Transcriptional organization of the phycocyanin subunit gene clusters of the cyanobacterium Anacystis nidulans UTEX 625

De novo sequence analysis and intact mass measurements for characterization of phycocyanin subunit isoforms from the blue-green alga Aphanizomenon flos-aquae

In this work, partial characterization of the primary structure of phycocyanin from the cyanobacterium Aphanizomenon flos-aquae (AFA) was achieved by mass spectrometry de novo sequencing with the aid of chemical derivatization. Combining N-terminal sulfonation of tryptic peptides by 4-sulfophenyl isothiocyanate (SPITC) and MALDI-TOF/TOF analyses, facilitated the acquisition of sequence information for AFA phycocyanin subunits. In fact, SPITC-derivatized peptides underwent facile fragmentation, predominantly resulting in y-series ions in the MS/MS spectra and often exhibiting uninterrupted sequences of 20 or more amino acid residues. This strategy allowed us to carry out peptide fragment fingerprinting and de novo sequencing of several peptides belonging to both alpha- and beta-phycocyanin polypeptides, obtaining a sequence coverage of 67% and 75%, respectively. The presence of different isoforms of phycocyanin subunits was also revealed; subsequently Intact Mass Measurements (IMMs) by both MALDI- and ESI-MS supported the detection of these protein isoforms. Finally, we discuss the evolutionary importance of phycocyanin isoforms in cyanobacteria, suggesting the possible use of the phycocyanin operon for a correct taxonomic identity of this species.

Analysis on the factors affecting start-up intensity in the upstream sequence of phycocyanin β subunit gene from Arthrospira platensis by site-directed mutagenesis

Six promoters in the 419 bp upstream sequence of the phycocyanin beta subunit gene of Arthrospira platensis FACHB341 have been previously cloned. Site-directed mutagenesis has now been used to introduce mutations in the -10 and -35 boxes of promoter 3, -10 box of promoter 4, and -35 box of promoter 6. The expression level of green fluorescent protein gene was measured by flow cytometry. Results showed that the effects of site-directed mutagenesis in different promoters were dissimilar: some increased and some declined.

Negative control of the high light-inducible hliA gene and implications for the activities of the NblS sensor kinase in the cyanobacterium Synechococcus elongatus strain PCC 7942

The hliA gene of the cyanobacterium Synechococcus elongatus PCC 7942 is known to be upregulated by high-intensity light through the activity of the NblS sensor kinase. In this work it was found that, within the hliA upstream region, changes to the sequence around -30 to -25 (relative to the transcriptional start site) resulted in elevated hliA expression, implicating this region in negative regulation of the gene. Electrophoretic mobility shift assays performed were consistent with a protein binding this region that acts to keep the gene off in lower light. A reduction in gene dosage of nblS in vivo resulted in enhanced hliA expression, suggesting that negative control of hliA is mediated through NblS. An extended version of the high light regulatory 1 (HLR1) motif (previously described in Synechocystis PCC 6803) was identified within the sequence surrounding -30 to -25 of hliA. The extended HLR1 sequence was found upstream of other NblS-controlled genes from S. elongatus and Synechocystis PCC 6803 and upstream of hli genes from a variety of cyanobacterial and related genomes. These results point to the evolutionary conservation of the HLR1 element and its importance in NblS-mediated signaling and yield new insight into NblS-mediated control of gene expression.

Thymine at -5 is crucial for cpc promoter activity of Synechocystis sp. strain PCC 6714

The levels of transcripts of the cpc operon were highly reduced in a PD-1 mutant of cyanobacterium Synechocystis sp. strain PCC 6714. This was due to a substitution of C for T that occurred at 5 bp upstream of the transcription initiation site of the cpc operon. Any substitution for T at the -5 position drastically reduced both in vivo and in vitro promoter activity in cyanobacterium Synechococcus sp. strain PCC 7942 but not the in vivo activity in Escherichia coli. This suggests that the requirement of -5T appears to be specific for a cyanobacterial RNA polymerase-promoter combination.

Interaction of Ferredoxin:NADP+ Oxidoreductase with Phycobilisomes and Phycobilisome Substructures of the Cyanobacterium Synechococcus sp. Strain PCC 7002

The enzyme ferredoxin-NADP(+) oxidoreductase (FNR) from Synechococcus sp. PCC 7002 has an extended structure comprising three domains (FNR-3D) (Schluchter, W. M., and Bryant, D. A. (1992) Biochemistry 31, 3092-3102). Phycobilisome (PBS) preparations from wild-type cells contained from 1.0 to 1.6 molecules of FNR-3D per PBS, with an average value of 1.3 FNR per PBS. A maximum of two FNR-3D molecules could be specifically bound to wild-type PBS via the N-terminal, CpcD-like domain of the enzyme when exogenous recombinant FNR-3D (rFNR-3D) was added. To localize the enzyme within the PBS, the interaction of PBS and their substructures with rFNR-3D was further investigated. The binding affinity of rFNR-3D for phycocyanin (PC) hexamers, which contained a 22-kDa proteolytic fragment derived from CpcG, the L(RC)(27) linker polypeptide, was higher than its affinity for PC hexamers containing no linker protein. PBS from a cpcD3 mutant, which lacks the 9-kDa, PC-associated rod linker, incorporated up to six rFNR-3D molecules per PBS. PBS of a cpcC mutant, which has peripheral rods that contain single PC hexamers, also incorporated up to six rFNR-3D molecules per PBS. Direct competition binding experiments showed that PBS from the cpcD3 mutant bound more enzyme than PBS from the cpcC mutant. These observations support the hypothesis that the enzyme binds preferentially to the distal ends of the peripheral rods of the PBS. These data also show that the relative affinity order of the PC complexes for FNR-3D is as follows: (alpha(PC)beta(PC))(6)-L(R)(33) > (alpha(PC)beta(PC))(6)-L(RC)(27) > (alpha(PC)beta(PC))(6). The data suggest that, during the assembly of the PBS, FNR-3D could be displaced to the periphery according to its relative binding affinity for different PC subcomplexes. Thus, FNR-3D would not interfere with the light absorption and energy transfer properties of PC in the peripheral rods of the PBS. The implications of this localization of FNR within the PBS with respect to its function in cyanobacteria are discussed.

Sensitivity of cyanobacterial antenna, reaction center and CO2 assimilation transcripts and proteins to moderate UVB: light acclimation potentiates resistance to UVB

We tested the hypothesis that cyanobacterial cells have sufficient acclimation potential to tolerate UVB when it is applied in a natural quantum ratio to growth photosynthetically active radiation (PAR). We grew Synechococcus under 50 (Low) or 300 (High) micromol PAR m(-2) x s(-1) and then exposed the cells to 0.125 (Low) or 0.75 (High) micromol UVB m(-2) x s(-1). The PAR:UVB quantum ratios were near natural for both the Low-PAR:Low-UVB and the High-PAR:High-UVB treatments, but UVB was in excess of typical aquatic PAR:UVB for Low-PAR:High-UVB treatments. The cellular light history determined the UVB responses of Synechococcus. High-PAR cells initially had fewer cpc transcripts encoding phycocyanin, lower phycocyanin content, and more psbAII/AIII transcripts encoding the D1:2 photosystem II (PSII) protein isoform. Higher PAR potentiated them to tolerate an appropriate UVB level without short-term inhibition of PSII or growth. Low-PAR cells rapidly altered psbAII/AIII and cpc gene expression and tolerated appropriate Low UVB. Low-PAR:High-UVB cells, in contrast, suffered short-term inhibition of PSII and growth. In all treatments UVB induced transient loss of cpc transcripts, possibly to free resources for psbAII/AIII expression, which is important for UVB resistance. The drop in cpc transcripts was not part of a general shock response because rbcL transcript pools were stable upon UVB exposure.

A phycocyanin-deficient mutant of synechocystis PCC 6714 with a single-base substitution upstream of the cpc operon

The structure and expression of the cpc operon encoding phycocyanin subunits and linker polypeptides in a phycocyanin-deficient mutant (PD-1) and the wild-type of Synechocystis PCC 6714 were analyzed. The results of sequence and Northern blot analyses of the wild type indicate that the cpc operon consists of cpcB, cpcA, cpcC1, cpcC2 and cpcD, in that order. The levels of the transcripts in PD-1 were one-tenth to one-sixth as high as those in the wild type. In the PD-1 genome, a single-base substitution of C for T has occurred at base 259 upstream of the translational initiation codon of cpcB (at three bases downstream of the putative -10 region). To evaluate the in vivo transcription activities of these promoters in a cyanobacterium, we constructed vectors for the transformation of Synechococcus PCC7942, pANY1 and pANY2, which contain the upstream region of cpcB of the wild type (pANY1) or PD-1 (pANY2) and the promoter-less luxAB fusion. The bioluminescence of the transformants with pANY2 was one-tenth to one-sixth as high as that with pANY1. The coincidence of the results of Northern analysis and the promoter assay shows that the phycocyanin deficiency of PD-1 is due to the single-base substitution in the upstream region of the cpc operon.

A role for cpeYZ in cyanobacterial phycoerythrin biosynthesis

Pigment mutant strain FdR1 of the filamentous cyanobacterium Fremyella diplosiphon is characterized by constitutive synthesis of the phycobiliprotein phycoerythrin due to insertional inactivation of the rcaC regulatory gene by endogenous transposon Tn5469. Whereas the parental strain Fd33 harbors five genomic copies of Tn5469, cells of strain FdR1 harbor six genomic copies of the element; the sixth copy in FdR1 is localized to the rcaC gene. Electroporation of FdR1 cells yielded secondary pigment mutant strains FdR1E1 and FdR1E4, which identically exhibited the FdR1 phenotype with significantly reduced levels of phycoerythrin. In both FdR1E1 and FdR1E4, a seventh genomic copy of Tn5469 was localized to the cpeY gene of the sequenced but phenotypically uncharacterized cpeYZ gene set. This gene set is located downstream of the cpeBA operon which encodes the alpha and beta subunits of phycoerythrin. Complementation experiments correlated cpeYZ activity to the phenotype of strains FdR1E1 and FdR1E4. The predicted CpeY and CpeZ proteins share significant sequence identity with the products of homologous cpeY and cpeZ genes reported for Pseudanabaena sp. strain PCC 7409 and Synechococcus sp. strain WH 8020, both of which synthesize phycoerythrin. The CpeY and CpeZ proteins belong to a family of structurally related cyanobacterial proteins that includes the subunits of the CpcE/CpcF phycocyanin alpha-subunit lyase of Synechococcus sp. strain PCC 7002 and the subunits of the PecE/PecF phycoerythrocyanin alpha-subunit lyase of Anabaena sp. strain PCC 7120. Phycobilisomes isolated from mutant strains FdR1E1 and FdR1E4 contained equal amounts of chromophorylated alpha and beta subunits of phycoerythrin at 46% of the levels of the parental strain FdR1. These results suggest that the cpeYZ gene products function in phycoerythrin synthesis, possibly as a lyase involved in the attachment of phycoerythrobilin to the alpha or beta subunit.

Cloning of the cpcE and cpcF genes from Synechococcus sp. PCC 6301 and their inactivation in Synechococcus sp. PCC 7942

Two open reading frames denoted as cpcE and cpcF were cloned and sequenced from Synechococcus sp. PCC 6301. The cpcE and cpcF genes are located downstream of the cpcB2A2 gene cluster in the phycobilisome rod operon and can be transcribed independently of the upstream cpcB2A2 gene cluster. The cpcE and cpcF genes were separately inactivated by insertion of a kanamycin resistance cassette in Synechococcus sp. PCC 7942 to generate mutants R2EKM and R2FKM, respectively, both of which display a substantial reduction in spectroscopically detectable phycocyanin. The levels of beta- and alpha-phycocyanin polypeptides were reduced in the R2EKM and R2FKM mutants although the phycocyanin and linker genes are transcribed at normal levels in the mutants as in the wild type indicating the requirement of the functional cpcE and cpcF genes for normal accumulation of phycocyanin. Two biliprotein fractions were isolated on sucrose density gradient from the R2EKM/R2FKM mutants. The faster sedimenting fraction consisted of intact phycobilisomes. The slower sedimenting biliprotein fraction was found to lack phycocyanin polypeptides, thus no free phycocyanin was detected in the mutants. Characterization of the phycocyanin from the mutants revealed that it was chromophorylated, had a lambda max similar to that from the wild type and could be assembled into the phycobilisome rods. Thus, although phycocyanin levels are reduced in the R2EKM and R2FKM mutants, the remaining phycocyanin seems to be chromophorylated and similar to that in the wild type with respect to phycobilisome rod assembly and energy transfer to the core.

A phosphorylated DNA-binding protein is specific for the red-light signal during complementary chromatic adaptation in cyanobacteria

Complementary chromatic adaptation is a mechanism by which some cyanobacteria that are able to synthesize phycoerythrin can adapt their pigment (phycobiliprotein) content to the incident wavelengths of the light. In Calothrix sp. PCC 7601 it concerns phycoerythrin (cpe operon), synthesized under green light, and phycocyanin-2 (cpc2 operon), expressed under red light, and involves transcriptional controls. With cell-free extracts from Calothrix sp. PCC 7601 grown under various light regimes, a protein designated RcaD was found by gel retardation experiments to specifically bind to the cpc2 promoter region and to be present only in red-light-grown cells. This protein was partially purified and its binding activity was shown to be sensitive to an alkaline phosphatase treatment. RcaD can protect two regions of the cpc2 promoter sequence against degradation by DNase I. Because its activity is detected only under the conditions required for cpc2 expression, we propose that RcaD is a positive effector of transcription.

The complete amino acid sequence of R-phycocyanin-I alpha and beta subunits from the red alga Porphyridium cruentum. Structural and phylogenetic relationships of the phycocyanins within the phycobiliprotein families

We present here the complete primary structure of R-phycocyanin-I alpha and beta subunits from the red alga Porphyridium cruentum. The alpha chain is composed of 162 amino acid residues (18049 Da, calculated from sequence, including chromophore) and carries a phycocyanobilin pigment covalently linked to Cys84. The beta chain contains 172 amino acids (19344Da, calculated from sequence, including chromophores) and carries a phycocyanobilin pigment covalently linked at Cys82 and a phycoerythrobilin pigment at Cys153. A gamma-N-methyl asparagine residue was also characterised at position beta 72 similar to other phycobiliprotein beta subunits. R-phycocyanin-I from Porphyridium cruentum shares high sequence identity with C-phycocyanins (69-83%), R-phycocyanins (66-70%) and in a less extent with phycoerythrocyanins (57-65%) from various sources. The presented phylogenetic trees are based on a comparison of all phycobiliprotein amino acid sequences known so far and confirm the clear affiliation of the R-phycocyanins in the phycocyanin family. In spite of their particular phycobilin pattern, they do not represent intermediate forms between the phycocyanin and the phycoerythrin family. Phycoerythrocyanin, a phycocyanin-related phycobiliprotein adapted to green light harvesting, is also shown to belong to the phycocyanin family. However, the phycoerythrocyanins diverge from phycocyanins in their different function and it is suggested that they should be assigned to a separate group within the phycocyanin family.

Organization and transcription of the genes encoding two differentially expressed phycocyanins in the cyanobacterium Pseudanabaena sp. PCC 7409

The cpc1 and cpc2 operons of the group III chromatically adapting cyanobacterium Pseudanabaena sp. PCC 7409 were isolated and their nucleotide sequences determined. The cpc1 operon consists of the genes cpcB1A1EF and gives rise to an abundant 1400-nucleotide transcript encoding the cpcB1A1 genes and two low-abundance transcripts of 1000 nucleotides and 1100 nucleotides encoding the cpcF gene. Two extremely low-abundance transcripts of approximately 2900 nucleotides and 4800 nucleotides possibly encode cpcB1A1E and cpcB1A1EF, respectively. All transcripts were present in cultures grown in either red or green light. The transcription start of the cpcB1A1 mRNA was mapped to a position 238 bp 5' to the cpcB1 translation start. The cloned fragment containing the cpcB2A2 genes was found to contain only a portion of the cpc2 operon and consisted of the cpcB2A2 genes and the 5' portion of the linker gene cpcH2. On the basis of biochemical evidence, as well as sequence data from other cpc operons, it is probable that the complete Pseudanabaena sp. PCC 7409 cpc2 operon consists of the genes cpcB2A2H2I2D2. This operon is almost exclusively transcribed in cells grown in red light and gives rise to an abundant mRNA 1400 nucleotides in length that encodes the cpcB2A2 genes. A second transcript of 2400 nucleotides encodes the cpcB2A2H2 genes. A third transcript of 3800 nucleotides encodes the cpcB2A2H2 genes and probably the cpcI2 and cpcD2 genes as well. Transcription of the cpc2 mRNAs inititates 219 bp 5' to the cpcB2 translation start. The promoter region of the Pseudanabaena sp. PCC 7409 cpc1 operon contains the sequence 5' ttGTATaa 3' that is also found to occur within 20 bp of the transcription initiation sites of a number of other constitutively expressed cpc promoters. A high level of sequence similarity also occurs between the red-light-inducible cpc2 promoters of Pseudanabaena sp. PCC 7409 and Calothrix sp. PCC 7601.

Regulation of phycobilisome rod proteins and mRNA at different light intensities in the cyanobacterium Synechococcus 6301

The regulation of the light-harvesting antennae, the phycobilisome (Pbs), and the cpcB1A1-cpcH-cpcI-cpcD operon encoding the structural proteins of the Pbs rod, was studied in the cyanobacterium, Synechococcus sp. PCC 6301, when grown at different light intensities (li). Pbs were purified and their linker protein (LP) profiles analyzed on SDS-polyacrylamide gels. At increasing li, the amount of the distal 30-kDa LP decreased prior to any change in the amount of the proximal 33-kDa LP, indicating a sequential increase in the Pbs rod length. While the amount of LP in the rod decreased with increasing li, the levels of the LP mRNAs increased. Post-transcriptional regulation of the expression of the polycistronic cpcB1A1-cpcH-cpcI-cpcD mRNA was inferred from these observations. The half-life of the mRNAs studied was typically found to be 7 min with four exceptions: (1 and 2) the half-lives for the 3.4- and 3.7-kb polycistronic LP mRNAs were 16 and 1 min at the low (lli) and high li (hli), respectively; (3) the half-life of the 1.4-kb cpcB1A1 mRNA was 2 min at lli; and (4) the 1.3-kb cpcB1A1 transcript had a half-life of 10 min at lli. At hli, it was found that the 1.3-kb cpcB1A1 transcript did not start to disappear until the amount of the 1.4-kb cpcB1A1 transcript had reached the level equal to that of the 1.3-kb mRNA, implying that the 1.4-kb transcript might be processed to the 1.3-kb form.

Isolation and characterization of the genes encoding allophycocyanin subunits and two linker proteins from Synechocystis 6714

Genes encoding the phycobilisome core subunits allophycocyanin alpha and beta and a small core linker protein in Synechocystis sp. strain PCC 6714 were cloned and sequenced. These genes form an operon, apcABC, with a single transcription start site and two possible termination sites, one following apcB and the other following apcC. The promoter region, like those of the apcABC operons of other cyanobacteria, does not resemble the consensus promoter sequences of Escherichia coli. However, the apcABC promoters identified in four strains of cyanobacteria have conserved sequences centered at -50 and -10 with respect to the start of transcription. The apcE gene, encoding the protein that links the phycobilisome core to the thylakoid membrane, was also cloned from Synechocystis 6714 and sequenced. It is unlinked to the apcABC operon. As in other Synechocystis strains, the LCM polypeptide encoded by the apcE gene contains three repeats of the basic phycobiliprotein linker domain. The apcE gene promoter sequence bears little resemblance to either the E. coli consensus or the apcABC promoter region, but it is similar to the corresponding regions of other cyanobacterial apcE genes. In these cases, there are conserved sequences centered at -40 and -10 with respect to the transcription start site. These conserved promoter elements from the apcABC and apcE genes were also identified in the corresponding 5'-flanking regions of eleven transcript starts for cpc genes encoding phycocyanin subunits in cyanobacteria and algal chloroplasts. These results suggest that a factor yet to be described participates in transcription of phycobiliprotein genes.

Cloning of the phycobilisome rod linker genes from the cyanobacterium Synechococcus sp. PCC 6301 and their inactivation in Synechococcus sp. PCC 7942

The phycobilisome rod linker genes in the two closely related cyanobacteria Synechococcus sp. PCC 6301 and Synechococcus sp. PCC 7942 were studied. Southern blot analysis showed that the genetic organization of the phycobilisome rod operon is very similar in the two strains. The phycocyanin gene pair is duplicated and separated by a region of about 2.5 kb. The intervening region between the duplicated phycocyanin gene pair was cloned from Synechococcus sp. PCC 6301 and sequenced. Analysis of this DNA sequence revealed the presence of three open reading frames corresponding to 273, 289 and 81 amino acids, respectively. Insertion of a kanamycin resistance cassette into these open reading frames indicated that they corresponded to the genes encoding the 30, 33 and 9 kDa rod linkers, respectively, as judged by the loss of specific linkers from the phycobilisomes of the insertional mutants. Amino acid compositions of the 30 and 33 kDa linkers derived from the DNA sequence were found to deviate from those of purified 33 and 30 kDa linkers in the amounts of glutamic acid/glutamine residues. On the basis of similarity of the amino acid sequence of the rod linkers between Synechococcus sp. PCC 6301 and Calothrix sp. PCC 7601 we name the genes encoding the 30, 33 and 9 kDa linkers cpcH, cpcI and cpcD, respectively. The three linker genes were found to be co-transcribed on an mRNA of 3700 nucleotides. However, we also detected a smaller species of mRNA, of 3400 nucleotides, which would encode only the cpcH and cpcI genes.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization and transcript analysis of the major phycobiliprotein subunit genes from Aglaothamnion neglectum (Rhodophyta)

The genes encoding the alpha and beta subunits of allophycocyanin, phycocyanin and phycoerythrin from the red alga Aglaothamnion neglectum were isolated and characterized. While the operons containing the different phycobiliprotein genes are dispersed on the plastid genome, the genes encoding the alpha and beta subunits for each phycobiliprotein are contiguous. The beta subunit gene is 5' for both the phycocyanin and phycoerythrin operons, while the alpha subunit gene is 5' for the allophycocyanin operon. The amino acid sequences of A. neglectum phycobiliproteins, as deduced from the nucleotide sequences of the genes, are 65-85% identical to analogous proteins from other red algae and cyanobacteria. The conserved nature of the plastid-encoded red algal and cyanobacterial phycobiliprotein genes supports the proposed origin of red algal plastids from cyanobacterial endosymbionts. Many environmental factors effect phycobilisome biosynthesis. The effect of both nutrient availability and light quantity on the level of A. neglectum phycobiliprotein subunits and the mRNA species encoding those subunits is described.

Gas vesicle synthesis in the cyanobacterium Pseudanabaena sp.: occurrence of a single photoregulated gene

Gas vesicles are subcellular inclusions found in a large number of aquatic prokaryotes. The gvpA gene, which frequently occurs as a multigene family, encodes the major gas vesicle structural protein. In several cyanobacteria, another gene, gvpC, encodes a different protein which might be a dispensable element for gas vesicle formation. We report here the molecular characterization of a gvpA gene in Pseudanabaena sp. PCC 6901. In this planktonic cyanobacterium, it is the only gvp gene which could be detected, and electrophoretic analysis of isolated gas vesicles revealed the presence of a single protein. A monocistronic mRNA species corresponds to the transcription of the gvpA gene and the abundance of the gvpA mRNA is inversely correlated with photosynthetic photon flux indicating that a light-dependent transcriptional regulation is likely to be involved in the control of gas vacuolation in this strain.

Genomic integration system based on pBR322 sequences for the cyanobacterium Synechococcus sp. PCC7942: transfer of genes encoding plastocyanin and ferredoxin

Synechococcus sp. PCC7942 recipient strains were constructed for the chromosomal integration of DNA fragments cloned in any pBR322-derived vector, which carries the ampicillin resistance (ApR) marker. The construction was based on the incorporation of specific recombination targets, the so-called 'integration platforms', into the chromosomal metF gene. These platforms consist of an incomplete bla gene (ApS) and the pBR322 ori separated from each other by a gene encoding an antibiotic (streptomycin or kanamycin) resistance (SmR or KmR). Recombination between a pBR322-derived donor plasmid and such a chromosomal platform results with high frequency in restoration of the bla gene and replacement of the chromosomal marker (SmR or KmR) by the insert of the donor plasmid. The integration into the platform depends on recombination between pBR322 ori and bla sequences only and is therefore independent of the DNA insert to be transferred. The desired recombinants are found by selection for a functional bla gene (ApR) and subsequent screening for absence of the chromosomal antibiotic marker. Gene transfer with this integration system was found to occur efficiently and reliably. Furthermore, the presence of the pBR322 ori in the platform allowed for 'plasmid rescue' of integrated sequences. The system was applied successfully for the transfer of the gene encoding plastocyanin (petE1) from Anabaena sp. PCC7937 and for the integration of an extra copy of the gene encoding ferredoxin I (petF1) from Synechococcus sp. PCC7942 itself.

Genes encoding both subunits of phycoerythrocyanin, a light-harvesting biliprotein from the cyanobacterium Mastigocladus laminosus

Phycocyanin (PC) and phycoerythrocyanin (PEC) are light-harvesting components of the phycobilisome (PbS) from the cyanobacterium Mastigocladus laminosus. These two biliproteins are closely related, and show a particularly high degree of sequence homology in the C-terminal part of their beta-subunits. A 198-bp gene fragment encoding this region of PC from M. laminosus was therefore used as a heterologous hybridization probe to identify the genes coding for PEC from the same organism. A 1.7-kb HindIII fragment was cloned and its sequence determined. Three open reading frames (ORFs) were found on this fragment. The gene coding for the beta-subunit of PEC (pecB) was followed downstream by the alpha-subunit encoding gene (pecA). This gene arrangement had also been found in the PC-encoding (cpc) gene pair from M. laminosus, and is conserved in cpc genes from other organisms. This finding is compatible with a model of evolution of the cpc and pec gene pairs as the product of gene duplication of an ancestral beta- and alpha-subunit-encoding pair. A third ORF starts downstream from pecA. It codes for the 34.5-kDa linker protein, which forms complexes with PEC with a 1:6 stoichiometry in the PbS. Biliprotein- and linker protein-encoding genes are frequently clustered, and this provides mechanisms for the production of the different stoichiometric amounts of these gene products required in the PbS and for coregulation by environmental factors.

Structure and mutation of a gene encoding a Mr 33,000 phycocyanin-associated linker polypeptide

The gene encoding a phycocyanin-associated linker polypeptide of Mr 33,000 from the cyanobacterium Synechococcus sp. PCC 7002 was found to be located adjacent and 3' to the genes encoding the alpha and beta subunits of phycocyanin. The identity of this gene, designated cpcC, was proven by matching the amino-terminal sequence of the authentic polypeptide with that predicted by the nucleotide sequence. A cpcC mutant strain of this cyanobacterium was constructed. The effect of the mutation was to prevent assembly of half the total phycocyanin into phycobilisomes. By electron microscopy, phycobilisomes from this mutant were shown to contain rod substructures composed of a single disc of hexameric phycocyanin, as opposed to two discs in the wild type. It was concluded that the Mr 33,000 linker polypeptide is required for attachment of the core-distal phycocyanin hexamer to the core-proximal one. Using absorption spectra of the wild type, CpcC-, and phycocyanin-less phycobilisomes, the in situ absorbances expected for specific phycocyanin-linker complexes were calculated. These data confirm earlier findings on isolated complexes regarding the influence of linkers on the spectroscopic properties of phycocyanin.

Duplication of the phycocyanin operon in the unicellular cyanobacterium Anacystis nidulans R2

Two phycocyanin (PC) operons, each containing alpha- and beta-subunit genes, have been isolated from the unicellular cyanobacterium Anacystis nidulans R2. Using oligodeoxyribonucleotide probes for the PC-coding regions, three PstI fragments were obtained and shown to contain the two operons, which are 2.7 kb apart, with a proposed gene order of 5'-(beta I-alpha I)-(beta II-alpha II)-3'. The nucleotide sequences of both alpha-subunit genes are identical, as are the beta-sequences and the 51-bp intergenic regions. However, significant nucleotide sequence differences are found in both the 5' and 3' untranslated regions of the two operons. Two mRNA species of 1.65 and 1.5 kb were detected in A. nidulans R2 RNA when probed with either the alpha-specific or the beta-specific probe. The results demonstrate the existence of two PC operons which are both transcriptionally active.

DNA sequence and regulation of the gene (cbpA) encoding the 42-kilodalton cytoplasmic membrane carotenoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942

The gene (cbpA) coding for a carotenoid-binding protein of the cyanobacterium Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) has been cloned and sequenced. A polyclonal antibody against the protein was used to identify immunoreactive clones from a lambda gt11 expression library of Synechococcus strain PCC 7942. The initial positive clone (lambda gtAN42) contained a 0.9-kilobase (kb) chromosomal fragment, which was used to detect a larger chromosomal fragment from a lambda EMBL3 library. The lambda EMBL3 recombinant, lambda EM109, contained an 18-kb portion of the Synechococcus strain PCC 7942 chromosome. The open reading frame of cbpA encoded 450 amino acids which give rise to a protein of 49,113 daltons. The hydrophobicity plot indicates that the protein may have a 49-residue signal sequence which is cleaved to yield a mature protein of 43,709 daltons. The protein has been localized in the cytoplasmic membrane by biochemical procedures as well as by electron microscopic immunocytochemistry. Northern (RNA) blot analysis indicates that transcription of cbpA is tightly regulated by DNA topology, light intensity, and iron concentration. Transcription is greatly induced by growth under high light intensities and repressed during growth under iron-deficient conditions. The DNA gyrase inhibitor novobiocin specifically inhibited the light-induced transcription. In Northern blots, the gene-specific probe hybridized to two size classes of RNA, with lengths of 2.0 and 6.2 kb. Since cbpA appears to be a component of the 6.2-kb transcript, it is likely part of a larger operon.

Genetic analysis of phycobilisome mutants in the cyanobacterium Synechococcus species PCC 6301

The chromophoric protein phycocyanin is the major protein in the phycobilisome rod of the cyanobacterium Synechococcus 6301 (formerly designated Anacystis nidulans sp. UTEX 625). The gene clusters coding for the beta- and alpha-subunits of phycocyanin are duplicated on the chromosome of Synechococcus 6301 and separated by an intergenic region 2.5 kb long. The structure of the phycocyanin operons of the phycobilisome mutant strains AN112 and AN135 was compared to that of wild-type Synechococcus 6301. Both mutants have an altered phycobilisome structure resulting in the appearance of rods of a shorter overall length. Genetic mapping indicated that the mutant strain AN112 completely lacked the intergenic region and carried only one set of phycocyanin subunit genes. No gross structural difference in the genetic organization of the corresponding region of mutant strain AN135 was detected. Northern blot analysis and primer extension experiments were used to monitor the transcriptional pattern of the phycocyanin rod operon. It was found that AN112 had lost the 3.7kb minor mRNA, which covers the intergenic region, and only produced two major 1.3 and 1.4kb mRNA species. These transcripts were identified as fusion products of the 5' end of the transcriptional unit originating from the promoter region of the left-hand phycocyanin gene cluster and the 3' end of the transcriptional unit covering the right-hand phycocyanin gene cluster. The mutant strain AN135 had a transcriptional pattern very similar to that of the wild type. The level of transcription of the major transcripts covering the phycocyanin gene clusters was similar in the wild-type and mutant strains.(ABSTRACT TRUNCATED AT 250 WORDS)

Genetic relationship of two highly studied Synechococcus strains designated Anacystis nidulans

The cyanobacteria Synechococcus sp. strain PCC 7942 and Synechococcus sp. strain PCC 6301 are very closely related and both have been designated by the binomial Anacystis nidulans. The only established difference between the two strains is the superior transformation properties of strain PCC 7942. Significant homology between the rRNA genes of these strains was demonstrated by the ability of an rRNA operon from strain PCC 6301, interrupted by a spectinomycin and streptomycin resistance marker, to transform strain PCC 7942 by recombining with and replacing an endogenous rRNA operon. Restriction fragment length polymorphism data indicated that the chromosomes of the two strains were conserved around the three psbA loci, the two rRNA operons, and the psbDI locus. However, multiple polymorphisms were detected downstream of the psbDII locus, identifying a DNA rearrangement such as an inversion, insertion, or deletion within the chromosome. Analysis of genome structure by pulsed-field gel electrophoresis of large NotI restriction fragments showed only two bands that were visibly shifted between the chromosomes of the two strains. These data support their very close genetic relationship and the feasibility of studying genes derived from strain PCC 6301 in the highly transformable PCC 7942 strain.