Cyanobacterial light-harvesting complex subunits encoded in two red light-induced transcripts

Responding to light signals: a comprehensive update on photomorphogenesis in cyanobacteria

Cyanobacteria are ancestors of chloroplast and perform oxygen-evolving photosynthesis similar to higher plants and algae. However, an obligatory requirement of photons for their growth results in the exposure of cyanobacteria to varying light conditions. Therefore, the light environment could act as a signal to drive the developmental processes, in addition to photosynthesis, in cyanobacteria. These Gram-negative prokaryotes exhibit characteristic light-dependent developmental processes that maximize their fitness and resource utilization. The development occurring in response to radiance (photomorphogenesis) involves fine-tuning cellular physiology, morphology and metabolism. The best-studied example of cyanobacterial photomorphogenesis is chromatic acclimation (CA), which allows a selected number of cyanobacteria to tailor their light-harvesting antenna called phycobilisome (PBS). The tailoring of PBS under existing wavelengths and abundance of light gives an advantage to cyanobacteria over another photoautotroph. In this work, we will provide a comprehensive update on light-sensing, molecular signaling and signal cascades found in cyanobacteria. We also include recent developments made in other aspects of CA, such as mechanistic insights into changes in the size and shape of cells, filaments and carboxysomes.

Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis

Chromatic acclimation (CA) encompasses a diverse set of molecular processes that involve the ability of cyanobacterial cells to sense ambient light colors and use this information to optimize photosynthetic light harvesting. The six known types of CA, which we propose naming CA1 through CA6, use a range of molecular mechanisms that likely evolved independently in distantly related lineages of the Cyanobacteria phylum. Together, these processes sense and respond to the majority of the photosynthetically relevant solar spectrum, suggesting that CA provides fitness advantages across a broad range of light color niches. The recent discoveries of several new CA types suggest that additional CA systems involving additional light colors and molecular mechanisms will be revealed in coming years. Here we provide a comprehensive overview of the currently known types of CA and summarize the molecular details that underpin CA regulation.

Emerging perspectives on the mechanisms, regulation, and distribution of light color acclimation in cyanobacteria

Chromatic acclimation (CA) provides many cyanobacteria with the ability to tailor the properties of their light-harvesting antennae to the spectral distribution of ambient light. CA was originally discovered as a result of its dramatic cellular phenotype in red and green light. However, discoveries over the past decade have revealed that many pairs of light colors, ranging from blue to infrared, can trigger CA responses. The capacity to undergo CA is widespread geographically, occurs in most habitats around the world, and is found within all major cyanobacterial groups. In addition, many other cellular activities have been found to be under CA control, resulting in distinct physiological and morphological states for cells under different light-color conditions. Several types of CA appear to be the result of convergent evolution, where different strategies are used to achieve the final goal of optimizing light-harvesting antenna composition to maximize photon capture. The regulation of CA has been found to occur primarily at the level of RNA abundance. The CA-regulatory pathways uncovered thus far are two-component systems that use phytochrome-class photoreceptors with sensor-kinase domains to control response regulators that function as transcription factors. However, there is also at least one CA-regulatory pathway that operates at the post-transcriptional level. It is becoming increasingly clear that large numbers of cyanobacterial species have the capacity to acclimate to a wide variety of light colors through the use of a range of different CA processes.

Sulfate-driven elemental sparing is regulated at the transcriptional and posttranscriptional levels in a filamentous cyanobacterium

Sulfur is an essential nutrient that can exist at growth-limiting concentrations in freshwater environments. The freshwater cyanobacterium Fremyella diplosiphon (also known as Tolypothrix sp. PCC 7601) is capable of remodeling the composition of its light-harvesting antennae, or phycobilisomes, in response to changes in the sulfur levels in its environment. Depletion of sulfur causes these cells to cease the accumulation of two forms of a major phycobilisome protein called phycocyanin and initiate the production of a third form of phycocyanin, which possesses a minimal number of sulfur-containing amino acids. Since phycobilisomes make up approximately 50% of the total protein in these cells, this elemental sparing response has the potential to significantly influence the fitness of this species under low-sulfur conditions. This response is specific for sulfate and occurs over the physiological range of sulfate concentrations likely to be encountered by this organism in its natural environment. F. diplosiphon has two separate sulfur deprivation responses, with low sulfate levels activating the phycobilisome remodeling response and low sulfur levels activating the chlorosis or bleaching response. The phycobilisome remodeling response results from changes in RNA abundance that are regulated at both the transcriptional and posttranscriptional levels. The potential of this response, and the more general bleaching response of cyanobacteria, to provide sulfur-containing amino acids during periods of sulfur deprivation is examined.

Functional characterization of a cyanobacterial OmpR/PhoB class transcription factor binding site controlling light color responses

Complementary chromatic acclimation (CCA) allows many cyanobacteria to change the composition of their light-harvesting antennae for maximal absorption of different wavelengths of light. In the freshwater species Fremyella diplosiphon, this process is controlled by the ratio of red to green light and allows the differential regulation of two subsets of genes in the genome. This response to ambient light color is controlled in part by a two-component system that includes a phytochrome class photoreceptor and a response regulator with an OmpR/PhoB class DNA binding domain called RcaC. During growth in red light, RcaC is able to simultaneously activate expression of red light-induced genes and repress expression of green light-induced genes through binding to the L box promoter element. Here we investigate how the L box functions as both an activator and a repressor under the same physiological conditions by analyzing the effects of changing the position, orientation, and sequence of the L box. We demonstrate that changes in the local sequences surrounding the L box affect the strength of its activity and that the activating and repressing functions of the L box are orientation dependent. Also, the spacing between the L box and the transcription start site is critical for it to work as an activator, while its repressing role during light regulation requires additional upstream and downstream DNA sequence elements. The latter result suggests that the repressing function of RcaC requires it to operate in association with multiple additional DNA binding proteins, at least one of which is functioning as an activator.

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.

A light regulated OmpR-class promoter element co-ordinates light-harvesting protein and chromophore biosynthetic enzyme gene expression

Co-ordination of chromophore and apoprotein biosynthesis is required during photosynthetic light-harvesting antennae production, such as occurs during complementary chromatic adaptation (CCA). This response to ambient light colour changes is controlled by a phytochrome-class photoreceptor and involves changes in the synthesis of cyanobacterial light-harvesting antennae. During growth in red light, CCA activates cpc2 transcription, an operon that encodes the light-harvesting protein phycocyanin. In order to function, this apoprotein must have covalently attached phycocyanobilin chromophores, which are synthesized by PcyA. We show that pcyA is also transcriptionally activated by CCA during red light growth and is not regulated via feedback that senses cpc2 RNA levels. The pcyA and cpc2 promoters contain a common regulatory element, a direct repeat typical of OmpR-class transcription factor binding sites, at similar positions relative to their red light-controlled transcription start sites. Deletion of this element from the pcyA promoter eliminated CCA-regulated transcription, and insertion of the element into a non-light responsive promoter conferred CCA regulation. We conclude that this element is necessary and sufficient to confer CCA transcriptional regulation and that it co-ordinates phycocyanin and phycocyanobilin biosynthesis in red light.

Responding to color: the regulation of complementary chromatic adaptation

The acclimation of photosynthetic organisms to changes in light color is ubiquitous and may be best illustrated by the colorful process of complementary chromatic adaptation (CCA). During CCA, cyanobacterial cells change from brick red to bright blue green, depending on their light color environment. The apparent simplicity of this spectacular, photoreversible event belies the complexity of the cellular response to changes in light color. Recent results have shown that the regulation of CCA is also complex and involves at least three pathways. One is controlled by a phytochrome-class photoreceptor that is responsive to green and red light and a complex two-component signal transduction pathway, whereas another is based on sensing redox state. Studies of CCA are uncovering the strategies used by photosynthetic organisms during light acclimation and the means by which they regulate these responses.

In vivo analysis of the roles of conserved aspartate and histidine residues within a complex response regulator

RcaC is the founding member of a group of large response regulators with complex domain combinations containing at least two receiver domains, an OmpR-class winged helix-turn-helix DNA binding domain, and a histidine phosphotransfer (HPt) domain. Within its two receiver and HPt domains, RcaC contains consensus phosphorylation sites at aspartates 51, 576 and histidine 316. RcaC operates in the pathway regulating transcription of genes encoding components of photosynthetic light harvesting antenna to changes in light colour. We show that phycocyanin gene expression requires RcaC. RcaC contributes to light regulation of phycoerythrin genes, but is not part of the second light regulation pathway controlling these genes. Substitutions at aspartate 51 or histidine 316 severely impaired light responsiveness while substitutions at aspartate 576 had little effect. Complete loss of light regulation, measured by phycocyanin gene expression, only occurred in the triple mutant. We conclude that aspartate 51 primarily controls light colour responsiveness and is regulated by histidine 316, and that these residues are likely phosphorylated in red light and dephosphorylated in green light. The carboxy-terminal receiver domain has a minor role in controlling this response. RcaC abundance is also light regulated and depends on aspartate 51 and histidine 316, but not aspartate 576.

Genomic DNA microarray analysis: identification of new genes regulated by light color in the cyanobacterium Fremyella diplosiphon

Many cyanobacteria use complementary chromatic adaptation to efficiently utilize energy from both green and red regions of the light spectrum during photosynthesis. Although previous studies have shown that acclimation to changing light wavelengths involves many physiological responses, research to date has focused primarily on the expression and regulation of genes that encode proteins of the major photosynthetic light-harvesting antennae, the phycobilisomes. We have used two-dimensional gel electrophoresis and genomic DNA microarrays to expand our understanding of the physiology of acclimation to light color in the cyanobacterium Fremyella diplosiphon. We found that the levels of nearly 80 proteins are altered in cells growing in green versus red light and have cloned and positively identified 17 genes not previously known to be regulated by light color in any species. Among these are homologs of genes present in many bacteria that encode well-studied proteins lacking clearly defined functions, such as tspO, which encodes a tryptophan-rich sensory protein, and homologs of genes encoding proteins of clearly defined function in many species, such as nblA and chlL, encoding phycobilisome degradation and chlorophyll biosynthesis proteins, respectively. Our results suggest novel roles for several of these gene products and highly specialized, unique uses for others.

CotB is essential for complete activation of green light-induced genes during complementary chromatic adaptation in Fremyella diplosiphon

The dramatic modifications of photosynthetic light harvesting antennae called phycobilisomes that occur during complementary chromatic adaptation in cyanobacteria are controlled by two separate photosensory systems. The first system involves the signal transduction components RcaE, RcaF and RcaC, which appear to make up a complex multistep phosphorelay. This system controls the light responsive expression of the cpcB2A2H2I2D2, cpeBA and cpeCDE operons, which encode phycobilisome proteins. The second system, which is not yet characterized, acts in concert with the first but only regulates the light responses of cpeBA and cpeCDE. We have generated and characterized a new mutant class, named the Tan mutants. In at least one member of this class, light-regulated RNA accumulation patterns are altered for cpeBA and cpeCDE, but not for cpcB2A2H2I2D2. Thus this mutant contains a lesion that may impair the operation of the second system. We demonstrate that several Tan mutants are the result of improper expression of the gene cotB. CotB has limited similarity to lyase class proteins, particularly those related to NblB, which is required for degradation of phycobilisomes in other cyanobacteria. Possible roles of CotB in the biogenesis of phycobilisomes are discussed.

CpeR is an activator required for expression of the phycoerythrin operon (cpeBA) in the cyanobacterium Fremyella diplosiphon and is encoded in the phycoerythrin linker-polypeptide operon (cpeCDESTR)

In the cyanobacteria, phycobilisomes are assembled from (alphabeta)(6) hexamers of the coloured phycobiliproteins, allophycocyanin, phycocyanin and phycoerythrin (PE). The precise architecture of the phycobilisome is determined by the various colourless linker proteins that bind to the biliprotein hexamers. Genes for beta and alpha subunits of PE make up one operon (cpeBA), whereas genes for PE-associated linker polypeptides are in a second operon. In the chromatically adapting cyanobacterium Fremyella diplosiphon green light is required for the transcription of both cpeBA and the operon encoding the PE-associated linkers (cpeCDE). From the genome of F. diplosiphon we have identified an open reading frame, cpeR, which, when expressed from a shuttle plasmid, is capable of suppressing various mutations that cause a decrease in PE synthesis. The introduction of a shuttle plasmid bearing cpeR+ into wild-type F. diplosiphon caused PE expression in red light. Fremyella diplosiphon cpeR-, created by in vitro mutagenesis and in vivo homologous recombination, is fully PE and, in this strain, cpeCDE is transcribed normally whereas the transcript from cpeBA is undetectable. Polymerase chain reaction (PCR) amplification of cDNA showed that cpeR is transcribed as part of the cpeCDE operon on an extended transcript. As CpeR is an activator required for expression of the cpeBA operon, we propose that at the onset of green light the operons cpeCDESTR and cpeBA are expressed in series as a genetic cascade.

Co-ordinated expression of phycobiliprotein operons in the chromatically adapting cyanobacterium Calothrix PCC 7601: a role for RcaD and RcaG

In the cyanobacterium Calothrix sp. PCC 7601 the cpc2 operon encoding phycocyanin 2 (PC2) is expressed if red radiations are available. RcaD was previously identified in extracts from red-light-grown cells as an alkaline phosphatase-sensitive protein that binds upstream of the transcription start point (TSP) of the cpc2 operon. In this work, RcaD was purified, and the corresponding gene cloned with a PCR probe obtained using degenerated primers based on RcaD peptide sequences (accession no. AJ319541). Purified RcaD binds to the cpc2 promoter region and also to those of the constitutive cpc1 and apc1 operons that encode phycocyanin 1 and allophycocyanin. Escherichia coli-overexpressed RcaD can bind to the cpc2 promoter region. The rcaD gene is upstream of an open reading frame (ORF) termed rcaG. Co-transcription of both genes was demonstrated by reverse transcription (RT)-PCR experiments, and found to be independent of the light wavelengths. A single TSP was mapped. Sequence features of RcaD and RcaG led us to propose a functional relationship between these two proteins. A rcaD mutant generated by allelic exchange exhibited altered expression of the cpc2, cpeBA, apc1 and cpc1 operons upon green to red-light shifts. RcaD seems to be a co-activator co-ordinating the transcription of the phycobiliprotein operons upon changes in light spectral quality.

A turquoise mutant genetically separates expression of genes encoding phycoerythrin and its associated linker peptides

During complementary chromatic adaptation (CCA), cyanobacterial light harvesting structures called phycobilisomes are restructured in response to ambient light quality shifts. Transcription of genes encoding components of the phycobilisome is differentially regulated during this process: red light activates cpcB2A2, whereas green light coordinately activates the cpeCDE and cpeBA operons. Three signal transduction components that regulate CCA have been isolated to date: a sensor-photoreceptor (RcaE) and two response regulators (RcaF and RcaC). Mutations in the genes encoding these components affect the accumulation of both cpcB2A2 and cpeBA gene products. We have isolated and characterized a new pigmentation mutant called Turquoise 1. We demonstrate that this mutant phenotype is due to a dramatic decrease in cpeBA transcript abundance and results from a lesion in the cpeR gene. However, in this mutant cpeCDE RNA levels remain near those found in wild-type cells. Our results show that the coordinate regulation of cpeBA and cpeCDE by green light can be uncoupled by the loss of CpeR, and we furnish the first genetic evidence that different regulatory mechanisms control these two operons. Sequence analysis of CpeR reveals that it shares limited sequence similarity to members of the PP2C class of protein serine/threonine phosphatases. We also demonstrate that cpeBA and cpeCDE retain light quality responsiveness in a mutant lacking the RcaE photoreceptor. This provides compelling evidence for the partial control of CCA through an as-yet-uncharacterized second light quality sensing system.

Differential expression of photosynthesis and nitrogen fixation genes in the cyanobacterium Plectonema boryanum

The filamentous non-heterocystous cyanobacterium Plectonema boryanum fixes dinitrogen at a high rate during microaerobic growth in continuous illumination by temporal separation of oxygen-evolving photosynthesis and oxygen-sensitive dinitrogen fixation. The onset of nitrogen fixation is preceded by a depression in photosynthesis that establishes a sufficiently low level of dissolved oxygen in the growth medium. A several-fold reduction in the level of transcripts coding for phycocyanin (cpcBA) and the chlorophyll a binding protein of photosystem II (psbC) and psbA accompanied the depression in photosynthetic oxygen evolution. Unlike most of the other organisms examined to date, in P. boryanum, psbC and psbD do not appear to be co-transcribed. The psbC transcripts were down-regulated several fold, while the psbD transcript declined marginally during the nitrogen fixation phase. A decrease in dissolved oxygen and a dramatic increase in the level of nifH transcripts and the enzyme activity of nitrogenase were characteristic of the nitrogen fixation phase. The level of transcript for glnA, which encodes glutamine synthetase, was not altered. Reciprocal regulation of gene expression was well orchestrated with the alternating cycles of photosynthesis and nitrogen fixation in P. boryanum.

Suppression of mutants aberrant in light intensity responses of complementary chromatic adaptation

Complementary chromatic adaptation is a process in which cyanobacteria alter the pigment protein (phycocyanin and phycoerythrin) composition of their light-harvesting complexes, the phycobilisomes, to help optimize the absorbance of prevalent wavelengths of light in the environment. Several classes of mutants that display aberrant complementary chromatic adaptation have been isolated. One of the mutant classes, designated "blue" or FdB, accumulates high levels of the blue chromoprotein phycocyanin in low-intensity green light, a condition that normally suppresses phycocyanin synthesis. We demonstrate here that the synthesis of the phycocyanin protein and mRNA in the FdB mutants can be suppressed by increasing the intensity of green light. Hence, these mutants have a decreased sensitivity to green light with respect to suppression of phycocyanin synthesis. Although we were unable to complement the blue mutants, we did isolate genes that could suppress the mutant phenotype. These genes, which have been identified previously, encode a histidine kinase sensor and response regulator protein that play key roles in controlling complementary chromatic adaptation. These findings are discussed with respect to the mechanism by which light quality and quantity control the biosynthesis of the phycobilisome.

New classes of mutants in complementary chromatic adaptation provide evidence for a novel four-step phosphorelay system

Complementary chromatic adaptation appears to be controlled by a complex regulatory system with similarity to four-step phosphorelays. Such pathways utilize two histidine and two aspartate residues for signal transduction. Previous studies of the signaling system controlling complementary chromatic adaptation have uncovered two elements of this pathway, a putative sensor, RcaE, and a response regulator, RcaC. In this work, we describe a second response regulator controlling complementary chromatic adaptation, RcaF, and identify putative DNA binding and histidine phosphoacceptor domains within RcaC. RcaF is a small response regulator with similarity to SpoOF of Bacillus subtilis; the latter functions in the four-step phosphorelay system controlling sporulation. We have also determined that within this phosphorelay pathway, RcaE precedes RcaF, and RcaC is probably downstream of RcaE and RcaF. This signal transduction pathway is novel because it appears to use at least five, instead of four, phosphoacceptor domains in the phosphorelay circuit.

Bradyrhizobium japonicum does not require alpha-ketoglutarate dehydrogenase for growth on succinate or malate

The sucA gene, encoding the E1 component of alpha-ketoglutarate dehydrogenase, was cloned from Bradyrhizobium japonicum USDA110, and its nucleotide sequence was determined. The gene shows a codon usage bias typical of non-nif and non-fix genes from this bacterium, with 89.1% of the codons being G or C in the third position. A mutant strain of B. japonicum, LSG184, was constructed with the sucA gene interrupted by a kanamycin resistance marker. LSG184 is devoid of alpha-ketoglutarate dehydrogenase activity, indicating that there is only one copy of sucA in B. japonicum and that it is completely inactivated in the mutant. Batch culture experiments on minimal medium revealed that LSG184 grows well on a variety of carbon substrates, including arabinose, malate, succinate, beta-hydroxybutyrate, glycerol, formate, and galactose. The sucA mutant is not a succinate auxotroph but has a reduced ability to use glutamate as a carbon or nitrogen source and an increased sensitivity to growth inhibition by acetate, relative to the parental strain. Because LSG184 grows well on malate or succinate as its sole carbon source, we conclude that B. japonicum, unlike most other bacteria, does not require an intact tricarboxylic acid (TCA) cycle to meet its energy needs when growing on the four-carbon TCA cycle intermediates. Our data support the idea that B. japonicum has alternate energy-yielding pathways that could potentially compensate for inhibition of alpha-ketoglutarate dehydrogenase during symbiotic nitrogen fixation under oxygen-limiting conditions.

Cyanobacterial protein with similarity to the chlorophyll a/b binding proteins of higher plants: evolution and regulation

We have isolated, from the prokaryotic cyanobacterium Synechococcus sp. strain PCC 7942, a gene encoding a protein of 72 amino acids [designated high light inducible protein (HLIP)] with similarity to the extended family of eukaryotic chlorophyll a/b binding proteins (CABs). HLIP has a single membrane-spanning alpha-helix, whereas both the CABs and the related early light inducible proteins have three membrane-spanning helices. Hence, HLIP may represent an evolutionary progenitor of the eukaryotic members of the CAB extended family. We also show that the gene encoding HLIP is induced by high light and blue/UV-A radiation. The evolution, regulation, and potential function of HLIP are discussed.

In vivo and in vitro characterization of the light-regulated cpcB2A2 promoter of Fremyella diplosiphon

When exposed to different spectral qualities of light, many cyanobacteria dramatically alter their phycobilisome rod composition in a process termed complementary chromatic adaptation. In the cyanobacterium Fremyella diplosiphon, this response is associated with differential expression of the cpcB2A2, cpeBA, and cpeCDE operons, which code for the phycobiliproteins phycocyanin and phycoerythrin and the phycoerythrin linker polypeptides, respectively. To define components of the signal transduction pathway involved in light-regulated expression of genes encoding phycobilisome polypeptides, we have used in vivo and in vitro techniques to identify cis-acting sequences and trans-acting factors necessary for the regulation of the red-light-inducible cpcB2A2 operon. Deletion of the cpcB2A2 upstream sequences to -76 bp with respect to the transcription start site had no effect on red-light induction of a cpcB2A2-beta-glucuronidase (GUS) chimeric gene, while deletion to -37 bp abolished GUS expression. Furthermore, a fragment of the cpcB2A2 gene from -76 to +25 bp linked to the untranslated leader of cpcB1A1 (a constitutively expressed operon encoding phycocyanin) is sufficient to drive high-level GUS expression in red light. Therefore, the sequence between positions -76 and -37 is necessary for the expression of cpcB2A2, and the region extending from -76 to +25 is sufficient for red-light induction of the operon. Attempts were made to correlate the in vivo data with protein binding in the region upstream of the transcription start site of cpcB2A2. Using in vitro analysis, we detected two protein-binding sites in the cpcB2A2 promoter which were localized to positions -162 to -122 and -37 to +25. Proteins from both red- and green-light-grown cells interacted with the former site, while only proteins present in extracts from red-light-grown cells interacted with the latter site. The data from both the in vivo and in vitro analyses suggest that while two regions upstream of the cpcB2A2 transcription initiation site specifically bind proteins, only the binding site bordering the transcription start site is important for complementary chromatic adaptation.

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.

Characterization of gene clusters encoding the fucoxanthin chlorophyll proteins of the diatom Phaeodactylum tricornutum

We are studying the multigene family encoding the fucoxanthin-chlorophyll binding proteins (fcp genes) that constitute the major component of the photosystem II-associated light harvesting complex in diatoms and brown algae. The characteristics of clusters of fcp genes on the genome of the diatom Phaeodactylum tricornutum are described. Sequence analysis of two genomic clones, PT5 and PT4, has demonstrated the presence of four fcp genes (fcpA, fcpB, fcpC, fcpD) on the former and two fcp genes (fcpE, fcpF) on the latter. The proteins encoded by the six characterized fcp genes range in similarity from 86% to 99%. The genes within each cluster are separated by short intergenic sequences (between 0.5 to 1.1 kb). None of these genes contain introns and all appear to be transcribed with short 5' transcribed, untranslated leader sequences; the transcription initiation sites were mapped 26 to 48 bases upstream of the ATG translation start site. Small conserved motifs are found among all of the genes just upstream of both the translation and the transcription start sites. The codon bias is similar in all of the fcp genes, with a predominance of pyrimidines in the third positions of codons of the four codon families. The two fcp genes that are most similar are fcpC and fcpD, and might represent a recent gene duplication. Southern analyses using fcp cDNAs as hybridization probes suggest that there may be additional sequences on the P. tricornutum genome that resemble the characterized fcp sequences.

The phycobilisome, a light-harvesting complex responsive to environmental conditions

Photosynthetic organisms can acclimate to their environment by changing many cellular processes, including the biosynthesis of the photosynthetic apparatus. In this article we discuss the phycobilisome, the light-harvesting apparatus of cyanobacteria and red algae. Unlike most light-harvesting antenna complexes, the phycobilisome is not an integral membrane complex but is attached to the surface of the photosynthetic membranes. It is composed of both the pigmented phycobiliproteins and the nonpigmented linker polypeptides; the former are important for absorbing light energy, while the latter are important for stability and assembly of the complex. The composition of the phycobilisome is very sensitive to a number of different environmental factors. Some of the filamentous cyanobacteria can alter the composition of the phycobilisome in response to the prevalent wavelengths of light in the environment. This process, called complementary chromatic adaptation, allows these organisms to efficiently utilize available light energy to drive photosynthetic electron transport and CO2 fixation. Under conditions of macronutrient limitation, many cyanobacteria degrade their phycobilisomes in a rapid and orderly fashion. Since the phycobilisome is an abundant component of the cell, its degradation may provide a substantial amount of nitrogen to nitrogen-limited cells. Furthermore, degradation of the phycobilisome during nutrient-limited growth may prevent photodamage that would occur if the cells were to absorb light under conditions of metabolic arrest. The interplay of various environmental parameters in determining the number of phycobilisomes and their structural characteristics and the ways in which these parameters control phycobilisome biosynthesis are fertile areas for investigation.

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.

Environmental effects on the light-harvesting complex of cyanobacteria

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Characterization of a light-regulated gene encoding a new phycoerythrin-associated linker protein from the cyanobacterium Fremyella diplosiphon

Cyanobacteria utilize multimeric protein complexes, the phycobilisomes, as their major light-harvesting antennae. Associated with the chromophorylated phycobiliproteins in these complexes are nonpigmented proteins, designated linker proteins. These linker proteins are believed to mediate assembly of the phycobilisome and energy transfer to the photosynthetic reaction center. We cloned and sequenced a gene, cpeE, encoding a previously uncharacterized linker protein which is expressed in green light in Fremyella diplosiphon. This gene is part of an operon containing two other phycoerythrin-associated linker genes, cpeC and cpeD. Transcription of the cpeCDE operon in green light results in two predominant species of mRNA of approximately 2,100 and 3,200 nucleotides. The shorter transcript encodes only CpeC and CpeD, while the longer contains the coding regions for all three linker proteins. By altering the pH of the resolving gel and the running buffer during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, this third linker protein CpeE can be resolved from the rod-core linker and the other rod linker proteins. The three proteins have an overall similarity of approximately 62%, and the genes encoding the three proteins are approximately 59% identical.

Molecular cloning and transcriptional analysis of the cpeBA operon of the cyanobacterium Pseudanabaena species PCC7409

The cpeBA operon of the Group III chromatically adapting cyanobacterium Pseudanabaena species PCC 7409 was cloned, sequenced and characterized. The cpeBA genes are transcribed in green-light-grown cells as an abundant 1400-nucleotide mRNA which initiates 69 nucleotides upstream from the cpeB translation start. Extensive sequence identity, extending 70 nucleotides 5' to the transcription start, occurs among cpeBA promoters of Group II and III chromatic adapters. Cell extracts of green-light-grown Calothrix species PCC 7601 contain an activity which specifically binds a restriction fragment containing the Pseudanabanea species PCC 7409 cpeBA promoter. Green-light-dependent cpeBA transcription in Group II and III chromatically adapting cyanobacteria is suggested to be similarly controlled by a transcriptional activator.

Isolation, transcription, and inactivation of the gene for an atypical alkaline phosphatase of Synechococcus sp. strain PCC 7942

The alkaline phosphatase of Synechococcus sp. strain PCC 7942 is 145 kDa, which is larger than any alkaline phosphatase previously characterized and approximately three times the size of the analogous enzyme in Escherichia coli. The gene for the alkaline phosphatase, phoA, was cloned and sequenced, and the protein that it encodes was found to have little similarity to other phosphatases. Some sequence similarities were observed between the Synechococcus sp. strain PCC 7942 alkaline phosphatase, the alpha subunit of the ATPase from bacteria and chloroplasts, and the UshA sugar hydrolase of E. coli. Also, limited sequence similarity was observed between a region of the phosphatase and a motif implicated in nucleotide binding. Interestingly, although the alkaline phosphatase is transported across the inner cytoplasmic membrane and into the periplasmic space, it does not appear to have a cleavable signal sequence at its amino terminus. The half-life of the mRNA encoding the alkaline phosphatase, measured after inhibition of RNA synthesis, is approximately 5 min. Similar kinetics for the loss of alkaline phosphatase mRNA occur upon the addition of phosphate to phosphate-depleted cultures, suggesting that high levels of this nutrient inhibit transcription from phoA almost immediately. The phoA gene also appears to be the first gene of an operon; the largest detectable transcript that hybridizes to a phoA gene-specific probe is 11 kb, over twice the size needed to encode the mature protein. Other phosphate-regulated mRNAs are also transcribed upstream of the phoA gene. Insertional inactivation of phoA results in the loss of extracellular, phosphate-regulated phosphatase activity but does not alter the capacity of the cell for phosphate uptake.

Use of a transposon with luciferase as a reporter to identify environmentally responsive genes in a cyanobacterium

Anabaena, a filamentous cyanobacterium, is of developmental interest because, when deprived of fixed nitrogen, it shows patterned differentiation of N2-fixing cells called heterocysts. To help elucidate its early responses to a decrease in nitrogen, we used a derivative of transposon Tn5 to generate transcriptional fusions of promoterless bacterial luciferase genes, luxAB, to the Anabaena genome. Genes that responded to removal of fixed nitrogen or to other environmental shifts by increased or decreased transcription were identified by monitoring the luminescence of colonies from transposon-generated libraries. The Tn5 derivative transposed in Anabaena at ca. 1-4 x 10(-5) per cell and permitted high-resolution mapping of its position and orientation in the genome and facile cloning of contiguous genomic DNA.

Characterization and mutagenesis of sulfur-regulated genes in a cyanobacterium: evidence for function in sulfate transport

A sulfur-regulated gene (cysA) that encodes the membrane-associated ATP-binding protein of the sulfate transport system of the cyanobacterium Synechococcus sp. strain PCC 7942 was recently isolated and sequenced. Adjacent to cysA and transcribed in the opposite direction is a gene encoding the sulfate-binding protein (sbpA). Two other genes, cysT and cysW, encode proteins that may form a channel for the transport of sulfate across the cytoplasmic membrane. A fourth gene, cysR, located between cysT, and cysW, encodes a polypeptide that has some homology to a family of prokaryotic regulatory proteins. Mutant strains in which cysA, cysT, or cysW was interrupted by a drug resistance marker were not viable when grown with sulfate as the sole sulfur source and exhibited essentially no sulfate uptake. In contrast, sbpA and cysR mutants grew on sulfate, although they did not exhibit the 20-fold increase in the Vmax (concentration of sulfate at half-maximal transport rate) for sulfate transport characteristic of wild-type cells grown under sulfur-limiting conditions. Three of the sulfur-regulated genes in Synechococcus sp. strain PCC 7942 are similar to genes encoded by the chloroplast genome of the primitive plant Marchantia polymorpha. These data suggest that a sulfate transport system similar to that of Synechococcus sp. strain PCC 7942 may exist in the chloroplast envelope of photosynthetic eukaryotes.

Isolation and characterization of a sulfur-regulated gene encoding a periplasmically localized protein with sequence similarity to rhodanese

During sulfur-limited growth, the cyanobacterium Synechococcus sp. strain PCC 7942 loses most of its photosynthetic pigments and develops an increased capacity to acquire sulfate. Sulfur deprivation also triggers the synthesis of several soluble polypeptides. We have isolated a prominent polypeptide of 33 kDa that accumulates specifically under sulfur-limiting conditions. This polypeptide was localized to the periplasmic space. The gene for this protein (designated rhdA) was isolated and discovered to lie within a region of the Synechococcus sp. strain PCC 7942 genome that encodes components of the sulfate permease system. The mRNA for the 33-kDa protein accumulates to high levels within an hour after the cells are deprived of sulfur and drops rapidly when sulfur is added back to the cultures. The amino acid sequence of the protein has similarity to bovine liver rhodanese, an enzyme that transfers the thiol group of thiosulfate to a thiophilic acceptor molecule, and a rhodaneselike protein of Saccharopolyspora erythraea. A strain in which rhdA was interrupted by a drug resistance marker exhibited marginally lower levels of rhodanese activity but was still capable of efficiently utilizing a variety of inorganic sulfur sources. The possible role of this protein in the transport of specific sulfur compounds is discussed.

Isolation, crystallization, crystal structure analysis and refinement of constitutive C-phycocyanin from the chromatically adapting cyanobacterium Fremyella diplosiphon at 1.66 A resolution

Constitutive phycocyanin from cyanobacterium Fremyella diplosiphon (Calothrix sp. PCC 7601) grown in green light, has been isolated and crystallized. The crystals belong to the space group R3 with cell constants a = b = 180.26 A, c = 61.24 A, alpha = beta = 90 degrees, gamma = 120 degrees. The crystal structure has been determined by Patterson search techniques using the molecular model of C-phycocyanin from the cyanobacterium Agmenellum quadruplicatum. The asymmetric unit of the crystal cell consists of two (alpha beta)-monomers related by a local dyad. Three asymmetric units are arranged around a crystallographic triad and form an (alpha beta)6-hexamer, the functional unit in the native antenna rod. The initial structure has been refined in a cyclic manner by energy-restrained crystallographic refinement and modelling until the conventional crystallographic R-factor converged at 18.1% with data to a resolution of 1.66 A. The molecular structure resembles closely the C-phycocyanins of Mastigocladus laminosus and A. quadruplicatum. The conformation and configuration of the alpha-84 and beta-84 chromophores is very similar to the corresponding chromophores in the trimeric C-phycocyanin of M. laminosus, whereas the beta-155 chromophore differs in configuration with C(4)-Z, C(10)-Z and C(15)-Z compared to C(4)-Z, C(10)-Z, C(15)-Z,E. The stereochemistry of the beta-155 chiral centres is C(2)-RC(3)-R and C(31)-S, respectively, whereas alpha-84 and beta-84 have C(2)-RC(3)-R and C(31)-R. The amino acid sequences of constitutive and inducible phycocyanin differ mainly in residues located on the surface of the beta-subunits that mediate the inter-hexameric contacts.

Light-harvesting proteins of diatoms: their relationship to the chlorophyll a/b binding proteins of higher plants and their mode of transport into plastids

We have cloned and characterized members of a gene family encoding polypeptide constituents of the fucoxanthin, chlorophyll a/c protein complex, a light-harvesting complex associated with photosystem II of diatoms and brown algae. Three cDNA clones encoding proteins associated with this complex in the diatom Phaeodactylum tricornutum have been isolated. As deduced from the nucleotide sequences, these light-harvesting proteins show homology to the chlorophyll a/b binding polypeptides of higher plants. Specifically, the N-terminal regions of the fucoxanthin, chlorophyll a/c-binding proteins are homologous to the chlorophyll a/b binding proteins in both the third membrane-spanning domain and the stroma-exposed region between membrane-spanning domains 2 and 3. Like the chlorophyll a/b-binding proteins, the mature fucoxanthin, chlorophyll a/c polypeptides have three hydrophobic alpha-helical domains which could span the membrane bilayer. The similarities between the two light-harvesting proteins might reflect the fact that both bind chlorophyll molecules and/or might be important for maintaining certain structural features of the complex. There is little similarity between the N-terminal sequences of the primary translation products of the fucoxanthin, chlorophyll a/c proteins and any transit sequences that have been characterized. Instead, the N-terminal sequences have features resembling those of signal sequences. Thus either transit peptides used in P. tricornutum show little resemblance to those of higher plants and green algae or the nuclear-encoded plastid proteins enter the organelle via a mechanism different from that used in higher plants.

Characterization of the light-regulated operon encoding the phycoerythrin-associated linker proteins from the cyanobacterium Fremyella diplosiphon

Many biological processes in photosynthetic organisms can be regulated by light quantity or light quality or both. A unique example of the effect of specific wavelengths of light on the composition of the photosynthetic apparatus occurs in cyanobacteria that undergo complementary chromatic adaptation. These organisms alter the composition of their light-harvesting organelle, the phycobilisome, and exhibit distinct morphological features as a function of the wavelength of incident light. Fremyella diplosiphon, a filamentous cyanobacterium, responds to green light by activating transcription of the cpeBA operon, which encodes the pigmented light-harvesting component phycoerythrin. We have isolated and determined the complete nucleotide sequence of another operon, cpeCD, that encodes the linker proteins associated with phycoerythrin hexamers in the phycobilisome. The cpeCD operon is activated in green light and expressed as two major transcripts with the same 5' start site but differing 3' ends. Analysis of the kinetics of transcript accumulation in cultures of F. diplosiphon shifted from red light to green light and vice versa shows that the cpeBA and cpeCD operons are regulated coordinately. A common 17-base-pair sequence is found upstream of the transcription start sites of both operons. A comparison of the predicted amino acid sequences of the phycoerythrin-associated linker proteins CpeC and CpeD with sequences of other previously characterized rod linker proteins shows 49 invariant residues, most of which are in the amino-terminal half of the proteins.

Highly repetitive DNA sequences in cyanobacterial genomes

We characterized three distinct families of repeated sequences in the genome of the cyanobacterium Calothrix sp. strain PCC 7601. These repeated sequences were present at a level of about 100 copies per Calothrix genome and consisted of tandemly amplified heptanucleotides. These elements were named short tandemly repeated repetitive (STRR) sequences. We used the three different Calothrix STRR sequences as probes to perform Southern hybridization experiments with DNAs extracted from various cyanobacterial strains, Bacillus subtilis, and Escherichia coli. The three different STRR sequences were found as repetitive genomic DNA components specific to the heterocystous strains tested. The role of the STRR sequences, as well as their possible use in taxonomic studies, is discussed.

Structure and light-regulated expression of phycoerythrin genes in wild-type and phycobilisome assembly mutants of Synechocystis sp. strain PCC 6701

Phycoerythrin is a major pigmented component of the phycobilisome, a cyanobacterial light-harvesting complex. It contains bilin-type chromophores that absorb and transfer light energy to chlorophyll protein complexes of the photosynthetic membranes. In many cyanobacteria, phycoerythrin expression is regulated by light wavelength in a response known as chromatic adaptation. Green light-grown cells contain higher levels of this biliprotein than do cells grown in red light. The phycoerythrin gene set from the unicellular cyanobacterium Synechocystis sp. strain PCC 6701 was cloned and sequenced, and the 5' end of the phycoerythrin mRNA was localized. The amino acid sequences of the phycoerythrin subunits from Synechocystis strain 6701 and Fremyella diplosiphon were 90% identical. As observed in F. diplosiphon, the Synechocystis strain 6701 phycoerythrin transcript accumulated to high levels in green light-grown cells and low levels in red light-grown cells. Similar nucleotide sequences, which might control gene expression, occurred upstream of the transcription initiation sites of the phycoerythrin genes in both organisms. While the phycoerythrin structure and light-regulated transcript accumulation were similar in Synechocystis strain 6701 and F. diplosiphon, the steady-state levels of phycoerythrin subunits during growth in red light were quite different for the two organisms. This observation suggests that control of phycoerythrin levels in Synechocystis strain 6701 is complex and may involve posttranscriptional processes. We also characterized the phycoerythrin genes and mRNA levels in two phycobilisome assembly mutants, UV16-40 and UV16.

Genes for phycocyanin subunits in Synechocystis sp. strain PCC 6701 and assembly mutant UV16

The cyanobacterial phycobilisome is a large protein complex located on the photosynthetic membrane. It harvests light energy and transfers it to chlorophyll for use in photosynthesis. Phycobilisome assembly mutants in the unicellular cyanobacterium Synechocystis sp. strain 6701 have been characterized. One such mutant, UV16, contains a defect in the assembly of the biliprotein phycocyanin. We report the cloning and sequencing of the phycocyanin genes from wild-type Synechocystis strain 6701 and demonstrate an alteration in the gene for the phycocyanin alpha subunit in UV16. Possible consequences of the lesion on phycobilisome assembly were assessed from its position in the phycocyanin tertiary and quaternary structures. The UV16 phenotype is complex and includes a reduced level of phycocyanin relative to that in the wild type. To determine whether the lower phycocyanin content results from lower transcript levels, a fragment of cpcBA was used as a probe for quantitating phycocyanin mRNA. Both the wild type and UV16 contained two phycocyanin transcripts of approximately 1.4 and 1.5 kilobases that were equal in abundance and that did not vary with light quality during cell growth. Equal levels of these transcripts in the wild type and UV16 suggest that the lower phycocyanin content in the mutant may be due to posttranscriptional events. The 5' ends of the two phycocyanin mRNAs were mapped at 100 and 223 base pairs upstream of the cpcB initiation codon. Homologous regions upstream of the putative transcription initiation sites may be important for maintaining high levels of transcription from the Synechocystis strain 6701 phycocyanin gene set.

A region of a cyanobacterial genome required for sulfate transport

Using the cysA locus of Salmonella typhimurium as a heterologous probe, we have cloned a region of the Anacystis nidulans R2 (Synechococcus PCC 7942) genome involved in sulfate assimilation. The 8.3-kilobase-pair region encodes at least five transcripts that cannot be detected unless the cells are deprived of sulfur. One of the genes in this region has been sequenced, and the protein that it encodes is homologous to a polypeptide component of other permease systems of Escherichia coli and Salmonella. Insertional inactivation of the putative sulfate permease gene, designated cysA, as well as of other genes within this region, results in cysteine auxotrophy, reduced sulfate uptake, and altered expression of soluble and cytoplasmic-membrane polypeptides associated with sulfur starvation.

Molecular characterization of phycobilisome regulatory mutants of Fremyella diplosiphon

Three classes of pigment mutants were generated in Fremyella diplosiphon in the course of electroporation experiments. The red mutant class had high levels of phycoerythrin in both red and green light and no inducible phycocyanin in red light. Thus, this mutant behaved as if it were always in green light, regardless of light conditions. Blue mutants exhibited normal phycoerythrin photoregulation, whereas the inducible phycocyanin was present at high levels in both red- and green-light-grown cells. Furthermore, the absolute amount of allophycocyanin was increased threefold in comparison with our wild-type strain. Green mutants lost the capacity to accumulate phycoerythrin in green light but showed normal photoregulation of phycocyanin. Analyses of transcript abundance in these mutants demonstrated that changes in the levels of the different phycobilisome components correlated with changes in the levels of mRNAs encoding those components. The characterization of these mutants supports hypotheses previously discussed concerning molecular mechanisms involved in the regulation of the phycobiliprotein gene sets during chromatic adaptation.

Genes encoding core components of the phycobilisome in the cyanobacterium Calothrix sp. strain PCC 7601: occurrence of a multigene family

The phycobilisome is the major light-harvesting complex of cyanobacteria. It is composed of a central core from which six rods radiate. Allphycocyanin, an alpha beta oligomer (alpha AP and beta AP), is the main component of the core which also contains three other phycobiliproteins (alpha APB, beta 18.3, and L92CM) and a small linker polypeptide (L7.8C). By heterologous DNA hybridization, two EcoRI DNA fragments of 3.5 and 3.7 kilobases have been cloned from the chromatically adapting cyanobacterium Calothrix sp. strain PCC 7601. Nucleotide sequence determination has allowed the identification of five apc genes: apcA1 (alpha AP1), apcA2 (alpha AP2), apcB1 (beta AP1), apcC (L7.8C), and apcE (L92CM). Four of these genes are adjacent on the chromosome and form the apcEA1B1C gene cluster. In contrast, no genes have been found close to the apcA2 gene which is carried by the 3.5-kilobase EcoRI fragment. Transcriptional analysis and 5'-end-mapping experiments were performed. The results obtained demonstrate that the apcEA1B1C gene cluster forms an operon from which segmented transcripts originate, whereas the apcA2 gene behaves as a monocistronic unit. Qualitatively, the same transcripts were identified regardless of the light wavelengths received during cell growth. The deduced amino acid sequences of the apc gene products are very similar to their known homologs of either cyanobacterial or eucaryotic origin. It was interesting, however, that in the apcA1 and apcA2 genes, whose products correspond to alpha-type allophycocyanin subunits, nucleotide sequences were more conserved (67%) than were the deduced amino acid sequences (59%).

Photoregulation of gene expression in the filamentous cyanobacterium Calothrix sp. PCC 7601: light-harvesting complexes and cell differentiation

Light plays a major role in many physiological processes in cyanobacteria. In Calothrix sp. PCC 7601, these include the biosynthesis of the components of the light-harvesting antenna (phycobilisomes) and the differentiation of the vegetative trichomes into hormogonia (short chains of smaller cells). In order to study the molecular basis for the photoregulation of gene expression, physiological studies have been coupled with the characterization of genes involved either in the formation of phycobilisomes or in the synthesis of gas vesicles, which are only present at the hormogonial stage.In each system, a number of genes have been isolated and sequenced. This demonstrated the existence of multigene families, as well as of gene products which have not yet been identified biochemically. Further studies have also established the occurrence of both transcriptional and post-transcriptional regulation. The transcription of genes encoding components of the phycobilisome rods is light-wavelength dependent, while translation of the phycocyanin genes may require the synthesis of another gene product irrespective of the light regime. In this report, we propose two hypothetical models which might be part of the complex regulatory mechanisms involved in the formation of functional phycobilisomes. On the other hand, transcription of genes involved in the gas vesicles formation (gvp genes) is turned on during hormogonia differentiation, while that of phycobiliprotein genes is simultaneously turned off. In addition, and antisense RNA which might modulate the translation of the gvp mRNAs is synthezised.

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

The phycocyanin subunit gene cluster is duplicated on the chromosome of the cyanobacterium Anacystis nidulans UTEX 625. The two gene clusters cpcB1A1 (left) and cpcB2A2 (right) are separated by about 2,500 base pairs, and in each cluster the beta-subunit gene is located upstream from the alpha-subunit gene. Filter hybridizations with phycocyanin-specific probes to total RNA detected at least two major transcripts that were 1,300 to 1,400 nucleotides long. Besides these major mRNA species, two minor transcripts of 3,400 and 3,700 nucleotides covering one of the gene clusters and the region between the clusters were found. No additional minor transcripts were found in the intergenic region between the two phycocyanin gene clusters. The lengths of the major mRNAs indicated that the beta- and alpha-subunit genes were cotranscribed. No apparent homologies were found when the DNA sequences located upstream from the proposed ribosome-binding site of the two phycocyanin beta-subunit genes were compared. Northern hybridizations with gene cluster-specific probes from the regions 5' of the beta-subunit genes, as well as S1 nuclease mapping and mRNA primer extension experiments, showed that both gene clusters were transcribed. The minor transcripts were found to initiate upstream from the left gene cluster. Two mRNA 5' ends were mapped upstream from the cpcB1A1 gene cluster, while only one 5' end was mapped in front of the cpcB2A2 gene cluster. All transcripts were present in RNA preparations from cultures grown under high levels of white light as well as under low levels of red light. The level of phycocyanin-specific mRNA, measured as part of the total RNA, was lower under low levels of red light compared with that under high levels of white light. Conserved sequence motifs were found when the promoter region of the cpcB1A1 gene cluster and promoter regions from other cyanobacterial photosynthesis genes were compared. The DNA sequences covering the proposed transcriptional attenuators and transcriptional stop signals contained several potential hairpin structures. One potential hairpin structure was located immediately downstream of the left phycocyanin gene cluster and was concluded to limit the level of transcription for the minor transcripts initiating upstream of the cpcB1A1 gene cluster.

Characterization of phycobiliprotein and linker polypeptide genes in Fremyella diplosiphon and their regulated expression during complementary chromatic adaptation

Phycobilisomes, comprised of both chromophoric (phycobiliproteins) and non-chromophoric (linker polypeptides) proteins, are light-harvesting complexes present in the prokaryotic cyanobacteria and the eukaryotic red algae. Many cyanobacteria exhibit complementary chromatic adaptation, a process which enables these organisms to optimize absorption of prevalent wavelengths of light by altering the composition of the phycobilisome. To examine the mechanisms involved in adjusting the levels of phycobilisome components during complementary chromatic adaptation, we have isolated and sequenced genes encoding phycobiliprotein and linker polypeptides in the cyanobacterium Fremyella diplosiphon, analyzed their transcriptional characteristics (transcript sizes and abundance when F. diplosiphon is grown in different light qualities) and mapped transcript initiation and termination sites. Our results demonstrate that genes encoding phycobilisome components are often cotranscribed as polycistronic messenger RNAs. Light quality regulates the composition of the phycobilisome by causing changes in the abundance of transcripts encoding specific components, suggesting that regulation is at the level of transcription (although not eliminating the possibility of changes in mRNA stability). The work presented here sets the foundation for analyzing the evolution of the different phycobilisome components and exploring signal transduction from photoperception to activation of specific genes using in vivo and in vitro genetic technology.

Structure and regulation of genes encoding phycocyanin and allophycocyanin from Anabaena variabilis ATCC 29413

Gene clones encoding phycocyanin and allophycocyanin were isolated from an Anabaena variabilis ATCC 29413-Charon 30 library by using the phycocyanin (cpc) genes of Agmenellum quadruplicatum and the allophycocyanin (apc) genes of Cyanophora paradoxa as heterologous probes. The A. variabilis cpcA and cpcB genes occur together in the genome, as do the apcA and apcB genes; the two sets of genes are not closely linked, however. The cpc and apc genes appear to be present in only one copy per genome. DNA-RNA hybridization analysis showed that expression of the cpc and apc genes is greatly decreased during nitrogen starvation; within 1 h no cpc or apc mRNA could be detected. The source of nitrogen for growth did not influence expression of the genes; vegetative cells from nitrogen-fixing and ammonia-grown cultures had approximately the same levels of cpc and apc mRNAs. Heterocysts had less than 5% as much cpc mRNA as vegetative cells from nitrogen-fixing cultures. Northern hybridization (RNA blot) analysis showed that the cpc genes are transcribed to give an abundant 1.4-kilobase (kb) RNA as well as two less prominent 3.8- and 2.6-kb species. The apc genes gave rise to two transcripts, a 1.4-kb predominant RNA and a minor 1.75-kb form.

Molecular characterization and evolution of sequences encoding light-harvesting components in the chromatically adapting cyanobacterium Fremyella diplosiphon

The major light-harvesting complex in eukaryotic red algae and prokaryotic cyanobacteria is the phycobilisome, a water-soluble complex located on the outer surface of the photosynthetic membranes and composed of both pigmented phycobiliproteins (85%) and non-pigmented linker (15%) polypeptides. The phycobiliproteins are encoded by a gene family and exhibit varying degrees of sequence homology (25 to 55%). Some cyanobacteria can maximize the absorption of prevalent wavelengths of light by adjusting the phycobiliprotein composition of the phycobilisome, a process called complementary chromatic adaptation. In the chromatically adapting species Fremyella displosiphon, there are at least two sets of phycocyanin genes; one is transcribed as two red light-induced transcripts and the other is encoded on a single transcript present in both red and green light. We have determined the complete nucleotide sequences of both sets of phycocyanin subunit genes and their associated 5' and 3' regulatory regions. Based on S1 nuclease protection experiments, the transcripts (1600 and 3800 bases) encoding the inducible phycocyanin subunits have the same 5' end, and possible mechanisms for their synthesis are presented. The 5' end of the 1500-base transcript encoding the constitutive phycocyanin subunits was determined and revealed an Escherichia coli-like "-10" and "-35" region, and sequences near the transcription initiation site homologous to the analogous region of the phycocyanin gene set of Anabaena sp. 7120. Determination of the 3' ends of the transcripts encoding both F. diplosiphon phycocyanin gene sets revealed regions of potential secondary structure that may be important for transcription termination and/or transcript stability. In addition, the sequence of an open reading frame (encoding a 30 kDa polypeptide), located 3' to the constitutive phycocyanin gene set in F. diplosiphon and highly conserved in at least three cyanobacterial species, is presented. The same high degree of sequence homology between the two F. diplosiphon PC alpha and PC beta sequences (85 and 77%, respectively) was found at both the nucleotide and amino acid levels, and similar results were obtained for interspecies comparisons. Implications of these homologies with regard to the evolution of phycobiliprotein subunits are discussed.