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

Nucleotide sequence of psbC, the gene encoding the CP-43 chlorophyll a-binding protein of Photosystem II, in the cyanobacterium Synechocystis 6803

The nucleotide sequence for the Photosystem II gene psbC has been determined for the cyanobacterium Synechocystis 6803. The gene overlaps the last 50 bases of the psbD gene, and both genes are transcribed in the same direction, but read in different frames. This arrangement is identical to that found in all chloroplast genomes for which psbC has been sequenced. The Synechocystis nucleotide sequence is 70% homologous to the tobacco gene and the predicted amino acid sequence shows 85% homology. A possible alternative translation start site for psbC has been conserved between seven plant sequences and the cyanobacterial sequence. The hydropathy plot for the cyanobacterial protein is very similar to plots determined for six plant species. Pairs of histidines that may play a role in binding chlorophyll are conserved between the cyanobacterial and plant amino acid sequences.

Primary structure of barley genes encoding quinone and chlorophyll a binding proteins of photosystem II

The psbA, psbD and psbC genes encoding the quinone binding D-1 and D-2 apoproteins and the 44 kD chlorophyll a-apoprotein 3 have been located in the chloroplast genome of barley. They are found on a 23 kbp SalI restriction endonuclease fragment in the large single copy region of the chloroplast DNA adjacent to the inverted repeat. As in other species the psbD and psbC genes have reading frames which overlap by 53 bp. They are transcribed in the same direction but translated with a frameshift of one nucleotide. Ten amino acid substitutions are found among the 18 N-terminal residues of the D-2 polypeptide if barley, spinach, tobacco, pea and the liverwort Marchantia are compared. Only 8 substitutions are present among the 335 other residues of the D-2 polypeptide. The amino acid residues located in the putative binding site for the special pair reaction center chlorophyll and the residues probably serving as ligands to non-heme iron in the D-1 and D-2 proteins of barley are strictly conserved when compared to those of purple bacteria and of other higher plants. Identity is also observed for the residues of importance in the binding of quinones.

In vitro transcription and translation of the psbD gene encoding the D-2 protein of photosystem II in barley

The plastoquinone-binding polypeptide D-2 of the reaction center complex of photosystem II in barley has been expressed in vitro using the expression vector pGem3 containing the psbD gene of chloroplast DNA as template. The full length D-2 polypeptide with an apparent mol. weight of 32 kD is a major product when mRNA is transcribed with SP6 RNA polymerase from an insert containing the psbD gene with a 36 bp 5' leader sequence and a 3' tail of 99 bp downstream of the stop codon. Translation of the mRNA had to be done in a rabbit reticulocyte lysate. Translation also occurred from the internal AUG codons giving rise to truncated D-2 polypeptides with sizes of 30, 25 and 17 kD. They are immunoprecipitable with antisera either raised against amino acid residues 235 to 241 or against 345 residues of the D-2 polypeptide. A truncated translation product of 12 kD probably initiated at codon 247 is not recognized by either antiserum. An additional immunoprecipitable protein with an apparent molecular weight of 46 kD is observed by SDS-PAGE and is interpreted as a homomeric aggregate of D-2 polypeptides. Upon addition of methanol solubilized 2,6 dichloro-p-benzoquinone or other quinones a preferential translation of the full-length and truncated D-2 polypeptides is observed. The use of in vitro synthesized D-2 polypeptides for studies of binding quinones, other electron carriers and chlorophyll chromophores is discussed.

The psbA gene of DCMU-resistant Euglena gracilis has an amino acid substitution at serine codon 265

The psbA gene coding for the herbicide binding QB protein of photosystem II has been sequenced previously (Karabin et al. 1984). A herbicide resistant mutant of Euglena, Euglena gracilis ZR, was studied by sequencing part of the psbA gene and its corresponding mRNA. Sequencing reactions were done by annealing a psbA specific, end-labeled DNA-oligomer to total chloroplast DNA or RNA and extending this primer with reverse transcriptase in the presence of the four dideoxynucleotides. An amino acid substitution from serine to alanine at position 265 was detected. All known herbicide resistant higher plants sequenced to date and the Chlamydomonas mutant DCMU-4 show a change at exactly this same position, but the substitution in higher plants is from serine to glycine.

A model for the mechanism of chloride activation of oxygen evolution in photosystem II

A hypothesis is proposed to explain the function of Cl(-) in activating the oxygenevolving complex (OEC) of photosystem II (PS II), based on the results of recent (35)Cl-NMR studies. The putative mechanism involves Cl(-) binding to two types of sites. An intrinsic site is suggested to be composed of three histidyl residues (His 332 and His 337 from D1 and His 337 D2). It is proposed that Cl(-) binding to this site accelerates the abstraction of H(+) from water by raising the pKa's of the histidine imidazole groups. Cl(-) binding also stimulates the transfer of H(+) from this intrinsic site to a set of extrinsic sites on the 33 kD extrinsic polypeptide. The extrinsic Cl(-) binding sites are suggested to involve four protein domains that are linked together by salt-bridge contacts. Chloride and H(+) donated from the intrinsic site attack these intramolecular salt-bridges in a defined sequence, thereby exposing previously inaccessible Cl(-) and H(+) binding sites and stimulating the oxidation of water. This hypothesis also proposes a possible structure for the Mn active site within the D1/D2 complex. Specific amino-acid residues that are likely to participate as Mn lignads are identified on the lumenal portions of the D1 and D2 proteins that are different from those in the L and M subunits of photosynthetic bacteria; the choice of these residues is based on the metal coordination chemistry of these residues, their location within the polypeptide chain, the regularity of their spacing, and their conservation through evolution. The catalytic Mn-binding residues are suggested to be D-61, E-65, E-92, E-98, D-103; D-308, E-329, E-342 and E-333 in D1, and H-62, E-70, H-88, E-97, D-101; E-313, D-334, E-338 and E-345 in D2. Finally, this hypothesis identifies sites on both D2 and the 33 kD extrinsic polypeptide that might be involved in high- and low-affinity Ca(2+) binding.

Sequencing and modification of psbB, the gene encoding the CP-47 protein of Photosystem II, in the cyanobacterium Synechocystis 6803

The Photosystem II protein CP-47 has been hypothesized to be involved in binding the reaction center chlorophyll. The psbB gene, encoding this protein, was cloned from the genome of the cyanobacterium Synechocystis 6803, and sequenced. The DNA sequence is 68% homologous with that of the psbB gene from spinach, whereas the predicted amino acid sequence is 76% homologous. The hydropathy patterns of Synechocystis and spinach CP-47 are almost indistinguishable, indicating the same general CP-47 folding pattern in the thylakoid membrane in the two species. There are five pairs of histidine residues in CP-47 that are spaced by 13 or 14 amino acids and that are located in hydrophobic regions of the protein; these histidine residues may be involved in chlorophyll binding. Interruption of the psbB gene by a DNA fragment carrying a gene conferring kanamycin resistance results in a loss of Photosystem II activity. This indicates that an intact CP-47 is required for a functional Photosystem II complex, but does not necessarily indicate that this protein would house the reaction center.

Identification of psbA and psbD gene products, D1 and D2, as reaction centre proteins of photosystem 2

A recent report (Nanba O, Satoh K: Proc. Natl. Acad. Sci. USA 84: 109-112, 1987) described the isolation from spinach of a putative photosystem 2 reaction centre which contained cytochrome b-559 and three other electrophoretically resolvable polypeptide bands, two of which have molecular weights comparable to the D1 and D2 polypeptides. We have used in vivo labelling with radioactive methionine and probed with D1 and D2 monospecific antibodies (raised against synthetically expressed sequences of the psbA and psbD genes) for specific detection of these proteins in a similarly prepared photosystem 2 reaction centre preparation. These techniques identified a 32 000 dalton D1 band, a 30 000 dalton D2 band and a 55 000 dalton D1/D2 aggregate, the latter apparently arising from the detergent treatments employed. Digestions with a lysine-specific protease further confirmed the identification of the lysine-free D1 polypeptide and also confirmed that the D1 molecules in the 55 000 dalton band were in aggregation with other bands and not in self-aggregates. The D1 and D2 polypeptides (including the aggregate) are considerably enriched in the photosystem two reaction centre preparation compared to the other resolved fractions.

Primary structure of the bc1 complex of Rhodopseudomonas capsulata. Nucleotide sequence of the pet operon encoding the Rieske cytochrome b, and cytochrome c1 apoproteins

The nucleotide sequence of the pet operon of Rhodopseudomonas capsulata strain SB1003 has been determined. This operon consists of the petA, petB and petC genes, which encode the Rieske Fe-S protein, cytochrome b and cytochrome c1, respectively, all components of the ubiquinol-cytochrome c2 oxidoreductase. The deduced amino acid sequences of the pet genes show homology to the corresponding proteins from other organisms, and particularly high homologies (over 90% for amino acid and nucleotide sequences) to the previously described fbc operon from a strain previously identified as Rhodopseudomonas spheroides GA. The amino acid sequences of the pet proteins are discussed with reference to the structure and function of the ubiquinol-cytochrome c2 oxidoreductase.

Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences

Protein coding sequences carry an additional message in the form of a universal three-base periodical pattern (G-non-G-N)n, which is expressed as a strong preference for guanines in the first positions of the codons in mRNA and lack of guanines in the second positions. This periodicity appears immediately after the initiation codon and is maintained along the mRNA as far as the termination triplet, where it disappears abruptly. Known cases of ribosome slippage during translation (leaky frameshifts, out-of-frame gene fusion) are analyzed. At the sites of the slippage the G-periodical pattern is found to be interrupted. It reappears downstream from the slippage sites, in a new frame that corresponds to the new translation frame. This suggests that the (G-non-G-N)n pattern in the mRNA may be responsible for monitoring the correct reading frame during translation. Several sites with complementary C-periodical structure are found in the Escherichia coli 16 S rRNA sequence. Only three of them are exposed to various interactions at the surface of the small ribosomal subunit: (517)gcCagCagCegC, (1395)caCacCgcC and (1531)auCacCucC. A model of a frame-monitoring mechanism is suggested based on the weak complementarity of G-periodical mRNA to the C-periodical sites in the ribosomal RNA. The model is strongly supported by the fact that the hypothetical frame-monitoring sites in the 16 S rRNA that are derived from the nucleotide sequence analysis are also the only sites known to be actually involved or implicated in rRNA-mRNA interactions.

Chloroplast genes encoding subunits of the H(+)-ATPase complex of Chlamydomonas reinhardtii are rearranged compared to higher plants: sequence of the atpE gene and location of the atpF and atpI genes

The chloroplast gene for the epsilon subunit (atpE) of the CF1/CF0 ATPase in the green alga Chlamydomonas reinhardtii has been localized and sequenced. In contrast to higher plants, the atpE gene does not lie at the 3' end of the beta subunit (atpB) gene in the chloroplast genome of C. reinhardtii, but is located at a position 92 kb away in the other single copy region. The uninterrupted open reading frame for the atpE gene is 423 bp, and the epsilon subunit exhibits 43% derived amino acid homology to that from spinach. Codon usage for the atpE gene follows the restricted pattern seen in other C. reinhardtii chloroplast genes.The genes for the CF0 subunits I (atpF) and IV (atpI) of the ATPase complex have also been mapped on the chloroplast genome of C. reinhardtii. The six chloroplast ATPase genes in C. reinhardtii are dispersed individually between the two single copy regions of the chloroplast genome, an organization strikingly different from the highly conserved arrangement in two operon-like units seen in chloroplast genomes of higher plants.

Phenylglyoxal modification of the Photosystem II reaction center

Time-resolved spectroscopic techniques, including optical flash photolysis and electron spin resonance (ESR), have been used in conjunction with fluorescence-induction and dye-reduction assays to monitor electron transport in Photosystem II (PS II) subchloroplast particles incubated with the covalent modifier, phenylglyoxal. Phenylglyoxal-modified digitonin (D-10) particles from spinach are characterized by a high initial fluorescence yield (Fi) and an abolition of the variable component of fluorescence (Fv); an inhibition of PS-II-mediated reduction of dichlorophenol indophenol (DPIP) by sym-diphenylcarbazide; an abolition of flash-induced absorption transients (t1/2 greater than 2 microseconds) at 820 nm attributed to the primary electron donor, P-680+; the inhibition of photoreduction of the acceptor Qa; and the elimination of the ESR Signal 2s and Signal 2f. These observations suggest the critical participation of specific arginine residues on both the oxidizing and reducing sides of Photosystem II and also implicate phenylglyoxal as a quinone-binding site inhibitor (Golbeck, J.H. and Warden, J.T. (1984) Biochim. Biophys. Acta 767, 263-271).

Primary structure of the reaction center from Rhodopseudomonas sphaeroides

The reaction center is a pigment-protein complex that mediates the initial photochemical steps of photosynthesis. The amino-terminal sequences of the L, M, and H subunits and the nucleotide and derived amino acid sequences of the L and M structural genes from Rhodopseudomonas sphaeroides have previously been determined. We report here the sequence of the H subunit, completing the primary structure determination of the reaction center from R. sphaeroides. The nucleotide sequence of the gene encoding the H subunit was determined by the dideoxy method after subcloning fragments into single-stranded M13 phage vectors. This information was used to derive the amino acid sequence of the corresponding polypeptide. The termini of the primary structure of the H subunit were established by means of the amino and carboxy terminal sequences of the polypeptide. The data showed that the H subunit is composed of 260 residues, corresponding to a molecular weight of 28,003. A molecular weight of 100,858 for the reaction center was calculated from the primary structures of the subunits and the cofactors. Examination of the genes encoding the reaction center shows that the codon usage is strongly biased towards codons ending in G and C. Hydropathy analysis of the H subunit sequence reveals one stretch of hydrophobic residues near the amino terminus; the L and M subunits contain five such stretches. From a comparison of the sequences of homologous proteins found in bacterial reaction centers and photosystem II of plants, an evolutionary tree was constructed. The analysis of evolutionary relationships showed that the L and M subunits of reaction centers and the D1 and D2 proteins of photosystem II are descended from a common ancestor, and that the rate of change in these proteins was much higher in the first billion years after the divergence of the reaction center and photosystem II than in the subsequent billion years represented by the divergence of the species containing these proteins.

The topology of a membrane protein: the orientation of the 32 kd Qb-binding chloroplast thylakoid membrane protein

Exposed portions of the 32 kd chloroplast membrane quinone-binding and triazine herbicide-binding protein of photosystem II have been mapped to the lumenal or to the outer (stromal) surface of the thylakoid by following reactions of antibodies generated against synthetic peptides corresponding to predicted hydrophilic amino acid sequences with normally oriented or everted membrane vesicles. These data have led to the construction of a model with five membrane-spanning domains. The model has been verified, in part, by immunoblots of fragments of the protein produced by trypsin treatment of thylakoids with peptide-specific antibodies. Some of the hydrophilic loops appear to be in close contact with proteins of the oxygen evolving complex of photosystem II inasmuch as their removal increases the antibody reaction.

Structure of a 3.2 kb region of pea chloroplast DNA containing the gene for the 44 kD photosystem II polypeptide

The gene for the 44 kD chlorophyll a-binding photosystem II polypeptide has been localized on the pea (Pisum sativum) chloroplast genome. The nucleotide sequence of the gene and its flanking regions has been analyzed. The gene codes for a polypeptide of 473 amino acid residues and is possibly cotranscribed with the gene for the D2 photosystem II polypeptide with which it has 50 bp in common. The amino acid sequences of the 44 kD polypeptides from pea, spinach and maize are approximately 95% homologous. Within the 1 kb fragment 3' to the 44 kD gene a 93 bp tRNA-Ser (UGA) gene and an open reading frame of 62 codons (ORF 62) were identified. Both show high homology to corresponding genes 3' to the 44 kD genes from spinach, maize and barley. The 44 kD gene and ORF 62 are encoded in the same strand, and have putative promoter sequences, ribosome binding sites and transcription termination signals.

Characterization of photosystem II mutants of Chlamydomonas reinhardii lacking the psbA gene

We have examined 78 chloroplast mutants of Chlamydomonas reinhardii lacking photosystem II activity. Most of them are unable to synthesize the 32 Kdalton protein. Analysis of 22 of these mutants reveals that they have deleted both copies of the psbA gene (which codes for the 32 Kdalton protein) in their chloroplast genome. Although these mutants are able to synthesize and to integrate the other photosystem II polypeptides in the thylakoid membranes, they are unable to assemble a stable functional photosystem II complex. The 32 Kprotein appears therefore to play an important role not only in photosystem II function, but also in stabilizing this complex.

The localization of genes for ribosomal, cytochrome b6/f complex and photosystems I and II polypeptides on the chloroplast chromosome of Vicia faba

Detailed studies of rearranged chloroplast genomes such as Vicia faba should give insights into the constraints governing the positional organization of the various gene clusters on the chloroplast chromosome. Seven polypeptide genes have already been mapped on the Vicia faba chloroplast genome (21, 22). In this report, ten additional chloroplast DNA-coded polypeptide genes have been mapped by heterologous hybridization. These genes include cytochrome b6 and subunit 4 of the cytochrome b6/f complex, the two P700 chlorophyll a apoproteins of photosystem I, the two chlorophyll a-binding proteins of photosystem II, cytochrome b559, the D2 polypeptide and two ribosomal proteins. The direction of transcription for five of these gene sequences has been established by utilizing 5' and 3' end specific gene probes. The genetic organization of the Vicia faba chloroplast genome was compared with the chloroplast maps of the standard conserved genome of spinach and the more rearranged genome of pea.

Inhibitors of photosystem II and the topology of the herbicide and QB binding polypeptide in the thylakoid membrane

The folding through the thylakoid membrane of the D-1 herbicide binding polypeptide and of the homologous D-2 subunit of photosystem II is predicted from comparison of amino acid sequences and hydropathy index plots with the folding of the subunits L and M of a bacterial photosystem. As the functional amino acids involved in Q and Fe binding in the bacterial photosystem of R. viridis, as indicated by the X-ray structure, are conserved in the homologous D-1 and D-2 subunits of photosystem II, a detailed topology of the binding niche of QB and of herbicides on photosystem II is proposed. The model is supported by the observed amino acid changes in herbicide tolerant plants and algae. These changes are all in the binding domain on the matrix side of the D-1 polypeptide, and turn out to be of functional significance in the QB binding.New inhibitors of QB function are described. Their chemical structure, i.e. pyridones, quinolones, chromones and benzodiones, contains the features of the phenolic type herbicides. Their essential elements, π-charges at particular atoms, QSAR and steric requirements for optimal inhibitory potency are discussed and compared with the "classical" herbicides of the urea/triazine type.

The sequence of the chloroplast atpB gene and its flanking regions in Chlamydomonas reinhardtii

The chloroplast (cp)-encoded CF1 ATPase beta-subunit gene (atpB) of Chlamydomonas reinhardtii and its flanking regions have been sequenced. The derived amino acid (aa) sequence is highly homologous to that of the beta-subunit gene in Escherichia coli, bovine heart mitochondria, and higher plant cp. In contrast to all other cp genomes, the CF1 epsilon subunit gene (atpE) does not lie at the 3' end of the atpB gene but maps to a position 92 kb away in the other single-copy region. Northern blots confirm that the beta subunit is not encoded as part of a dicistronic message as it is in higher plants. The region just upstream from the atpB gene in C. reinhardtii contains two small open reading frames (ORFs) and not the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase as is found in cp genomes of higher plants. No transcripts for either ORF were detected, but the codon usage in these ORFs as well as in the atpB gene follows the unique pattern of codon usage previously seen in other cp genes in C. reinhardtii.

Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3Å resolution

The molecular structure of the photosynthetic reaction centre from Rhodopseudomonas viridis has been elucidated using X-ray crystallographic analysis. The central part of the complex consists of two subunits, L and M, each of which forms five membrane-spanning helices. We present the first description of the high-resolution structure of an integral membrane protein.

Organization of the thylakoid membrane from the heterotrophic cyanobacterium, Aphanocapsa 6714

The polypeptide composition of thylakoid membrane fractions from the heterotrophic cyanobacterium Aphanocapsa 6714 was examined by electrophoretic and immunoblotting procedures. We have identified thylakoid cytochromes f, b6, c-550 and c-553 by tetramethylbenzidine staining of lithium dodecyl sulfate polyacrylamide gels; we also have identified the Rieske Fe-S center protein and subunit 4 of the cytochrome b6/f complex. We have characterized phycobilisomes and active core preparations of PS I and PS II. PS I is comprised of five polypeptides (62 kDa, 14.5 kDa, 10 kDa, and two proteins of less than 10 kDa), and our PS II preparation is highly enriched for three chlorophyll-binding proteins of 48, 45 and 36 kDa. Furthermore, we have resolved the chlorophyll-binding complexes on non-denaturing gels and have determined the polypeptide composition of each chlorophyll-containing band. Three bands are associated with PS I (I, IIa and IIb) and three bands are PS II components (III', IIIa and IIIb) as judged by low-temperature fluorescence emission spectra. Band III' contains a 64 kDa antenna polypeptide, IIIa contains the 48 kDa and 45 kDa polypeptides, and IIIb is comprised solely of a 36 kDa protein. The IIIb apoprotein represents a novel PS II component; its possible role in photochemistry is discussed.

Plastid gene expression during fruit ripening in tomato

A tomato chloroplast genome map has been constructed with the restriction enzymes Hpa I, Pvu II, and Sal I. Twelve plastid genes have been located on the tomato plastid genome (159 kb).The expression of plastid genes during tomato fruit ripening has been studied. The levels of transcripts of various genes coding for proteins of the photosystem I (psaA), photosystem II (psbA, psbB, psbC, psbD) and the stroma (rbcL) decrease when plastids differentiate from chloroplasts to chromoplasts. The amount of plastid ribosomal RNA also decreases. Transcripts of the genes for the P700 reaction center protein (psaA), for the photosystem II-associated proteins (psbC, psbD) and for the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) cannot be detected in chromoplasts. In contrast, a relatively high level of mRNA is present for the 32 kD protein ('herbicide-binding protein', psbA) in red fruit.

Gene map for the Cyanophora paradoxa cyanelle genome

The genes for the following proteins were localized by hybridization analysis on the cyanelle genome of Cyanophora paradoxa: the alpha and beta subunits of phycocyanin (cpcA and cpcB); the alpha and beta subunits of allophycocyanin (apcA and apcB); the large and small subunits of ribulose-1,5-bisphosphate carboxylase (rbcL and rbcS); the two putative chlorophyll alpha-binding apoproteins of the photosystem I-P700 complex (psaA and psaB); four apoproteins believed to be components of the photosystem II core complex (psbA, psbB, psbC, and psbD); the two apoprotein subunits of cytochrome b-559 which is also found in the core complex of photosystem II (psbE and psbF); three subunits of the ATP synthase complex (atpA and atpBE); and the cytochrome f apoprotein (petA). Eighty-five percent of the genome was cloned as BamHI, BglII, or PstI fragments. These cloned fragments were used to construct a physical map of the cyanelle genome and to localize more precisely some of the genes listed above. The genes for phycocyanin and allophycocyanin were not clustered and were separated by about 25 kilobases. Although the rbcL gene was adjacent to the atpBE genes and the psbC and psbD genes were adjacent, the arrangement of other genes encoding various polypeptide subunits of protein complexes involved in photosynthetic functions was dissimilar to that observed for known chloroplast genomes. These results are consistent with the independent development of this cyanelle from a cyanobacterial endosymbiont.

Chloroplast DNA variation in Chlamydomonas and its potential application to the systematics of this genus

We have estimated the extent of chloroplast DNA (cpDNA) variation in three species of green algae belonging to the genus Chlamydomonas to determine if this variation could be used for taxonomic studies. The overall arrangement of sequences in the chloroplast genome of Chlamydomonas eugametos was compared with that of the closely related C. moewusii and that of the more distantly related C. reinhardtii. The results show that the chloroplast genomes of C. eugametos and C. moewusii are essentially co-linear and are highly homologous in sequence while those of C. eugametos and C. reinhardtii have been extensively rearranged and share a relatively low overall sequence homology. This wide range of chloroplast genome organization suggests that the analysis of cp-DNA variation will be useful for the classification of algae belonging to the Chlamydomonas genus.