Analysis of the Structure of the PsbO Protein and its Implications

The PsbO protein is a ubiquitous extrinsic subunit of Photosystem II (PS II), the water splitting enzyme of photosynthesis. A recently determined 3D X-ray structure of a cyanobacterial protein bound to PS II has given an opportunity to conduct complete analyses of its sequence and structural characteristics using bioinformatic methods. Multiple sequence alignments for the PsbO family are constructed and correlated with the cyanobacterial structure. We identify the most conserved regions of PsbO and the mapping of their positions within the structure indicates their functional roles especially in relation to interactions of this protein with the lumenal surface of PS II. Homologous models for eukaryotic PsbO were built in order to compare with the prokaryotic protein. We also explore structural homology between PsbO and other proteins for which 3D structures are known and determine its structural classification. These analyses contribute to the understanding of the function and evolutionary origin of the PS II manganese stabilising protein.     

The role of ApcD and ApcF in energy transfer from phycobilisomes to PS I and PS II in a cyanobacterium

The role of the phycobilisome core components, ApcD and ApcF, in transferring energy from the phycobilisome to PS I and PS II in the cyanobacterium Synechocystis sp. PCC6803 has been investigated. The genes encoding these proteins have been disrupted in the genomes of wild type Synechocystis sp. PCC6803 and a PS II deficient mutant, PsbD1CD2^-, by inserting antibiotic resistance genes into their coding regions. Data from fluorescence emission spectra and pigment content analysis for these inactivation mutants is presented. These data suggest that both ApcD and ApcF are involved in the energy transfer route to PS II and PS I. In both cases, the energy transfer may to the reaction centres may be via the chromophore of ApcE (the L cm) or anchor polypeptide). The major route of energy transfer to both kinds of reaction centre appears to involve ApcF rather than ApcD. When both ApcF and ApcD are absent, the phycobilisomes are unable to transfer energy to either reaction centre. We suggest a model for the pathways of energy transfer from the phycobilisomes to PS I and PS II.     

Sequence similarity between Photosystems I and II. Identification of a Photosystem I reaction center transmembrane helix that is similar to transmembrane helix IV of the D2 subunit of Photosystem II and the M subunit of the non-sulfur purple and flexible green bacteria

There are basic structural similarities between plant PS II and bacterial RCs of the Chloroflexaceae and Rhodospirillaceae. These RCs are referred to as PS II-type RCs. A similar relationship of PS I RC to PS II-type RCs has not been established. Although plant PS I and PS II RCs show structural and functional differences, they also share similarities. Therefore, the A and B polypeptides of PS I were searched for PS II D1 and D2 polypeptide-like sequences. An alignment without gaps was found between PS II-type D2/M helix IV and PS I B helix X, as well as a weaker alignment of PS II-type D1/L with PS I B helix X. No comparable alignment with PS I A was found. In the M/D2 alignment there were eight identities and some conservative substitutions in twenty nine residues. PS I B helix X appeared to contain a modified chlorophyll dimer and monomer binding site and a modified non-heme iron-quinone binding site. The conserved residue sequence was found only in RC polypeptides. The proposed chlorophyll dimer-monomer binding site was located transmembrane from the iron-sulfur cluster X binding site. The conserved residues generally are those that interact with prosthetic groups. Half of the conserved residues are located on the same side of the helix. Thus, although there are impediments to concluding firmly that PS I B helix X has a functional and evolutionary relatedness to the D2 PS II and bacterial M RC polypeptides, our analysis gives reasonable support to the idea.Abbreviation RC reaction center     

Degradation and release from the thylakoid membrane of Photosystem II subunits after UV-B irradation of the liverwort Conocephalum conicum

The effect of ultraviolet-B (UV-B) radiation on the amount of various Photosystem (PS) II subunits has been studied in the thalloid liverwort Conocephalum conicum. UV-B irradiation led to a drastic decrease of the reaction center proteins D1 and D2 and the outer light harvesting antenna (LHC II). A minor reduction was found in the levels of the CP 43 polypeptide of the inner antenna and the 33, 23 and 16 kDa extrinsic polypeptides of PS II. During UV-B irradiation, the extrinsic polypeptides accumulated in the soluble protein fraction, but D1 and D2 were not dedectable. Streptomycin, but not cycloheximide inhibited the repair process of PS II, indicating that only protein synthesis in the chloroplast is necessary for recovery. This indicates that the extrinsic proteins of PS II dissociate from the membrane during UV-B treatment and reassociate with PS II in the course of the repair process. We conclude that the reaction center core is a target of UV-B radiation in C. concicum. The extrinsic proteins of PS II are not directly affected by UV-B, but their release is the consequence of UV-B-induced degradation of the D1 and D2 proteins.     

Photoinhibition – a historical perspective

Photoinhibition is a state of physiological stress that occurs in all oxygen evolving photosynthetic organisms exposed to light. The primary damage occurs within the reaction center of Photosystem II (PS II). While irreversible photoinduced damage to PS II occurs at all light intensities, the efficiency of photosynthetic electron transfer decreases markedly only when the rate of damage exceeds the rate of its repair, which requires de novo PS II protein synthesis. Photoinhibition has been studied for over a century using a large variety of biochemical, biophysical and genetic methodologies. The discovery of the light induced turnover of a protein, encoded by the plastid psbA gene (the D1 protein), later identified as one of the photochemical reaction center II proteins, has led to the elucidation of the underlying mechanism of photoinhibition and to a deeper understanding of the PS II `life cycle.' This revised version was published online in August 2006 with corrections to the Cover Date.     

Prolonged high light treatment of plant cells results in changes of the amount,the localization and the electrophoretic behavior of several thylakoid membrane proteins

The effect of a 30 h high light treatment on the amount and the localization of thylakoid proteins was analysed in low light grown photoautotrophic cells of Marchantia polymorpha and Chenopodium rubrum. High light treatment resulted in a net loss of D1 protein which was accompanied by comparable losses of other proteins of the PS II core (reaction center with inner antenna). LHC II proteins were not reduced correspondingly, indicating that these complexes are less affected by prolonged high light. High light influenced the distribution of PS II components between the grana and the stroma region of the thylakoid membrane, probably by translocation of the respective PS II proteins. Additionally, modifications of several thylakoid proteins were detected in high light treated cells of C. rubrum. These effects are discussed in relation to photoinhibitory damage and repair processes.Abbreviations BCA bioinchonic acid - chl chlorophyll - CF₁ coupling factor - CYC cycloheximide - GT grana thylakoids - HL high light - LL low light - PAGE polyacrylamide gel electrophoresis - PFD photon flux density - PS I Photosystem I - PS II Photosystem II - RC reaction center - SDS sodium dodecylsulfate - ST stroma thylakoids - Thyl unfractionated thylakoids     

The reaction centre from green sulphur bacteria: progress towards structural elucidation

The reaction centre (RC) of green sulphur bacteria is a FeS-type RC, as are the RCs of Photosystems I (PS I) of oxygenic photosynthetic organisms and of heliobacteria. The core domains of both green sulphur bacterial and heliobacterial RCs are considered to be homodimeric, in contrast to those of purple bacteria, PS I and Photosystem II (PS II). This paper briefly describes the techniques of electron microscopy and image processing suited to investigate the structure of these proteins. Recent advances in the study of the structure of the green sulphur bacterial RC, primarily achieved by the application of scanning transmission electron microscopy, are reviewed.This revised version was published online in October 2005 with corrections to the Cover Date.     

Response of Tradescantia albiflora to growth irradiance: Change versus changeability

Most chloroplasts undergo changes in composition, function and structure in response to growth irradiance. However, Tradescantia albiflora, a facultative shade plant, is unable to modulate its light-harvesting components and has the same Chl a/Chl b ratios and number of functional PS II and PS I reaction centres on a Chl basis at all growth irradiances. With increasing growth irradiance, Tradescantia leaves have the same relative amount of chlorophyll—proteins of PS II and PS I, but increased xanthophyll cycle components and more zeaxanthin formation under high light. Despite high-light leaves having enhanced xanthophyll cycle content, all Tradescantia leaves acclimated to varying growth irradiances have similar non-photochemical quenching. These data strongly suggest that not all of the zeaxanthin formed under high light is necessarily non-covalently bound to major and minor light-harvesting proteins of both photosystems, but free zeaxanthin may be associated with LHC II and LHC I or located in the lipid bilayer. Under the unusual circumstances in light-acclimated Tradescantia where the numbers of functional PS II and PS I reaction centres and their antenna size are unaltered during growth under different irradiances, the extents of PS II photoinactivation by high irradiances are comparable. This is due to the extent of PS II photoinactivation being a light dosage effect that depends on the input (photon exposure, antenna size) and output (photosynthetic capacity, non-radiative dissipation) parameters, which in Tradescantia are not greatly varied by changes in growth irradiance.This revised version was published online in October 2005 with corrections to the Cover Date.     

Proteins of the cyanobacterial photosystem I.

Cyanobacterial photosystem (PS) I is remarkably similar to its counterpart in the chloroplast of plants and algae. Therefore, it has served as a prototype for the type I reaction centers of photosynthesis. Cyanobacterial PS I contains 11-12 proteins. Some of the cyanobacterial proteins are modified post-translationally. Reverse genetics has been used to generate subunit-deficient cyanobacterial mutants, phenotypes of which have revealed the functions of the missing proteins. The cyanobacterial PS I proteins bind cofactors, provide docking sites for electron transfer proteins, participate in tertiary and quaternary organization of the complex and protect the electron transfer centers. Many of these mutants are now being used in sophisticated structure-function analyses. Yet, the roles of some proteins of the cyanobacterial PS I are unknown. It is necessary to examine functions of these proteins on a global scale of cell physiology, biogenesis and evolution.     

Reality of P-680 chlorophyll protein – Identification of the site of primary photochemistry in oxygenic photosynthesis

Until recently nearly all available experimental evidence seemed to indicate that the largest subunit of about 50 kDa in the photosystem II core complex ( psb B gene product) is the site of primary photochemistry, and thus the name "P-680 apoprotcin" has been given to this subunit. The notion, however, has also been challenged on the basis of deduced amino acid sequence homology between the proteins in the photosystem II and those of the purple bacterial reaction center. The actual preparation of a functionally active photosystem II reaction center completely devoid of the psb B gene product, but consisting of D-1 and D-2 proteins and cytochrome b -559, has now been achieved.     

A three-dimensional model of the Photosystem II reaction centre of Pisum sativum

A three-dimensional model of the core proteins D1 and D2, including the cofactors, that form the Photosystem II reaction centre of pea (Pisum sativum), has been generated. This model was built with a rule-based computer modelling system using the information from the crystal structures of the photosynthetic reaction centres of Rhodopseudomonas viridis and Rhodobacter sphaeroides. An alignment of the primary sequences of twenty three D1, nine D2, eight bacterial L and eight bacterial M subunits predicts strong similarity between bacterial and higher plant reaction centres, especially in the transmembrane region where the cofactors responsible for electron transport are located. The sequence to be modelled was aligned to the bacterial structures using environment-dependent substitution tables to construct matrices, improving the alignment procedure. The ancestral relationship between the bacteria and higher plant sequences allowed both the L and M subunits to be used as structural templates as they were equally related to the higher plant polypeptides. The regions with the highest predicted structural homology were used as a framework for the construction of the structurally conserved regions. The structurally conserved region of the model shows strong similarity to the bacterial reaction centre in the transmembrane helices. The stromal and lumenal loops show greater sequence variation and are therefore predicted to be the structurally variable regions in the model. The key sidechain assignments and residues that may interact with cofactors are discussed.Abbreviations D Tyr161 in the D2 polypeptide - PS II Photosystem II - Q_A primary plastoquinone acceptor of Photosystem II - Q_B secondary plastoquinone acceptor of Photosystem II - Z Tyr161 in the D1 polypeptide     

Removal of both Ycf48 and Psb27 in Synechocystis sp. PCC 6803 disrupts Photosystem II assembly and alters QA oxidation in the mature complex

The Photosystem II (PS II) assembly factors Psb27 and Ycf48 are transiently associated with PS II during its biogenesis and repair pathways. We investigated the function of these proteins by constructing knockout mutants in Synechocystis sp. PCC 6803. In ΔYcf48 cells, PS II electron transfer and stable oxygen evolution were perturbed. Additionally, Psb27 was required for photoautotrophic growth of cells lacking Ycf48 and assembly beyond the RC47 assembly complex in ΔYcf48:ΔPsb27 cells was impeded. Our results suggest the RC47 complex formed in ΔYcf48 cells is defective and that this deficiency is exacerbated if CP43 binds in the absence of Psb27.     

Nuclear mutations affecting plastoquinone accumulation in maize

We have isolated and characterized two nuclear mutations which affect plastoquinone accumulation in maize. The mutations, hcf103 and hcf114, modify the same genetic locus. Plants homozygous for either mutant allele exhibit reduced PS II electron transport activity, reduced variable chlorophyll fluorescence and reduced delayed fluorescence yield. In these ways, hcf103 and hcf114 resemble previously described PS II mutants which lack stably assembled PS II reaction center complexes. However, unlike most previously described PS II mutants, hcf103 and hcf114 possess stable membrane-associated PS II complexes. Plastoquinone (PQ-9), which performs a variety of redox functions essential to normal non-cyclic electron transport, is severely depleted in the mutants. The lack of PS II electron transport activity is attributed to the absence of PQ-9. This is the first report of mutants deficient in PQ which do not also suffer serious pleiotropic defects.Abbreviations PS II Photosystem II - PQ plastoquinone - Q_A and Q_B primary and secondary stable electron acceptors of PS II - HPLC high pressure liquid chromatography - LDS-PAGE lithium dodecyl sulfate polyacrylamide gel electrophoresis - TLC thin layer chromatography     

Bacterial secretins: Mechanisms of assembly and membrane targeting

Secretion systems are employed by bacteria to transport macromolecules across membranes without compromising their integrities. Processes including virulence, colonization, and motility are highly dependent on the secretion of effector molecules toward the immediate cellular environment, and in some cases, into the host cytoplasm. In Type II and Type III secretion systems, as well as in Type IV pili, homomultimeric complexes known as secretins form large pores in the outer bacterial membrane, and the localization and assembly of such 1 MDa molecules often relies on pilotins or accessory proteins. Significant progress has been made toward understanding details of interactions between secretins and their partner proteins using approaches ranging from bacterial genetics to cryo electron microscopy. This review provides an overview of the mode of action of pilotins and accessory proteins for T2SS, T3SS, and T4PS secretins, highlighting recent near‐atomic resolution cryo‐EM secretin complex structures and underlining the importance of these interactions for secretin functionality.     

Similarity between electron donor side reactions in the solubilized Photosystem II–LHC II supercomplex and Photosystem-II-containing membranes

The PS II–LHC II supercomplex is a novel type of oxygen evolving Photosystem II (PS II) core particle that contains the light harvesting complex proteins Lhcb1/2/4/5 in addition to the PS II reaction centre, oxygen evolving complex (OEC) and inner antennae [Hankamer et al. (1997) Eur J Biochem 243: 422–429]. The 33 and 23 kDa extrinsic proteins in these particles have been localised by image analysis of electron micrographs and averaging techniques [Boekema et al. (1998) Eur J Biochem 252: 268–276]. To assay the functionality of the water splitting complex, we compared the single flash P680⁺ reduction kinetics in these supercomplexes with those of PS II-rich granal stack membranes (BBYs). We found that the P680⁺ reduction kinetics in PS II–LHC II supercomplexes were indistinguishable from those in BBYs. We also examined a number of PS II core particles lacking the Lhcb components. All of these had different P680⁺ reduction kinetics, which we attributed to partial loss of OEC function before and during the measurements.     

Is the 9 kDa thylakoid membrane phosphoprotein functionally and structurally analogous to the 'H' subunit of bacterial reaction centres?

Although the amino acid sequence of the 9 kDa (phospho)protein of chloroplasts has been determined, the function of this thylakoid membrane protein in photosynthetic electron transport and the reason for its physiological control remains unclear. In this paper, I briefly review the evidence which indicates that the phosphorylation of the 9 kDa protein results in a partial inhibition of photosynthetic oxygen evolution by increasing the stability of the semiquinone bound to QA the primary, plastoquinone-binding site of photosystem II (PS II). I propose that in its dephosphorylated state, the 9 kDa thylakoid membrane protein may serve PS II to ensure efficient photochemical charge separation by aiding the transfer of reducing equivalents out of the reaction centre to the attendant plastoquinone pool. This function is analogous to that proposed for the H-subunit of the reaction centre of photosynthetic eubacteria. Whether these two proteins have evolved from a common ancestral reaction centre protein is discussed in the light of a comparison of their amino acid sequences and predicted secondary structures.     

Global spectral-kinetic analysis of room temperature chlorophyll a fluorescence from light-harvesting antenna mutants of barley

This study presents a novel measurement, and simulation, of the time-resolved room temperature chlorophyll a fluorescence emission spectra from leaves of the barley wild-type and chlorophyll-b-deficient chlorina (clo) f2 and f104 mutants. The primary data were collected with a streak-camera-based picosecond-pulsed fluorometer that simultaneously records the spectral distribution and time dependence of the fluorescence decay. A new global spectral-kinetic analysis programme method, termed the double convolution integral (DCI) method, was developed to convolve the exciting laser pulse shape with a multimodal-distributed decay profile function that is again convolved with the spectral emission band amplitude functions. We report several key results obtained by the simultaneous spectral-kinetic acquisition and DCI methods. First, under conditions of dark-level fluorescence, when photosystem II (PS II) photochemistry is at a maximum at room temperature, both the clo f2 and clo f104 mutants exhibit very similar PS II spectral-decay contours as the wild-type (wt), with the main band centred around 685 nm. Second, dark-level fluorescence is strongly influenced beyond 700 nm by broad emission bands from PS I, and its associated antennae proteins, which exhibit much more rapid decay kinetics and strong integrated amplitudes. In particular a 705-720 nm band is present in all three samples, with a 710 nm band predominating in the clo f2 leaves. When the PS II photochemistry becomes inhibited, maximizing the fluorescence yield, both the clo f104 mutant and the wt exhibit lifetime increases for their major distribution modes from the minimal 205-500 ps range to the maximal 1500-2500 ps range for both the 685 nm and 740 nm bands. The clo f2 mutant, however, exhibits several unique spectral-kinetic properties, attributed to its unique PS I antennae and thylakoid structure, indicating changes in both PS II fluorescence reabsorption and PS II to PS I energy transfer pathways compared to the wt and clo f104. Photoprotective energy dissipation mediated by the xanthophyll cycle pigments and the PsbS protein was uninhibited in the clo f104 mutant but, as commonly reported in the literature, significantly inhibited in the clo f2; the inhibited energy dissipation is partly attributed to its thylakoid structure and PS II to PS I energy transfer properties. It is concluded that it is imperative with steady-state fluorometers, especially for in vivo studies of PS II efficiency or photoprotective energy dissipation, to quantify the influence of the PS I spectral emission.     

A knowledge-based three dimensional model of the Photosystem II reaction center of Chlamydomonas reinhardtii

In this Minireview, a comparison of the binding niches of the PS II cofactors from several existing models of the PS II reaction center is provided. In particular, it discusses a three dimensional model of the Photosystem II (PS II) reaction center including D1, D2 and cytochrome b559 proteins from the green alga Chlamydomonas reinhardtii that was specifically generated for this Minireview. This model is the most complete to date and includes accessory chlorophyll_zs, a manganese cluster, two molecules of -carotene and cytochrome b559, all of which are essential components of the PS II reaction center. The modeling of the D1 and D2 proteins was primarily based on homology with the L and M subunits of the anoxygenic purple bacterial photosynthetic reaction centers. The non-homologous loop regions were built using a sequence specific approach by searching for the best-matched protein segments in the Protein Data Bank, and by imposing the matching conformations on the corresponding D1 and D2 regions. Cytochrome b559 which is in close proximity to D1 and D2 was tentatively modeled in / conformation and docked on the Q_B side of the PS II reaction center according to experimental suggestions. An alternate docking on the Q_A side is also shown for comparison. The cofactors in the PS II reaction center were modeled either by adopting the structures from the bacterial counterparts, when available, with modifications based on existing experimental data or by de novo modeling and docking in the most probable positions in the reaction center complex. The specific features of this model are the inclusion of the tetramanganese cluster (with calcium and chloride ions) in a open, C-shaped structure modeled within the D1/D2/cytochrome b559 complex with D1-D170, D1-E189, D1-D342 and D1-A344 as putative ligands; and the modeling of two cis -carotenes and two accessory chlorophyll_zs liganded by D1-H118 and D2-H117. We also analyzed residues in the model which may be involved in the D1 and D2 inter-protein interactions, as well as residues which may be involved in putative bicarbonate and water binding and transport.     

Structural organization of proteins on the oxidizing side of photosystem II. Two molecules of the 33-kDa manganese-stabilizing proteins per reaction center.

The 33-kDa manganese-stabilizing protein stabilizes the manganese cluster in the oxygen-evolving complex. There has been, however, a considerable amount of controversy concerning the stoichiometry of this photosystem II (PS II) component. In this paper, we have verified the extinction coefficient of the manganese-stabilizing protein by amino acid analysis, determined the manganese content of oxygen-evolving photosystem II membranes and reaction center complex using inductively coupled plasma spectrometry, and determined immunologically the amount of the manganese-stabilizing protein associated with photosystem II. Oxygen-evolving photosystem II membranes and reaction center complex preparations contained 258 +/- 11 and 67 +/- 3 chlorophyll, respectively, per tetranuclear manganese cluster. Immunoquantification of the manganese-stabilizing protein using mouse polyclonal antibodies on "Western blots" demonstrated the presence of 2.1 +/- 0.2 and 2.0 +/- 0.3 molecules of the manganese-stabilizing protein/tetranuclear manganese cluster in oxygen-evolving PS II membranes and highly purified PS II reaction center complex, respectively. Since the manganese-stabilizing protein co-migrated with the D2 protein in our electrophoretic system, accurate immunoquantification required the inclusion of CaCl2-washed PS II membrane proteins or reaction center complex proteins in the manganese-stabilizing protein standards to compensate for the possible masking effect of the D2 protein on the binding of the manganese-stabilizing protein to Immobilon-P membranes. Failure to include these additional protein components in the manganese-stabilizing protein standards leads to a marked underestimation of the amount of the manganese-stabilizing protein associated with these photosystem II preparations.