes from a higher plant (Hordeum vulgare L.) were identified by the primary sequence of hydrophilic intermembrane peptide domains using nano ESI-MS/MS-analysis. Peptide analysis revealed that lysine residues of membrane proteins are primarily situated in the intermembrane domains. We concluded that esterification of lysine residues with fluorescent dyes may open the opportunity to label membrane proteins still localized in native protein complexes within the membrane phase. We demonstrate that covalent labelling of membrane proteins with the fluorescent dye Cy3 allows high sensitive visualization of protein complexes after 2-D BN/SDS-PAGE. We show that pre-electrophoretic labelling of protein subunits supplements detection of proteins by post-electrophoretic staining with silver and CBB and assists in completing the identification of the membrane proteome.

Refinement of the structural model for the Photosystem II supercomplex of higher plants

Recent X-ray structures determined for the Photosystem II (PSII) core complex isolated from cyanobacteria have provided important information for understanding the functionality of this photosynthetic enzyme including its water splitting activity. As yet, no high-resolution structure is available for PSII of plants or eukaryotes in general. However, crystal structures have been determined for some components of plant PSII which together with the cyanobacterial structure can be used to interpret lower resolution structures of plant PSII derived from electron cryomicroscopy (cryo-EM). Here, we utilise the published X-ray structures of a cyanobacterial PSII core, Light Harvesting Complex II (LHCII), PsbP and PsbQ proteins to construct a model of the plant LHCII-PSII supercomplex using a 17 A resolution 3D electron density map of the spinach supercomplex determined by cryo-EM and single particle analysis. In so doing, we tentatively identify the relative positioning of the chlorophylls within the supercomplex and consider energy transfer pathways between the different subunits. The modelling has also allowed density to be assigned to the three extrinsic proteins of plant PSII, PsbO, PsbP and PsbQ associated with the water splitting centre and concluded that although the position of PsbO is the same as in cyanobacteria, PsbP and PsbQ are located in different positions to the cyanobacterial extrinsic PsbU and PsbV proteins.

Absence of the psbH gene product destabilizes the Photosystem II complex and prevents association of the Photosystem II-X protein in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1

PS II-H is a small hydrophobic protein that is universally present in the PS II core complex of cyanobacteria and plants. The role of PS II-H was studied by directed mutagenesis and biochemical analysis in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. The psbH disruptant could grow photoautotrophically; however, its growth was much slower than that of the wild type cell. Chromatography enabled the isolation of active oxygen-evolving PS II complexes from both the mutant and the wild type. The mutant yielded a relatively large amount of inactive PS II complex that lacked the following extrinsic proteins: the 33-kDa protein, the 12-kDa protein, and cytochrome c ( 550 ). There were differences between the psbH disruptant and the wild type in terms of the oxygen evolution activities of the cells, thylakoids, and PS II complexes. At high concentrations of 2,6-DCBQ, the activity was much lower in the mutant than in the wild type. Gel filtration chromatography of the PS II complexes showed that both active and inactive PS II complexes isolated from the mutant were mostly in the monomeric form, while the active PS II complex from the wild type was in the dimeric form. The polypeptide composition of both active and inactive PS II complexes from the mutant showed the absence of another small polypeptide, PS II-X. These results suggest that the PS II-H protein is essential for stable assembly of native dimeric PS II complex containing PS II-X.

PsbP protein, but not PsbQ protein, is essential for the regulation and stabilization of photosystem II in higher plants

PsbP and PsbQ proteins are extrinsic subunits of photosystem II (PSII) and participate in the normal function of photosynthetic water oxidation. Both proteins exist in a broad range of the oxygenic photosynthetic organisms; however, their physiological roles in vivo have not been well defined in higher plants. In this study, we established and analyzed transgenic tobacco (Nicotiana tabacum) plants in which the levels of PsbP or PsbQ were severely down-regulated by the RNA interference technique. A plant that lacked PsbQ showed no specific phenotype compared to a wild-type plant. This suggests that PsbQ in higher plants is dispensable under the normal growth condition. On the other hand, a plant that lacked PsbP showed prominent phenotypes: drastic retardation of growth, pale-green-colored leaves, and a marked decrease in the quantum yield of PSII evaluated by chlorophyll fluorescence. In PsbP-deficient plant, most PSII core subunits were accumulated in thylakoids, whereas PsbQ, which requires PsbP to bind PSII in vitro, was dramatically decreased. PSII without PsbP was hypersensitive to light and rapidly inactivated when the repair process of the damaged PSII was inhibited by chloramphenicol. Furthermore, thermoluminescence studies showed that the catalytic manganese cluster in PsbP-deficient leaves was markedly unstable and readily disassembled in the dark. The present results demonstrated that PsbP, but not PsbQ, is indispensable for the normal PSII function in higher plants in vivo.

Localization of the PsbH subunit in photosystem II from the Synechocystis 6803 using the His-tagged Ni–NTA Nanogold labeling

The PsbH protein belongs to a group of small protein subunits of photosystem II (PSII) complex. This protein is predicted to have a single transmembrane helix and it is important for the assembly of the PSII complex as well as for the proper function at the acceptor side of PSII. To identify the location of the PsbH subunit, the PSII complex with His-tagged PsbH protein was isolated from the cyanobacterium Synechocystis sp. PCC 6803 and labeled by Ni(2+)-nitrilo triacetic acid Nanogold. Electron microscopy followed by single particle image analysis identified the location of the labeled His-tagged PsbH protein at the periphery of the dimeric PSII complex. These results indicate that the N terminus of the PsbH protein is located at the stromal surface of the PSII complex and close to the CP47 protein.

Supramolecular organization of thylakoid membrane proteins in green plants

The light reactions of photosynthesis in green plants are mediated by four large protein complexes, embedded in the thylakoid membrane of the chloroplast. Photosystem I (PSI) and Photosystem II (PSII) are both organized into large supercomplexes with variable amounts of membrane-bound peripheral antenna complexes. PSI consists of a monomeric core complex with single copies of four different LHCI proteins and has binding sites for additional LHCI and/or LHCII complexes. PSII supercomplexes are dimeric and contain usually two to four copies of trimeric LHCII complexes. These supercomplexes have a further tendency to associate into megacomplexes or into crystalline domains, of which several types have been characterized. Together with the specific lipid composition, the structural features of the main protein complexes of the thylakoid membranes form the main trigger for the segregation of PSII and LHCII from PSI and ATPase into stacked grana membranes. We suggest that the margins, the strongly folded regions of the membranes that connect the grana, are essentially protein-free, and that protein-protein interactions in the lumen also determine the shape of the grana. We also discuss which mechanisms determine the stacking of the thylakoid membranes and how the supramolecular organization of the pigment-protein complexes in the thylakoid membrane and their flexibility may play roles in various regulatory mechanisms of green plant photosynthesis.

Conservative sorting in a primitive plastid. The cyanelle of Cyanophora paradoxa

Higher plant chloroplasts possess at least four different pathways for protein translocation across and protein integration into the thylakoid membranes. It is of interest with respect to plastid evolution, which pathways have been retained as a relic from the cyanobacterial ancestor ('conservative sorting'), which ones have been kept but modified, and which ones were developed at the organelle stage, i.e. are eukaryotic achievements as (largely) the Toc and Tic translocons for envelope import of cytosolic precursor proteins. In the absence of data on cyanobacterial protein translocation, the cyanelles of the glaucocystophyte alga Cyanophora paradoxa for which in vitro systems for protein import and intraorganellar sorting were elaborated can serve as a model: the cyanelles are surrounded by a peptidoglycan wall, their thylakoids are covered with phycobilisomes and the composition of their oxygen-evolving complex is another feature shared with cyanobacteria. We demonstrate the operation of the Sec and Tat pathways in cyanelles and show for the first time in vitro protein import across cyanobacteria-like thylakoid membranes and protease protection of the mature protein.

Structural differences in the inner part of photosystem II between higher plants and cyanobacteria

A detailed comparison of key components in the Photosystem II complexes of higher plants and cyanobacteria was carried out. While the two complexes are overall very similar, significant differences exist in the relative orientation of individual components relative to one another. We compared a three-dimensional map of the inner part of plant PS II at 8 A resolution, and a 5.5 A projection map of the same complex determined by electron crystallography, to the recent 3.5-3.8 A X-ray structures of cyanobacterial complexes. The largest differences were found in the rotational alignment of the cyt b(;)559 subcomplex, and of the CP47 core antenna with respect to the D1/D2 reaction centre. Within the D1/D2 proteins, there are clear differences between plants and cyanobacteria at the stromal ends of membrane-spanning helices, even though these proteins are highly homologous. Notwithstanding these differences in the protein scaffold, the distances between the critical photosynthetic pigment cofactors seem to be precisely conserved. The different protein arrangements in the two complexes may reflect an adaptation to the two very different antenna systems, membrane-extrinsic phycobilisomes for cyanobacteria, and membrane-embedded chlorophyll a/b proteins in plants.

PSII-Tc Protein Plays an Important Role in Dimerization of Photosystem II

We cloned and determined the nucleotide sequence of PSII genes, psbB and psbTc, from the thermophilic cyanobacterium, Thermosynechococcus elongatus strain BP-1. PSII-Tc, encoded by psbTc, is a small membrane-spanning subunit of the PSII core complex of cyanobacteria and plants. However, its role has not been fully elucidated. We generated an insertional disruptant of psbTc and studied the role of the PSII-Tc protein in cyanobacterial PSII. The following observations were made: (i) The psbTc disruptant could grow photoautotrophically at a rate similar to that of wild-type T. elongatus under a wide range of light conditions. (ii) Thylakoids and oxygen-evolving PSII complexes were successfully isolated from the psbTc disruptant as well as the wild type. There was no significant difference in the oxygen evolution activities of cells, thylakoids or PSII complexes between the psbTc disruptant and the wild type. This is in contrast to the lower activities in the other PSII mutants of T. elongatus. (iii) Chromatographic separation of monomeric and dimeric PSII revealed that recovery of dimeric PSII was dramatically reduced in the psbTc disruptant. (iv) SDS-urea-PAGE showed a complete loss of the 4.7-kDa band in the mutant PSII. Since this band in wild-type PSII consists of PSII-M and PSII-Tc, we assume that PSII-Tc is critical for the binding of PSII-M in the PSII complex and is involved directly and indirectly in the dimerization of PSII. These results appear to be in good agreement with the recent structural model of the dimeric PSII complex.

The low molecular mass subunits of the photosynthetic supracomplex, photosystem II

The photosystem II (PSII) complex is located in the thylakoid membrane of higher plants, algae and cyanobacteria and drives the water oxidation process of photosynthesis, which splits water into reducing equivalents and molecular oxygen by solar energy. Electron and X-ray crystallography analyses have revealed that the PSII core complex contains between 34 and 36 transmembrane alpha-helices, depending on the organism. Of these helices at least 12-14 are attributed to low molecular mass proteins. However, to date, at least 18 low molecular mass (<10 kDa) subunits are putatively associated with the PSII complex. Most of them contain a single transmembrane span and their protein sequences are conserved among photosynthetic organisms. In addition, these proteins do not have any similarity to any known functional proteins in any type of organism, and only two of them bind a cofactor. These findings raise intriguing questions about why there are so many small protein subunits with single-transmembrane spans in the PSII complex, and their possible functions. This article reviews our current knowledge of this group of proteins. Deletion mutations of the low molecular mass subunits from both prokaryotic and eukaryotic model systems are compared in an attempt to understand the function of these proteins. From these comparisons it seems that the majority of them are involved in stabilization, assembly or dimerization of the PSII complex. The small proteins may facilitate fast dynamic conformational changes that the PSII complex needs to perform an optimal photosynthetic activity.

Homologs of plant PsbP and PsbQ proteins are necessary for regulation of photosystem ii activity in the cyanobacterium Synechocystis 6803

The mechanism of oxygen evolution by photosystem II (PSII) has remained highly conserved during the course of evolution from ancestral cyanobacteria to green plants. A cluster of manganese, calcium, and chloride ions, whose binding environment is optimized by PSII extrinsic proteins, catalyzes this water-splitting reaction. The accepted view is that in plants and green algae, the three extrinsic proteins are PsbO, PsbP, and PsbQ, whereas in cyanobacteria, they are PsbO, PsbV, and PsbU. Our previous proteomic analysis established the presence of a PsbQ homolog in the cyanobacterium Synechocystis 6803. The current study additionally demonstrates the presence of a PsbP homolog in cyanobacterial PSII. Both psbP and psbQ inactivation mutants exhibited reduced photoautotrophic growth as well as decreased water oxidation activity under CaCl(2)-depleted conditions. Moreover, purified PSII complexes from each mutant had significantly reduced activity. In cyanobacteria, one PsbQ is present per PSII complex, whereas PsbP is significantly substoichiometric. These findings indicate that both PsbP and PsbQ proteins are regulators that are necessary for the biogenesis of optimally active PSII in Synechocystis 6803. The new picture emerging from these data is that five extrinsic PSII proteins, PsbO, PsbP, PsbQ, PsbU, and PsbV, are present in cyanobacteria, two of which, PsbU and PsbV, have been lost during the evolution of green plants.

Structural characterization of photosystem II complex from red alga Porphyridium cruentum retaining extrinsic subunits of the oxygen-evolving complex

The structure of photosystem II (PSII) complex isolated from thylakoid membranes of the red alga Porphyridium cruentum was investigated using electron microscopy followed by single particle image analysis. The dimeric complexes observed contain all major PSII subunits (CP47, CP43, D1 and D2 proteins) as well as the extrinsic proteins (33 kDa, 12 kDa and the cytochrome c(550)) of the oxygen-evolving complex (OEC) of PSII, encoded by the psbO, psbU and psbV genes, respectively. The single particle analysis of the top-view projections revealed the PSII complex to have maximal dimensions of 22 x 15 nm. The analysis of the side-view projections shows a maximal thickness of the PSII complex of about 9 nm including the densities on the lumenal surface that has been attributed to the proteins of the OEC complex. These results clearly demonstrate that the red algal PSII complex is structurally very similar to that of cyanobacteria and to the PSII core complex of higher plants. In addition, the arrangement of the OEC proteins on the lumenal surface of the PSII complex is consistent to that obtained by X-ray crystallography of cyanobacterial PSII.

Pleiotropic effects of inactivating a carboxyl-terminal protease, CtpA, in Borrelia burgdorferi

A gene encoding a putative carboxyl-terminal protease (CtpA), an unusual type of protease, is present in the Borrelia burgdorferi B31 genome. The B. burgdorferi CtpA amino acid sequence exhibits similarities to the sequences of the CtpA enzymes of the cyanobacterium Synechocystis sp. strain PCC 6803 and higher plants and also exhibits similarities to the sequences of putative CtpA proteins in other bacterial species. Here, we studied the effect of ctpA gene inactivation on the B. burgdorferi protein expression profile. Total B. burgdorferi proteins were separated by two-dimensional gel electrophoresis, and the results revealed that six proteins of the wild type were not detected in the ctpA mutant and that nine proteins observed in the ctpA mutant were undetectable in the wild type. Immunoblot analysis showed that the integral outer membrane protein P13 was larger and had a more acidic pI in the ctpA mutant, which is consistent with the theoretical change in pI for P13 not processed at the carboxyl terminus. Matrix-assisted laser desorption ionization-time of flight data indicated that in addition to P13, the BB0323 protein may serve as a substrate for carboxyl-terminal processing by CtpA. Complementation analysis of the ctpA mutant provided strong evidence that the observed effect on proteins depended on inactivation of the ctpA gene alone. We show that CtpA in B. burgdorferi is involved in the processing of proteins such as P13 and BB0323 and that inactivation of ctpA has a pleiotropic effect on borrelial protein synthesis. To our knowledge, this is the first analysis of both a CtpA protease and different substrate proteins in a pathogenic bacterium.

Water, water everywhere, and its remarkable chemistry

Photosystem II (PSII), the multisubunit pigment-protein complex localised in the thylakoid membranes of oxygenic photosynthetic organisms, uses light energy to drive a series of remarkable reactions leading to the oxidation of water. The products of this oxidation are dioxygen, which is released to the atmosphere, and reducing equivalents destined to reduce carbon dioxide to organic molecules. The water oxidation occurs at catalytic sites composed of four manganese atoms (Mn(4)-cluster) and powered by the redox potential of an oxidised chlorophyll a molecule (P680(*+)). Gerald T (Jerry) Babcock and colleagues showed that electron/proton transfer processes from substrate water to P680(*+) involved a tyrosine residue (Y(Z)) and proposed an attractive reaction mechanism for the direct involvement of Y(Z) in the chemistry of water oxidation. The 'hydrogen-atom abstract/metalloradical' mechanism he formulated is an expression of his genius and a highlight of his many other outstanding contributions to photosynthesis research. A structural basis for Jerry's model is now being revealed by X-ray crystallography.

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

The psbEFLJ operon of tobacco plastids encodes four bitopic low molecular mass transmembrane components of photosystem II. Here, we report the effect of inactivation of psbL on the directional forward electron flow of photosystem II as compared to that of the wild type and the psbJ deletion mutant, which is impaired in PSII electron flow to plastoquinone [Regel et al. (2001) J. Biol. Chem. 276, 41473-41478]. Exposure of Delta psbL plants to a saturating light pulse gives rise to the maximal fluorescence emission, Fm(L), which is followed within 4-6 s by a broader hitherto not observed second fluorescence peak in darkness, Fm(D). Conditions either facilitating oxidation or avoiding reduction of the plastoquinone pool do not affect the Fm(L) level of Delta psbL plants but prevent the appearance of Fm(D). The level of Fm(D) is proportional to the intensity and duration of the light pulse allowing reduction of the plastoquinone pool in dark-adapted leaves prior to the activation of PSI and oxidation of plastoquinol. Lowering the temperature decreases the Fm(D) level in the Delta psbL mutant, whereas it increases considerably the lifetime of Q(A)*- in the Delta psbJ mutant. The thermoluminescence signal generated by Q(A)*-/S(2) charge recombination is not affected; on the other hand, charge recombination of Q(B)*-/S(2,3) could not be detected in Delta psbL plants. PSII is highly sensitive to photoinhibition in Delta psbL. We conclude that PsbL prevents reduction of PSII by back electron flow from plastoquinol protecting PSII from photoinactivation, whereas PsbJ regulates forward electron flow from Q(A)*- to the plastoquinone pool. Therefore, both proteins contribute substantially to ensure unidirectional forward electron flow from PSII to the plastoquinone pool.

In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database

An extensive analysis of the Arabidopsis thaliana peripheral and integral thylakoid membrane proteome was performed by sequential extractions with salt, detergent, and organic solvents, followed by multidimensional protein separation steps (reverse-phase HPLC and one- and two-dimensional electrophoresis gels), different enzymatic and nonenzymatic protein cleavage techniques, mass spectrometry, and bioinformatics. Altogether, 154 proteins were identified, of which 76 (49%) were alpha-helical integral membrane proteins. Twenty-seven new proteins without known function but with predicted chloroplast transit peptides were identified, of which 17 (63%) are integral membrane proteins. These new proteins, likely important in thylakoid biogenesis, include two rubredoxins, a potential metallochaperone, and a new DnaJ-like protein. The data were integrated with our analysis of the lumenal-enriched proteome. We identified 83 out of 100 known proteins of the thylakoid localized photosynthetic apparatus, including several new paralogues and some 20 proteins involved in protein insertion, assembly, folding, or proteolysis. An additional 16 proteins are involved in translation, demonstrating that the thylakoid membrane surface is an important site for protein synthesis. The high coverage of the photosynthetic apparatus and the identification of known hydrophobic proteins with low expression levels, such as cpSecE, Ohp1, and Ohp2, indicate an excellent dynamic resolution of the analysis. The sequential extraction process proved very helpful to validate transmembrane prediction. Our data also were cross-correlated to chloroplast subproteome analyses by other laboratories. All data are deposited in a new curated plastid proteome database (PPDB) with multiple search functions (http://cbsusrv01.tc.cornell.edu/users/ppdb/). This PPDB will serve as an expandable resource for the plant community.

Protein assembly of photosystem II and accumulation of subcomplexes in the absence of low molecular mass subunits PsbL and PsbJ

The protein assembly and stability of photosystem II (PSII) (sub)complexes were studied in mature leaves of four plastid mutants of tobacco (Nicotiana tabacum L), each having one of the psbEFLJ operon genes inactivated. In the absence of psbL, no PSII core dimers or PSII-light harvesting complex (LHCII) supercomplexes were formed, and the assembly of CP43 into PSII core monomers was extremely labile. The assembly of CP43 into PSII core monomers was found to be necessary for the assembly of PsbO on the lumenal side of PSII. The two other oxygen-evolving complex (OEC) proteins, PsbP and PsbQ, were completely lacking in Delta psbL. In the absence of psbJ, both intact PSII core monomers and PSII core dimers harboring the PsbO protein were formed, whereas the LHCII antenna remained detached from the PSII dimers, as demonstrated by 77 K fluorescence measurements and by the lack of PSII-LHCII supercomplexes. The Delta psbJ mutant was characterized by a deficiency of PsbQ and a complete lack of PsbP. Thus, both the PsbL and PsbJ subunits of PSII are essential for proper assembly of the OEC. The absence of psbE and psbF resulted in a complete absence of all central PSII core and OEC proteins. In contrast, very young, vigorously expanding leaves of all psbEFLJ operon mutants accumulated at least traces of D2, CP43 and the OEC proteins PsbO and PsbQ, implying developmental control of the expression of the PSII core and OEC proteins. Despite severe problems in PSII assembly, the thylakoid membrane complexes other than PSII were present and correctly assembled in all psbEFLJ operon mutants.

Calcium-Dependent Conformational Change and Thermal Stability of the Isolated PsbO Protein Detected by FTIR Spectroscopy

The structure and function of the photosystem II PsbO extrinsic protein is under intense research, being an essential part of the biomolecular engine that carries out water oxidation and oxygen production. This paper presents a structural analysis of the isolated PsbO protein by FTIR spectroscopy, reporting detailed secondary structure quantification and changes in the secondary structure content of the protein attributed to the effect of calcium (Ca(2+)). Measurements in H(2)O and D(2)O have allowed us to see the effect of calcium on the conformation of the protein. The results indicate that (i) the protein presents a major content of beta-structure (i.e., beta-sheet, beta-strands, beta-turns) as detected by the infrared bands at 1624-1625, 1678-1679, 1688-1689 cm(-1), which account for about 38% in water and 33% in heavy water, in the presence of calcium; and (ii) the amount of this beta-structure fraction increases 7-10% in the absence of calcium, with a concomitant decrease in loops and nonordered structure. The thermal denaturation profile of the protein in the presence of calcium showed low stability with T(m) approximately 56 degrees C. This profile also shows a second phase of denaturation above 60 degrees C and the appearance of aggregation signals above 70 degrees C. Our observations indicate that calcium is able to modify the conformation of the protein at least in solution and confirm that PsbO is mainly a beta-protein where beta-sheet is the major ordered secondary structure element of the protein core.

Functional differences of photosystem II from Synechococcus elongatus and spinach characterized by flash induced oxygen evolution patterns

Detailed comparative studies of flash induced oxygen evolution patterns in thylakoids from the thermophilic cyanobacterium Synechococcus elongatus (S. elongatus; also referred to as Thermosynechococcus elongatus) and from spinach led to the following results: (i) the miss parameter alpha of S. elongatus thylakoids exhibits a pronounced temperature dependence with a minimum of 7% at 25 degrees C and values of 17 and 10% at 3 and 35 degrees C, respectively, while for spinach thylakoids alpha decreases continuously from 18% at 35 degrees C down to 8% at 3 degrees C; (ii) at all temperatures, the double hit probability beta exceeds in S. elongatus the corresponding values of spinach by an increment Delta beta of about 3%; (iii) at 20 degrees C the slow relaxation of the oxidation states S(2) and S(3) is about 15 and 30 times, respectively, slower in S. elongatus than in spinach, while the reduction of these S states by tyrosine Y(D) is 2-3 times faster; (iv) the reaction S(0)Y(D)(ox) --> S(1)Y(D) is slower by a factor of 4 in S. elongatus as compared to spinach; and (v) the activation energies of S state dark relaxations in S. elongatus are all within a factor of 1.5 as compared to the previously reported values from spinach thylakoids [Vass, I., Deak, Z., and Hideg, E. (1990) Biochim. Biophys. Acta 1017, 63-69; Messinger, J., Schröder, W. P., and Renger, G. (1993) Biochemistry 32, 7658-7668], but the difference between the activation energies of the slow S(2) and S(3) decays is significantly larger in S. elongatus than in spinach. These results are discussed in terms of differences between cyanobacteria and higher plants on the acceptor side of PSII and a shift of the redox potential of the couple Y(D)/Y(D)(ox). The obtained data are also suitable to address questions about effects of the redox state of Y(D) on the miss probability and the possibility of an S state dependent miss parameter.

Origin and evolution of transmembrane Chl-binding proteins: hydrophobic cluster analysis suggests a common one-helix ancestor for prokaryotic (Pcb) and eukaryotic (LHC) antenna protein superfamilies

All chlorophyll (Chl)-binding proteins constituting the photosynthetic apparatus of both prokaryotes and eukaryotes possess hydrophobic domains, corresponding to membrane-spanning alpha-helices (MSHs). Hydrophobic cluster analysis of representative members of the different Chl protein superfamilies revealed that all Chl proteins except the five-helix reaction center II proteins and the small subunits of photosystem I possess related domains. As a major conclusion, we found that the eukaryotic antennae likely share a common precursor with the prokaryotic Chl a/b antennae from Chl-b-containing oxyphotobacteria. From these data, we propose a global scheme for the evolution of these proteins from a one-MSH ancestor.

Acceptor and donor-side interactions of phenolic inhibitors in Photosystem II

Certain phenolic compounds represent a distinct class of Photosystem (PS) II Q(B) site inhibitors. In this paper, we report a detailed study of the effects of 2,4,6-trinitrophenol (TNP) and other phenolic inhibitors, bromoxynil and dinoseb, on PS II energetics. In intact PS II, phenolic inhibitors bound to only 90-95% of Q(B) sites even at saturating concentrations. The remaining PS II reaction centers (5-10%) showed modified Q(A) to Q(B) electron transfer but were sensitive to urea/triazine inhibitors. The binding of phenolic inhibitors was 30- to 300-fold slower than the urea/triazine class of Q(B) site inhibitors, DCMU and atrazine. In the sensitive centers, the S(2)Q(A)(-) state was 10-fold less stable in the presence of phenolic inhibitors than the urea/triazine herbicides. In addition, the binding affinity of phenolic herbicides was decreased 10-fold in the S(2)Q(A)(-) state than the S(1)Q(A) state. However, removal of the oxygen-evolving complex (OEC) and associated extrinsic polypeptides by hydroxylamine (HA) washing abolished the slow binding kinetics as well as the destabilizing effects on the charge-separated state. The S(2)-multiline electron paramagnetic resonance (EPR) signal and the 'split' EPR signal, originating from the S(2)Y(Z) state showed no significant changes upon binding of phenolic inhibitors at the Q(B) site. We thus propose a working model where Q(A) redox potential is lowered by short-range conformational changes induced by phenolic inhibitor binding at the Q(B) niche. Long-range effects of HA-washing eliminate this interaction, possibly by allowing more flexibility in the Q(B) site.

Structural analysis of the photosystem I supercomplex of cyanobacteria induced by iron deficiency

Here we describe the three-dimensional structure of the newly discovered CP43'-photosystem I (PSI) supercomplex of cyanobacteria calculated by single-particle analysis of images obtained by electron cryomicroscopy (cryo-EM). This large membrane protein complex has a molecular mass of approximately 2 MDa and is found in cyanobacteria when grown in iron deficient media. It is composed of a reaction center trimer surrounded by 18 subunits of the chlorophyll a binding CP43'protein, encoded by the isiA gene, which increases the light harvesting capacity of PSI by approximately 70%. By modeling higher-resolution structural data obtained from X-ray crystallography into the three-dimensional (3D) cryo-EM map, we have been able to gain a better understanding of the structure and functional properties of this supermolecular complex. We have identified three separate clusters of chlorophyll molecules at the periphery of the PSI core which may aid energy transfer from the CP43' antenna ring to the reaction center. Moreover, it is shown that despite the replacement of ferredoxin with flavodoxin as an electron acceptor under iron stress conditions, the 3D map has density to accommodate the extrinsic proteins, PsaC, PsaD, and PsaE. The presence of these three proteins was also confirmed by immunoblotting.