Sequence homology between the 32K dalton and the D2 chloroplast membrane polypeptides of Chlamydomonas reinhardii

Translation of partially overlapping psbD-psbC mRNAs in chloroplasts: the role of 5'-processing and translational coupling

The chloroplast psbD and psbC genes encode the D2 and CP43 proteins of the photosystem II complex, and they are generally cotranscribed. We report studies on the basic translation process of tobacco psbD-psbC mRNAs using an in vitro translation system from tobacco chloroplasts. The primary transcript has an unusually long 5'-UTR (905 nt). We show that it is translatable. Processing of the 5'-UTR greatly enhances the translation efficiency of the psbD cistron. A striking feature is that psbD and psbC cistrons overlap by 14 nt. Removal of the psbD 5'-UTR plus the start codon and introduction of a premature termination codon in the psbD cistron considerably reduce the translation efficiency of the downstream psbC cistron. These results indicate that translation of the psbC cistron depends largely on that of the upstream psbD cistron and thus shows translational coupling; however, a portion is independently translated. These observations, together with the presence of monocistronic psbC mRNAs, suggest that the psbD and psbC cistrons are translated via multiple processes to produce necessary amounts of D2 and CP43 proteins.

Herbicide resistance and cross-resistance: changes at three distinct sites in the herbicide-binding protein

Plants and algae resistant to the commonly used s-triazine herbicides display a wide spectrum of cross-resistance to other herbicides that act in a similar manner. Analysis of uniparental mutants of the green alga Chlamydomonas reinhardi showed that three different amino acid residues in the 32-kilodalton thylakoid membrane protein can be independently altered to produce three different patterns of resistance to s-triazine and urea-type herbicides. These results clarify the molecular basis for herbicide resistance and cross-resistance. Two of the mutations do not alter normal electron transport and thus may have applications of agronomic interest.

The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas viridis

The history and methods of membrane protein crystallization are described. The solution of the structure of the photosynthetic reaction center from the bacterium Rhodopseudomonas viridis is described, and the structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Conclusions about the structure of the photosystem II reaction center from plants are drawn, and aspects of membrane protein structure are discussed.

Protein-pigments and the photosystem II reaction center: a glimpse into the history of research and reminiscences

This article provides a glimpse into the dawning of research on chlorophyll-protein complexes and a brief recollection of the path that led us to the identification of the photosystem II reaction center, i.e., the polypeptides that carry the site of primary charge separation in oxygenic photosynthesis. A preliminary version of the personal review on the latter topic has already appeared in this journal (Satoh Photosynth Res 76:233-240, 2003).

The mystery of oxygen evolution: analysis of structure and function of photosystem II, the water-plastoquinone oxido-reductase

Photosystem II (PS II) of thylakoid membrane of photosynthetic organisms has drawn attention of researchers over the years because it is the only system on Earth that provides us with oxygen that we breathe. In the recent past, structure of PS II has been the focus of research in plant science. The report of X-ray crystallographic structure of PS II complex by the research groups of James Barber and So Iwata in UK is a milestone in the area of research in photosynthesis. It follows the pioneering and elegant work from the laboratories of Horst Witt and W. Saenger in Germany, and J. Shen in Japan. It is time to analyze the historic events during the long journey made by the researchers to arrive at this point. This review makes an attempt to critically review the growth of the advancement of concepts and knowledge on the photosystem in the background of technological development. We conclude the review with perspectives on research and technology that should reveal the complete story of PS II of thylakoid in the future.

The Photosynthetic Reaction Centre from the Purple Bacterium Rhodopseudomonasviridis

We first describe the history and methods of membrane protein crystallization, and show how the structure of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis was solved. The structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Finally we draw conclusions on the structure of the photosystem II reaction centre from plants and discuss the aspects of membrane protein structure.

Photosystem II: the solid structural era

Understanding the precise role of photosystem II as an element of oxygenic photosynthesis requires knowledge of the molecular structure of this membrane protein complex. The past few years have been particularly exciting because the structural era of the plant photosystem II has begun. Although the atomic structure has yet to be determined, the map obtained at 6 A resolution by electron crystallography allows assignment of the key reaction center subunits with their associated pigment molecules. In the following, we first review the structural details that have recently emerged and then discuss the primary and secondary photochemical reaction pathways. Finally, in an attempt to establish the evolutionary link between the oxygenic and the anoxygenic photosynthesis, a framework structure common to all photosynthetic reaction centers has been defined, and the implications have been described.

cis- and trans-Acting determinants for translation of psbD mRNA in Chlamydomonas reinhardtii

Chloroplast translation is mediated by nucleus-encoded factors that interact with distinct cis-acting RNA elements. A U-rich sequence within the 5' untranslated region of the psbD mRNA has previously been shown to be required for its translation in Chlamydomonas reinhardtii. By using UV cross-linking assays, we have identified a 40-kDa RNA binding protein, which binds to the wild-type psbD leader, but is unable to recognize a nonfunctional leader mutant lacking the U-rich motif. RNA binding is restored in a chloroplast cis-acting suppressor. The functions of several site-directed psbD leader mutants were analyzed with transgenic C. reinhardtii chloroplasts and the in vitro RNA binding assay. A clear correlation between photosynthetic activity and the capability to bind RNA by the 40-kDa protein was observed. Furthermore, the data obtained suggest that the poly(U) region serves as a molecular spacer between two previously characterized cis-acting elements, which are involved in RNA stabilization and translation. RNA-protein complex formation depends on the nuclear Nac2 gene product that is part of a protein complex required for the stabilization of the psbD mRNA. The sedimentation properties of the 40-kDa RNA binding protein suggest that it interacts directly with this Nac2 complex and, as a result, links processes of chloroplast RNA metabolism and translation.

Characterization of mutants with alterations of the phosphorylation site in the D2 photosystem II polypeptide of chlamydomonas reinhardtii

We have changed the potential phosphorylation site, a threonine residue at position 2 of the D2 polypeptide of the photosystem II complex of Chlamydomonas reinhardtii, to alanine, valine, aspartate, proline, glycine, or glutamate. Mutants with neutral amino acid changes did not display any phenotype with regard to photoautotrophic growth, light sensitivity, fluorescence transients, or photoinhibition. Pulse labeling of these mutants with 32P indicated that a phosphorylated protein of the same size as D2 is absent in these mutants, suggesting that threonine-2 is indeed the unique phosphorylation site of D2. In contrast, mutants in which threonine-2 has been replaced with acidic residues are deficient in photosystem II. Use of chimeric genes containing the psbD 5'-untranslated region revealed that the initiation of translation was not affected in these mutants, but the mutations interfered with a later step of D2 synthesis and accumulation.

Processing of the psbA 5' untranslated region in Chlamydomonas reinhardtii depends upon factors mediating ribosome association

The 5' untranslated region of the chloroplast psbA mRNA, encoding the D1 protein, is processed in Chlamydomonas reinhardtii. Processing occurs just upstream of a consensus Shine-Dalgarno sequence and results in the removal of 54 nucleotides from the 5' terminus, including a stem-loop element identified previously as an important structure for D1 expression. Examination of this processing event in C. reinhardtii strains containing mutations within the chloroplast or nuclear genomes that block psbA translation reveals a correlation between processing and ribosome association. Mutations within the 5' untranslated region of the psbA mRNA that disrupt the Shine-Dalgarno sequence, acting as a ribosome binding site, preclude translation and prevent mRNA processing. Similarly, nuclear mutations that specifically affect synthesis of the D1 protein specifically affect processing of the psbA mRNA. In vitro, loss of the stem-loop element does not prohibit the binding of a message-specific protein complex required for translational activation of psbA upon illumination. These results are consistent with a hierarchical maturation pathway for chloroplast messages, mediated by nuclear-encoded factors, that integrates mRNA processing, message stability, ribosome association, and translation.

A common ancestor for oxygenic and anoxygenic photosynthetic systems: a comparison based on the structural model of photosystem I

The 4 A structural model of photosystem I (PSI) has elucidated essential features of this protein complex. Inter alia, it demonstrates that the core proteins of PSI, PsaA and PsaB each consist of an N-terminal antenna-binding domain, and a C-terminal reaction center (RC)-domain. A comparison of the RC-domain of PSI and the photosynthetic RC of purple bacteria (PbRC), reveals significantly analogous structures. This provides the structural support for the hypothesis that the two RC-types (I and II) share a common evolutionary origin. Apart from a similar set of constituent cofactors of the electron transfer system, the analogous features include a comparable cofactor arrangement and a corresponding secondary structure motif of the RC-cores. Despite these analogies, significant differences are evident, particularly as regards the distances between and the orientation of individual cofactors, and the length and orientation of alpha-helices. Inferred roles of conserved amino acids are discussed for PSI, photosystem II (PSII), photosystem C (PSC, green sulfur bacteria) and photosystem H (PSH, heliobacteria). Significant sequence homology between the N-terminal, antenna-binding domains of the core proteins of type-I RCs, PsaA, PsaB, PscA and PshA (of PSI, PSC and PSH respectively) with the antenna-binding subunits CP43 and CP47 of PSII indicate that PSII has a modular structure comparable to that of PSI.

Nuclear-gene mutations suppress a defect in the expression of the chloroplast-encoded large subunit of ribulose-1,5-bisphosphate Carboxylase/Oxygenase

The green alga Chlamydomonas reinhardtii mutant 76-5EN lacks photosynthesis because of a nuclear-gene mutation that specifically inhibits expression of the chloroplast gene encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39). Photosynthesis-competent revertants were selected from mutant 76-5EN to explore the possibility of increasing Rubisco expression. Genetic analysis of 10 revertants revealed that most arose from suppressor mutations in nuclear genes distinct from the original 76-5EN mutant gene. The revertant strains have regained various levels of Rubisco holoenzyme, but none of the suppressor mutations increased Rubisco expression above the wild-type level in either the presence or absence of the 76-5EN mutation. One suppressor mutation, S107-4B, caused a temperature-conditional, photosynthesis-deficient phenotype in the absence of the original 76-5EN mutation. The S107-4B strain was unable to grow photosynthetically at 35 degreesC, but it expressed a substantial level of Rubisco holoenzyme. Whereas the 76-5EN gene encodes a nuclear factor that appears to be required for the transcription of the Rubisco large-subunit gene, the S107-4B nuclear gene may be required for the expression of other chloroplast genes.

A nuclear-encoded subunit of the photosystem II reaction center

A nuclear-encoded polypeptide of 6.1 kDa was identified in isolated photosystem II (PSII) reaction center from Spinacia oleracea. The hydrophobic membrane protein easily escapes staining procedures such as Coomassie R-250 or silver staining, but it is clearly detected by immunodecoration with peptide-directed IgG. This additional subunit was found to be present in PSII reaction centers previously known to contain only the D1/D2/cytb559 proteins and the psbI gene product. Furthermore, cross-linking experiments using 1-(3-dimethylaminopropyl-) 3-ethylcarbodiimide showed that the nearest neighbors were the D1 and D2 proteins and the cytb559. The 6.1-kDa protein was purified by immune affinity chromatography. N-terminal sequence analysis of the isolated protein confirmed the identity of the 6.1-kDa protein and enabled finding of strong similarities with a randomly obtained cDNA from Arabidopsis thaliana. Using enzyme-linked immunosorbent assay in combination with thylakoid membrane preparations of different orientation, the N terminus of the protein, predicted to span the membrane once, is suggested to be exposed at the lumen side of the membrane. Consequently the 6.1-kDa protein seems to be the only subunit in the PSII reaction center that is nuclear encoded and has its N terminus on the lumen side of the membrane. These findings open for new interesting suggestions concerning the properties of photosystem II reaction center with respect to the photosynthetic activity, regulation and assembly in higher plants.

The D-E region of the D1 protein is involved in multiple quinone and herbicide interactions in photosystem II

The region between helices D and E (D-E region) of the D1 protein of photosystem II (PSII) is exposed at the stromal side of the photosynthetic membrane, contains the secondary plastoquinone (QB) binding niche, and is involved in processes at the reducing side of PSII. The role of the D-E region was studied in 27 site-directed mutants generated in the psbAII gene of the cyanobacterium Synechocystis sp. PCC 6803. The photochemical performance of the modified PSII reaction centers was assessed with respect to photoautotrophic growth, oxygen evolution, fluorescence induction, and herbicide inhibition. A few mutations, located at positions presumably involved in essential interactions in the QB binding niche, greatly interfered with PSII performance. On the other hand, mutations in the presumptive loop region between helices D and de resulted in relatively minor effects, indicating a flexible region not critical for photochemical function. Indeed, although more than 80% of the D-E region is phylogenetically invariant, the bulk of the mutations affected the measured parameters only moderately. The significance of the conserved residues appears to be in subtle interactions that optimize the thermodynamic balance between some of the redox components of PSII, as indicated by mild changes in the steady state fluorescence. Many mutations modified tolerances to PSII herbicides. The dispersion of these mutations throughout the D-E region indicates the complex nature of the interactions, direct and indirect, affecting herbicide binding in the QB niche. Mutation of codons Ser221 and Ser222 to Leu221 and Ala222 revealed a new location coordinating the herbicide diuron in the D1 protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Evolution of heliobacteria: Implications for photosynthetic reaction center complexes

The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein shows rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.

Isolation and characterization of PSII core complexes from a brown alga, Laminaria saccharina

PSII-enriched particles, active for DCIP-reduction, were prepared from Laminaria saccharina chloroplasts, and PSII core complexes were further purified by ion-exchange chromatography. They contained several polypeptides, four of them cross-reacting with antibodies raised against CP47, CP43, D1 and D2 of green plants. A second chromatography was required to separate: (i) a core antenna, composed of 51 kDa polypeptide subunits, binding 11 beta-carotene, 4 chlorophyll (Chl) c and 7 fucoxanthin for 100 Chl a, and reacting with CP47 antibodies; and (ii) a reaction center complex consisting of two main polypeptides of 34 and 36 kDa. The pigment stoichiometry was of 5 Chl a and 0.5 beta-carotene for 2 pheophytin a. The 34 and 36 kDa components cross-reacted with anti-D1 and anti-D2 antibodies, respectively. The presence of cytochrome b-559 was substantiated by spectrophotometry.

Structure and organization of rhodophyte and chromophyte plastid genomes: implications for the ancestry of plastids

Plastid genomes of two rhodophytes (Porphyra yezoensis and Griffithsia pacifica) and two chromophytes (Olisthodiscus luteus and Ochromonas danica) were compared with one another and with green plants in terms of overall structure, gene complement and organization. The rhodophyte genomes are moderately colinear in terms of gene organization, and are distinguished by three rearrangements that can most simply be explained by transpositions and a large (approximately 40 kb) inversion. Porphyra contains two loci for ppcBA and Griffithsia has two loci for rpoA. Although there is little similarity in gene organization between the rhodophytes and consensus green plant genome, certain gene clusters found in green plants appear to be conserved in the rhodophytes. The chromophytes Olisthodiscus and Ochromonas contain relatively large plastid inverted repeats that encode several photosynthetic genes in addition to the rRNA genes. With the exception of rbcS, the plastid gene complement in Olisthodiscus is similar to that of green plants, at least for the subset of genes tested. The Ochromonas genome, in contrast, appears unusual in that several of the green plant gene probes hybridizing to Olisthodiscus DNA did not detect similar sequences in Ochromonas DNA. Gene organization within the chromophytes is scrambled relative to each other and to green plants, despite the presence of putatively stabilizing inverted repeats. However, some gene clusters conserved in green plants and rhodophytes are also present in the chromophytes. Comparison of the entire rhodophyte, chromophyte and green plant plastid genomes suggests that despite differences in gene organization, there remain overall similarities in architecture, gene content, and gene sequences among in three lineages. These similarities are discussed with reference to the ancestry of the different plastid types.

Origin and early evolution of photosynthesis

Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the earth's history, and that a presumed phase of evolution involving non-oxygen evolving photosynthetic organisms took place even earlier. The evolutionary relationships of the reaction center complexes found in all the classes of currently existing organisms have been analyzed using sequence analysis and biophysical measurements. The results indicate that all reaction centers fall into two basic groups, those with pheophytin and a pair of quinones as early acceptors, and those with iron sulfur clusters as early acceptors. No simple linear branching evolutionary scheme can account for the distribution patterns of reaction centers in existing photosynthetic organisms, and lateral transfer of genetic information is considered as a likely possibility. Possible scenarios for the development of primitive reaction centers into the heterodimeric protein structures found in existing reaction centers and for the development of organisms with two linked photosystems are presented.

A preparative method for the isolation of the 43 kDa, 47 kDa and the D1-D 2-Cyt b 559 species directly from thylakoid membranes

Using the non-ionic detergent dodecyl-β-D-maltoside we have developed a preparative method for the isolation of the 43 kDa, 47 kDa and D1-D2-Cyt b 559 species directly from thylakoid membranes. In contrast to previous procedures the photosynthetic membrane was exposed only to one mild detergent and that resulted in more stable preparations. The isolated species were examined spectroscopically and it was found that even under these mild conditions the D1-D2-Cyt b 559 did not retain the primary quinone QA.

Glu-69 of the D2 protein in photosystem II is a potential ligand to Mn involved in photosynthetic oxygen evolution

To probe the involvement of amino acid residues of the D2 protein in the water-splitting process in photosystem II, site-directed mutagenesis was applied to identify D2 residues that might contribute to binding the Mn cluster involved in oxygen evolution. Mutation of Glu-69 to Gln or Val in D2 of the cyanobacterium Synechocystis sp. PCC 6803 was found to lead to a loss of photoautotrophic growth. However, in cells of the Gln mutant (E69Q) a significant Hill reaction rate could be observed upon the start of illumination, but the oxygen evolution rate declined with a half-time of approximately 1 min. Addition of 1 mM Mn2+ stabilized oxygen evolution in E69Q thylakoids. Other divalent cations were ineffective in specific stabilization. When the water-splitting system was bypassed, the rate of electron transport remained stable during illumination, indicating that the inactivation of oxygen evolution is localized in the water-splitting complex. We interpret these observations to indicate that Glu-69 is a Mn ligand and that the loss of oxygen evolution in the E69Q mutant upon turnover of PS II is initiated by changes in the Mn cluster, possibly leading to Mn release from the water-splitting complex. The addition of exogenous Mn to E69Q thylakoids may help to keep the Mn cluster active for a longer time, perhaps by providing Mn to rebind in the cluster after release of one Mn and before the Mn cluster had disintegrated.(ABSTRACT TRUNCATED AT 250 WORDS)

Chloride binding proteins: mechanistic implications for the oxygen-evolving complex of Photosystem II

Chloride plays a key role in activating the photosynethetic oxygen-evolving complex (OEC) of Photosystem II, but the OEC is only one of many enzymes affected by this anion. Some of the mechanistic features of Cl(-) involvement in water-splitting resemble those of other proteins whose structure and chemistry are known in detail. An overview of the similarities and differences between these Cl(-)-binding systems is presented.

The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis

We first describe the history and methods of membrane protein crystallization, and show how the structure of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis was solved. The structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Finally we draw conclusions on the structure of the photosystem II reaction centre from plants and discuss the aspects of membrane protein structure.

Transfer RNA genes and the genetic code in Chlamydomonas reinhardtii mitochondria

Only three tRNA genes are present within a sequenced 12.35 kbp region of the 15.8 kbp mtDNA of Chlamydomonas reinhardtii, a unicellular green alga. The corresponding tRNAs, whose anticodons are specific for TGG (Trp), CAA/G (Gln) and ATG (Met) codons, all display conventional secondary structures. The tRNA(Met) gene encodes an elongator rather than initiator species. The standard genetic code is used in C. reinhardtii mitochondria, but codon distribution is highly biased: in a collection of six identified protein coding genes, nine codons (including TGA) are not used at all, while four other sense codons occur very infrequently. In spite of the absence of certain codons, a minimum of 23 tRNAs (assuming separate initiator and elongator tRNAs(Met) are used) is needed to translate the C. reinhardtii mitochondrial genetic code. It appears unlikely that this minimal tRNA set is encoded by C. reinhardtii mtDNA.

Structural determination of the photosystem II core complex from spinach

A photosystem II core complex was purified with high yield from spinach by solubilization with beta-dodecylmaltoside. The complex consisted of polypeptides with molecular mass 47, 43, 34, 31, 9 and 4 kDa and some minor components, as detected by silver-staining of polyacrylamide gels. There was no indication for the chlorophyll-a/b-binding, light-harvesting complex polypeptides. The core complex revealed electron-transfer activity (1,5-diphenylcarbazide----2,6-dichloroindophenol) of about 30 mumol reduced 2,6-dichloroindophenol/mg chlorophyll/h. The structural integrity was analyzed by electron microscopy. The detergent-solubilized protein complex has the shape of a triangular disk with a maximum diameter of 13 nm and a maximum height of 6.8 nm. The shape of this core complex differs considerably from that of cyanobacterial photosystem II membrane fragments, which are elongated particles. The structural differences between both the complexes of higher plants and cyanobacteria are discussed with special emphasis on their association with the antenna apparatus in the photosynthetic membranes.

Structure and organization of Marchantia polymorpha chloroplast genome. II. Gene organization of the large single copy region from rps'12 to atpB

The nucleotide sequence (56,410 base-pairs) of the large single-copy region of chloroplast DNA from the liverwort Marchantia polymorpha has been determined. The sequence starts from one end (JLA) of the large single-copy region and encompasses genes for 21 tRNAs, six ATPase subunits (atpA, atpB, atpE, atpF, atpH and atpI), two photosystem I polypeptides (psaA and psaB), four photosystem II polypeptides (psbA, psbC, psbD and psbG), five ribosomal proteins (rps2, rps4, rps7, rps'12 and rps14), and three RNA polymerase subunits (rpoB, rpoC1 and rpoC2). In addition, we detected 18 open reading frames ranging from 29 to 2136 amino acid residues long, four of which share significant amino acid sequence homology to those of an Escherichia coli malK protein (designated mbpX), human mitochondrial ND2 (ndh2) and ND3 (ndh3) of a respiratory chain NADH dehydrogenase, or a bacterial antenna protein of a light-harvesting complex (lhcA). Sequence analysis suggests that four tRNA genes and six protein genes might be split by introns; they are trnG(UCC), trnK(UUU), trnL(UAA), trnV(UAC), atpF, ndh2, rpoC1, rps'12, ORF135 and ORF167. In the large single-copy region described here, the gene organization deduced is highly conserved with respect to that of higher plants, but an inversion of some 30,000 base-pairs flanked by trnL(CAA) and trnD(GUC) was seen between the liverwort and tobacco chloroplast genomes.