Nucleotide sequence of the psbA3 gene from the cyanobacterium Synechocystis PCC 6803

Genomic structure of the cyanobacterium Synechocystis sp. PCC 6803 strain GT-S

Synechocystis sp. PCC 6803 is the most popular cyanobacterial strain, serving as a standard in the research fields of photosynthesis, stress response, metabolism and so on. A glucose-tolerant (GT) derivative of this strain was used for genome sequencing at Kazusa DNA Research Institute in 1996, which established a hallmark in the study of cyanobacteria. However, apparent differences in sequences deviating from the database have been noticed among different strain stocks. For this reason, we analysed the genomic sequence of another GT strain (GT-S) by 454 and partial Sanger sequencing. We found 22 putative single nucleotide polymorphisms (SNPs) in comparison to the published sequence of the Kazusa strain. However, Sanger sequencing of 36 direct PCR products of the Kazusa strains stored in small aliquots resulted in their identity with the GT-S sequence at 21 of the 22 sites, excluding the possibility of their being SNPs. In addition, we were able to combine five split open reading frames present in the database sequence, and to remove the C-terminus of an ORF. Aside from these, two of the Insertion Sequence elements were not present in the GT-S strain. We have thus become able to provide an accurate genomic sequence of Synechocystis sp. PCC 6803 for future studies on this important cyanobacterial strain.

Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. strain PCC 6803

We report the results of whole-genome transcriptional profiling of the light-to-dark transition with the model photosynthetic prokaryote Synechocystis sp. strain PCC 6803 (Synechocystis). Experiments were conducted by growing Synechocystis cultures to mid-exponential phase and then exposing them to two cycles of light/dark conditions, during which RNA samples were obtained. These samples were probed with a full-genome DNA microarray (3,169 genes, 20 samples) as well as a partial-genome microarray (88 genes, 29 samples). We concluded that (i) 30-min sampling intervals accurately captured transcriptional dynamics throughout the light/dark transition, (ii) 25% of the Synechocystis genes (783 genes) responded positively to the presence of light, and (iii) the response dynamics varied greatly for individual genes, with a delay of up to 120 to 150 min for some genes. Four classes of genes were identified on the basis of their dynamic gene expression profiles: class I (108 genes, 30-min response time), class II (279 genes, 60 to 90 min), class III (258 genes, 120 to 150 min), and class IV (138 genes, 180 min). The dynamics of several transcripts from genes involved in photosynthesis and primary energy generation are discussed. Finally, we applied Fisher discriminant analysis to better visualize the progression of the overall transcriptional program throughout the light/dark transition and to determine those genes most indicative of the lighting conditions during growth.

Novel psbA1 gene from a naturally occurring atrazine-resistant cyanobacterial isolate

A naturally occurring atrazine-resistant cyanobacterial isolate, strain SG2, was isolated from an atrazine-containing wastewater treatment system at the Syngenta atrazine production facility in St. Gabriel, La. Strain SG2 was resistant to 1,000 microg of atrazine per ml but showed relatively low resistance to diuron [3-(3,4-dichlorophenyl)-1,1-dimethyl urea]. Analyses of 16S ribosomal DNA indicated that strain SG2 falls into the Synechocystis/Pleurocapsa/Microcystis group. Photosynthetically driven oxygen evolution in strain SG2 was only slightly inhibited (about 10%) by 2,000 microg of atrazine per ml, whereas in the control strain Synechocystis 6803, oxygen evolution was inhibited 90% by 1,000 microg of atrazine per ml. No atrazine accretion, mineralization, or metabolites were detected when strain SG2 was grown with [(14)C]atrazine. Strain SG2 contained three copies of the psbA gene, which encodes the D(1) protein of the photosystem II reaction center. Nucleotide sequence analyses indicated that the psbA2 and psbA3 genes encoded predicted proteins with the same amino acid sequence. However, the psbA1 gene product contained five extra amino acids, which were not found in PsbA proteins from five other cyanobacteria. Moreover, the PsbA1 protein from strain SG2 had an additional 13 amino acid changes compared to the PsbA2/PsbA3 proteins and contained 10 amino acid alterations compared to conserved residues found in other cyanobacteria. Reverse transcriptase PCR analysis indicated that the psbA1 gene and the psbA2/psbA3 gene(s) were expressed in photosynthetically grown cells in the presence of atrazine. These results suggest that strong selection pressure conferred by the continual input of atrazine has contributed to the evolution of a herbicide-resistant, yet photosynthetically efficient, psbA gene in a cyanobacterium.

Engineering of the protein environment around the redox-active TyrZ in photosystem II. The role of F186 and P162 in the D1 protein of Synechocystis 6803

The photosystem II reaction centre protein D1 is encoded by the psbA gene. By activation of the silent and divergent psbA1 gene in the cyanobacterium Synechocystis 6803, a novel D1 protein, D1', was produced [Salih, G. & Jansson, C. (1997) Plant Cell 9, 869-878]. The D1' protein was found to be fully operational although it deviates from the normal D1 protein in 54 out of 360 amino acids. Two notable amino-acid substitutions in D1' are the replacements of F186 by a leucine and P162 by a serine. The F186 and P162 positions are located in the vicinity of the reaction centre chlorophyll dimer P680 and the redox-active Y161 (TyrZ), and F186 has been implicated in the electron transfer between Y161 and P680. The importance of F186 was addressed by construction of engineered D1 proteins in Synechocystis 6803. F186 was replaced by leucine, serine, alanine, tyrosine or tryptophan. Only the leucine replacement yielded a functional D1 protein. Other substitutions did not support photoautotrophic growth and the corresponding mutants showed no or very poor oxygen evolving activity. In the F186Y and F186W mutants, the D1 protein failed to accumulate to appreciable levels in the thylakoid membrane. The F186S mutation severely increased the light sensitivity of the D1 protein, as indicated by the presence of a 16-kDa proteolytic degradation product. We conclude that the hydrophobicity and van der Waals volume are the most important features of the residue at position 186. Exchanging P162 for a serine yielded no observable phenotype.

Exposure of Synechocystis 6803 cells to series of single turnover flashes increases the psbA transcript level by activating transcription and down-regulating psbA mRNA degradation

Exposure of Synechocystis sp. PCC 6803 cells to series of single turnover flashes increases specifically the level of psbA and psbD2 messages, encoding the D1 and D2 proteins of photosystem II, as compared to light exposed cells. This increase is due to maintenance the transcription rate as high as in growth light and to the down-regulation of transcript degradation as in darkness. Inhibition of the plastoquinone pool reduction by DCMU or its oxidation by DBMIB does not diminish the transcription of the psbA gene under growth conditions. However, the degradation rate of psbA transcript, as well as of other transcripts encoding proteins of thylakoid complexes, is down-regulated in all conditions leading to the oxidation of the plastoquinone pool. We conclude that single turnover flashes are sensed as 'light' by transcription machinery of the cells irrespective of the plastoquinone pool reduction state and as 'dark' by the transcript degradation system.

UV-B-induced differential transcription of psbA genes encoding the D1 protein of photosystem II in the Cyanobacterium synechocystis 6803

UV-B irradiation of intact Synechocystis sp. PCC 6803 cells results in the loss of photosystem II activity, which can be repaired via de novo synthesis of the D1 (and D2) reaction center subunits. In this study, we investigated the effect of UV-B irradiation on the transcription of the psbA2 and psbA3 genes encoding identical D1 proteins. We show that UV-B irradiation increases the level of psbA2 mRNA 2-3-fold and, more dramatically, it induces a 20-30-fold increase in the accumulation of the psbA3 mRNA even at levels of irradiation too low to produce losses of either photosystem II activity or D1 protein. The induction of psbA3 transcript accumulation is specific for UV-B light (290-330 nm). Low intensity UV-A emission (330-390 nm) and white light induce only a small, at most, 2-3-fold enhancement, whereas no effect of blue light was observed. Expression patterns of chimeric genes containing the promoter regions of the psbA2, psbA3 genes fused to the firefly luciferase (luc) reporter gene indicate that (i) transcription of psbA2/luc and psbA3/luc transgenes was elevated, similarly to that of the endogenous psbA genes, by UV-B irradiation, and that (ii) a short, 80-base pair psbA3 promoter fragment is sufficient to maintain UV-B-induced transcription of the luc reporter gene. Furthermore, our findings indicate that UV-B-induced expression of the psbA2 and psbA3 genes is a defense response against UV-B stress, which is regulated, at least, partially at the level of transcription and does not require active electron transport.

Activation of the silent psbA1 gene in the cyanobacterium Synechocystis sp strain 6803 produces a novel and functional D1 protein

The photosystem II reaction center protein D1 in Synechocystis sp strain 6803 is encoded by the psbA2 and psbA3 genes of the three-membered psbA gene family. The silent and divergent psbA1 copy of the psbA gene family was activated by exchanging part of its upstream region with a corresponding fragment of the psbA2 copy. The light-regulated expression of the activated psbA1 gene showed that the inserted psbA2 segment contains the information necessary for light-dependent as well as high-light-stimulated transcription. The activated psbA1 gene expressed a novel D1 protein, D1'. A mutant strain containing psbA1 as the only active psbA gene grew photoautotrophically at a rate comparable to that of the wild type. This finding demonstrates that despite its unusual amino acid sequence, D1 is exchangeable for D1 in the photosystem II complex, at least under normal laboratory conditions. The D1' protein was found to have a degradation rate similar to that of the D1 protein under low- or high-light conditions. Another mutant containing the activated psbA1 gene together with the psbA2 and psbA3 genes produced both the D1 and D1' proteins.

Site-directed mutations near the L-subunit D-helix of the purple bacterial reaction center: a partial model for the primary donor of photosystem II

We have engineered a photosynthetically competent mutant of the purple non-sulfur bacterium Rhodobacter capsulatus which seeks to mimic the behavior of the primary electron donor (P) of the plant photosystem II (PS II) reaction center (RC). To construct this mutant (denoted D1-ILMH), four residues in the bacterial L subunit were mutagenized, such that an 11-residue segment was made identical to the analogous segment from the D1 subunit of PS II. The electronic properties of the bacteriochlorophyll (Bchl) dimer which constitutes the primary donor are substantially altered by these modifications, to the degree that the dimer becomes functionally much more "monomeric". The changes include (1) an increase in the values of the zero-field splitting (ZFS) parameters, as measured by electron paramagnetic resonance (EPR), for the spin-polarized triplet state, 3P, from /D/ = 185 x 10(-4) cm(-1) and /E/ = 31 x 10(-4) cm(-1) in wild-type (WT) chromatophore membranes to /D/ = 200 x 10(-4) cm(-1) and /E/ = 44 x 10(-4) cm(-1) in the mutant and (2) an increase in the EPR line width of the oxidized state, P+, from 0.97 mT in WT to 1.09 mT in D1-ILMH RCs. However, unlike the PS II primary donor (P680), the orientation of 3P in the D1-ILMH mutant is the same as in WT bacteria and does not display the unusual orientation found for PS II. And whereas the redox couple P/P+ has a very high midpoint potential in PS II, P/P+ in the D1-ILMH mutant has a lower midpoint (90 mV more negative) than in WT Rb. capsulatus. In addition, Raman measurements indicate that the hydrogen bond between HisL168 and the C2 acetyl carbonyl oxygen of the Bchl on the active electron transfer pathway (P(A)) is absent in the mutant, due to the fact that HisL168 in the WT sequence has been replaced by a leucine in D1-ILMH. However, the Raman data also reveal the presence of a new hydrogen bond in the D1-ILMH RCs, between the C9 keto carbonyl oxygen of P(A) and an unknown hydrogen-bond donor. Thus, although the protein environment around one of the Bchls of the special pair is significantly changed in D1-ILMH, the chimeric RC does not, as a result of these changes, have a primary donor that is oriented like the one in PS II.

The NADP-glutamate dehydrogenase of the cyanobacterium Synechocystis 6803: cloning, transcriptional analysis and disruption of the gdhA gene

The gdhA gene of Synechocystis PCC 6803, which encodes an NADP-dependent glutamate dehydrogenase (NADP-GDH), has been cloned by complementation of an Escherichia coli glutamate auxotroph. This gene was found to code for a polypeptide of 428 amino acid residues, whose sequence shows high identity with those of archaebacteria (42-47%), some Gram-positive bacteria (40-44%) and mammals (37%). The minimal fragment of Synechocystis DNA required for complementation (2kb) carries the gdhA gene preceded by an open reading frame (ORF2) encoding a polypeptide of 130 amino acids. ORF2 and gdhA are co-transcribed as a 1.9 kb mRNA, but shorter transcripts including only gdhA were also detected. Two promoter regions were identified upon transcriptional fusion to the cat reporter gene of a promoter probe plasmid. Transcription from the promoter upstream of ORF2 was found to be regulated depending on the growth phase of Synechocystis, in parallel to NADP-GDH activity. This promoter is expressed in Escherichia coli too, in contrast to the second promoter, located between ORF2 and gdhA, which was silent in E. coli and did not respond to the stage of growth in Synechocystis. Disruption of the cyanobacterial gdhA gene with a chloramphenicol resistance cassette yielded a mutant strain totally lacking NADP-GDH activity, demonstrating that this gene is not essential to Synechocystis 6803 under our laboratory conditions.

Characterization of the single psbA gene of Prochlorococcus marinus CCMP 1375 (Prochlorophyta)

DNA sequence, copy number, expression and phylogenetic relevance of the psbA gene from the abundant marine prokaryote P. marinus CCMP 1375 was analyzed. The 7 amino acids near the C-terminus missing in higher plant and in Prochlorothrix hollandica D1 proteins are present in the derived amino acid sequence. P. marinus contains only a single psbA gene. Thus, this organism lacks the ability to adapt its photosystem II by replacement of one type of D1 by another, as several cyanobacteria do. Phylogenetic trees suggested the D1-1 iso-form from Synechococcus PCC 7942 as the next related D1 protein and place P. marinus separately from Prochlorothrix hollandica among the cyanobacteria.

The ctpA gene encodes the C-terminal processing protease for the D1 protein of the photosystem II reaction center complex

The D1 protein of the photosystem II (PSII) complex in the thylakoid membrane of oxygenic photosynthetic organisms is synthesized as a precursor polypeptide (pD1) with a C-terminal extension. Posttranslational processing of the pD1 protein is essential to establish water oxidation activity of the PSII complex. We have recently identified a gene, ctpA, a mutation in which resulted in a loss of PSII activity in the cyanobacterium Synechocystis sp. PCC 6803. To study the function of the CtpA protein, we inactivated the ctpA gene by inserting a kanamycin-resistance gene into its coding sequence. The resultant mutant strain, T564, had no PSII-mediated water oxidation activity, but it had normal cytochrome b6f and photosystem I activities. Measurements of thermoluminescence profiles and rates of reduction of 2,6-dichlorophenolindophenol indicated that PSII complexes in the mutant cells had functional reaction centers that were unable to accept electrons from water. Immunoblot analysis showed that D1, D2, CP47, CP43, and the alpha subunit of cytochrome b559, five integral membrane proteins of PSII, were present in T564 cells. Interestingly, the D1 protein in the mutant cells was 2 kDa larger than that in wild-type cells, due to the presence of a C-terminal extension. We conclude that the CtpA protein is a processing enzyme that cleaves off the C-terminal extension of the D1 protein. Interestingly, the CtpA protein shows significant sequence similarity to the interphotoreceptor retinoid-binding proteins in the bovine, human, and insect eye systems.

Differential expression of the psbA genes in the cyanobacterium Synechocystis 6803

The 5' region and transcription initiation sites of the psbA-2 and psbA-3 genes of Synechocystis 6803 were determined. The otherwise highly homologous genes were shown to diverge significantly in the 5' noncoding regions. The transcription start site for the psbA-2 gene was mapped to position -49 upstream of the coding region and for the psbA-3 gene to position -88, i.e. 38 bp upstream of the psbA-2 transcription start point. Both genes exhibit promoter elements, which conform in sequence and position to Escherichia coli consensus motifs. The two genes share identical -35 sequences but differ in their -10 sequences. Primer extension analysis demonstrated that the psbA-2 and psbA-3 genes are differentially expressed, with > 90% of the total psbA transcripts being produced by the psbA-2 gene and the rest by the psbA-3 gene. Inactivation of the psbA-2 gene resulted in an eightfold up-regulation of the psbA-3 gene. The strikingly higher stability of the psbA transcripts in darkness compared to light, and the accumulation of a specific decay intermediate under dark conditions was reported previously. We show here that this dark-stability applies to both the psbA-2 and psbA-3 transcripts. The psbA-3 transcript did not appear to produce the processed intermediate, arguing for the involvement of the 5' non-coding region as a determinant in psbA transcript degradation.

Functional analysis of the two homologous psbA gene copies in Synechocystis PCC 6714 and PCC 6803

The cyanobacteria Synechocystis 6803 and 6714 contain three genes (psbA) coding for the D1 protein. This protein is an essential subunit of photosystem II (PSII) and is the target for herbicides. We have used herbicide-resistant mutants to study the role of the two homologous copies of the psbA genes in both strains (the third copy is not expressed). Several herbicide resistance mutations map within the psbAI gene in Synechocystis 6714 (G. Ajlani et al., Plant Mol. Biol. 13 (1989): 469-479). We have looked for mutations in copy II. Results show that in Synechocystis 6714, only psbAI contains herbicide resistance mutations. Relative expression of psbAI and psbAII has been measured by analysing the proportions of resistant and sensitive D1 in the thylakoid membranes of the mutants. In normal growth conditions, 95% resistant D1 and 5% sensitive D1 were found. In high light conditions, expression of psbAII was enhanced, producing 15% sensitive D1. This enhancement is specifically due to high light and not to the decrease of D1 concentration caused by photoinhibition. Copy I of Synechocystis 6714 corresponds to copy 2 of Synechocystis 6803 since it was always psbA2 which was recombined in Synechocystis 6803 transformants. PSII of the transformant strains was found to be 95% resistant to herbicides as in resistant mutants of Synechocystis 6714.

Role of the carboxy terminus of polypeptide D1 in the assembly of a functional water-oxidizing manganese cluster in photosystem II of the cyanobacterium Synechocystis sp. PCC 6803: assembly requires a free carboxyl group at C-terminal position 344

The D1 polypeptide of the photosystem II (PSII) reaction center is synthesized as a precursor polypeptide which is posttranslationally processed at the carboxy terminus. It has been shown in spinach that such processing removes nine amino acids, leaving Ala344 as the C-terminal residue [Takahashi, M., Shiraishi, T., & Asada, K. (1988) FEBS Lett. 240, 6-8; Takahashi, Y., Nakane, H., Kojima, H., & Satoh, K. (1990) Plant Cell Physiol. 31, 273-280]. We show here that processing on the carboxy side of Ala344 also occurs in the cyanobacterium Synechocystis 6803, resulting in the removal of 16 amino acids. By constructing a deletion strain of Synechocystis 6803 that lacks the three copies of the psbA gene encoding D1, we have developed a system for generating psbA mutants. Using this system, we have constructed mutants of Synechocystis 6803 that are modified in the region of the C-terminus of the D1 polypeptide. Characterization of these mutants has revealed that (1) processing of the D1 polypeptide is blocked when the residue after the cleavage site is changed from serine to proline (mutant Ser345Pro) with the result that the manganese cluster is unable to assemble correctly; (2) the C-terminal extension of 16 amino acid residues can be deleted with little consequence either for insertion of D1 into the thylakoid membrane or for assembly of D1 into a fully active PSII complex; (3) removal of only one more residue (mutant Ala344stop) results in a loss of assembly of the manganese cluster; and (4) the ability of detergent-solubilized PSII core complexes (lacking the manganese cluster) to bind and oxidize exogenous Mn2+ by the secondary donor, Z+, is largely unaffected in the processing mutants (the Ser345Pro mutant of Synechocystis 6803 and the LF-1 mutant of Scenedesmus obliquus) and the truncation mutant Ala344stop. Our results are consistent with a role for processing in regulating the assembly of the photosynthetic manganese cluster and a role for the free carboxy terminus of the mature D1 polypeptide in the ligation of one or more manganese ions of the cluster.