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

The increasing role of structural proteomics in cyanobacteria

Cyanobacteria, also known as blue–green algae, are ubiquitous organisms on the planet. They contain tremendous protein machineries that are of interest to the biotechnology industry and beyond. Recently, the number of annotated cyanobacterial genomes has expanded, enabling structural studies on known gene-coded proteins to accelerate. This review focuses on the advances in mass spectrometry (MS) that have enabled structural proteomics studies to be performed on the proteins and protein complexes within cyanobacteria. The review also showcases examples whereby MS has revealed critical mechanistic information behind how these remarkable machines within cyanobacteria function.

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.

Transcriptional analysis of the jamaicamide gene cluster from the marine cyanobacterium Lyngbya majuscula and identification of possible regulatory proteins

Background

The marine cyanobacterium Lyngbya majuscula is a prolific producer of bioactive secondary metabolites. Although biosynthetic gene clusters encoding several of these compounds have been identified, little is known about how these clusters of genes are transcribed or regulated, and techniques targeting genetic manipulation in Lyngbya strains have not yet been developed. We conducted transcriptional analyses of the jamaicamide gene cluster from a Jamaican strain of Lyngbya majuscula, and isolated proteins that could be involved in jamaicamide regulation.

Results

An unusually long untranslated leader region of approximately 840 bp is located between the jamaicamide transcription start site (TSS) and gene cluster start codon. All of the intergenic regions between the pathway ORFs were transcribed into RNA in RT-PCR experiments; however, a promoter prediction program indicated the possible presence of promoters in multiple intergenic regions. Because the functionality of these promoters could not be verified in vivo, we used a reporter gene assay in E. coli to show that several of these intergenic regions, as well as the primary promoter preceding the TSS, are capable of driving β-galactosidase production. A protein pulldown assay was also used to isolate proteins that may regulate the jamaicamide pathway. Pulldown experiments using the intergenic region upstream of jamA as a DNA probe isolated two proteins that were identified by LC-MS/MS. By BLAST analysis, one of these had close sequence identity to a regulatory protein in another cyanobacterial species. Protein comparisons suggest a possible correlation between secondary metabolism regulation and light dependent complementary chromatic adaptation. Electromobility shift assays were used to evaluate binding of the recombinant proteins to the jamaicamide promoter region.

Conclusion

Insights into natural product regulation in cyanobacteria are of significant value to drug discovery and biotechnology. To our knowledge, this is the first attempt to characterize the transcription and regulation of secondary metabolism in a marine cyanobacterium. If jamaicamide is light regulated, this mechanism would be similar to other cyanobacterial natural product gene clusters such as microcystin LR. These findings could aid in understanding and potentially assisting the management of toxin production by Lyngbya in the environment.

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.

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.

Interference of an apcA insertion with complementary chromatic adaptation in the diazotrophic Synechocystis sp. strain BO 8402

Complementary chromatic adaptation was studied in two unicellular diazotrophic Synechocystis-type cyanobacteria, strains BO 8402 and BO 9201. Strain BO 8402 was isolated from Lake Constance as a mutant lacking phycobilisomes due to an insertion sequence element in the gene apcA, encoding alpha-allophycocyanin. Strain BO 9201 recovered the ability to assemble functional phycobilisomes after a spontaneous excision of the insertion sequence element in apcA. Simultaneously, the strain became able to perform group II complementary chromatic adaptation by regulating the synthesis of phycoerythrin. The two strains had identical phycoerythrin operons, cpeBA, and similar-sized transcripts were formed upon induction by green light. However, in strain BO 8402 the cpeBA transcript level was approx. 20-fold lower than in strain BO 9201. Because strain BO 8402 cannot synthesize allophycocyanin and phycocyanin is sequestered in paracrystalline inclusion bodies, non-assembled phycoerythrin may accumulate inside the cells. It was examined whether non-assembled phycoerythrin or other effects caused by the absence of phycobilisomes, such as a permanently oxidized redox status of the photosynthetic electron transport chain or a distorted ratio of C and N assimilation mediated the repression of cpeBA transcription in strain BO 8402. No such links could be established. We therefore concluded that in these diazotrophic Synechocystis-type cyanobacteria the green light-induced transcription of the cpe operon directly required a functional apc operon.

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.

How do cyanobacteria sense and respond to light?

Cyanobacteria exhibit numerous responses to changes in the intensity and spectral quality of light. What sensors do cyanobacteria use to detect light and what are the mechanisms of signal transduction? The publication in 1996 of the complete genome sequence of the cyanobacterium Synechocystis 6803 provided a tremendous stimulus for research in this field, and many light-sensors and signal transducers have now been identified. However, our knowledge of cyanobacterial light-signal transduction remains fragmentary. This review summarizes what we know about the ways in which cyanobacteria perceive light, some of the ways which they respond to light signals and some recent achievements in elucidating the signal transduction mechanisms. Some problems in characterizing cyanobacterial signal transduction pathways are outlined and alternative experimental strategies are discussed.

Deletion mutagenesis of the 5' psbA2 region in Synechocystis 6803: identification of a putative cis element involved in photoregulation

Three Synechocystis 6803 mutants, with deletions in the upstream region of the light-regulated psbA2 gene, were constructed. All three mutants grew photoautotrophically but they were affected in psbA2 expression. In one of the mutants, DeltaU80, psbA2 transcription levels were not suppressed under low light conditions and production of psbA2 transcripts occurred also in darkness, in contrast to the situation in the control strain. Comparative sequence analyses of the mutants identified a hexanucleotide repeat as possible cis element in psbA2 light regulation. Electrophoresis mobility shift assays showed that protein binding to the hexanucleotide repeat decreased with light intensity, consistent with a hypothesis that the repeat harbors a binding site for a repressor protein. Repeats similar to that in psbA2 were found also in the upstream region of other light-regulated genes in Synechocystsis 6803. We refer to these hexanucleotide repeats as High Light Regulatory 1 (HLR1) sequences.

Protein phosphorylation and its possible involvement in the induction of the high-affinity CO2 concentrating mechanism in cyanobacteria

Cyanobacteria as well as eukaryotic algae possess a CO2 concentrating mechanism that enables the cells to use low CO2 concentrations very efficiently for photosynthesis. The efficiency of the CO2 concentrating mechanism changes in response to environmental changes, especially the availability of inorganic carbon, but the underlying mechanisms that are involved in the regulation of the induction are unknown. This review deals with the occurrence of protein phosphorylation in cyanobacteria and highlights the possible involvement of post-translational modifications of existing proteins in the induction process, which leads to a high-affinity state of the CO2 concentrating mechanism.Key words: cyanobacteria, CO2 concentrating mechanism, protein kinase, protein phosphorylation, post-translational regulation.

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.

Complementary chromatic adaptation alters photosynthetic strategies in the cyanobacterium Calothrix

The cyanobacterium Calothrix sp. strain PCC 7601 drastically changes phycobiliprotein composition and colour in response to light quality, through complementary chromatic adaptation (CCA). Red light promotes phycocyanin-II and inhibits phycoerythrin synthesis, while green light has the opposite effect, through changes in transcription regulated by a putative green/red photoreceptor(s). The effects of CCA on photosynthesis were characterized by measuring oxygen evolution and chlorophyll fluorescence parameters. Cells fully acclimated to either red or green light achieve a similar photosynthetic quantum yield of oxygen evolution (light-use efficiency). Shifting acclimated cells from green to red or from red to green light caused similar 40% drops in photosynthetic quantum yield. Therefore, full CCA significantly increases light use efficiency, which is of great importance under light-limited growth. Cells growing under red light are in state I, with very low PS II to PS I energy transfer, since red light is absorbed both by phycocyanin in the phycobilisome/PS II supracomplex and by PS I chlorophyll. Cells growing under green light are in state II, with high transfer of excitation energy from the phycobilisome/PS II supracomplex to PS I. This transfer allows green light captured by phycoerythrin to ultimately drive both PS I and PS II photochemistry.

Effect of the nitrogen source on phycobiliprotein synthesis and cell reserves in a chromatically adapting filamentous cyanobacterium

Cyanobacteria can utilize nitrate or ammonium as a source of fixed nitrogen for cell growth. In the filamentous Calothrix sp. strain PCC 7601, these two sources of nitrogen differently influenced the phycobiliprotein composition of the phycobilisomes, the major light-harvesting antennae. When compared to nitrate, growth in the presence of ammonium resulted in intracellular steady-state levels 35% lower for phycoerythrin and 46% higher for phycocyanin. Besides these differences in cell pigmentation, a rapid but transient accumulation of cyanophycin granule polypeptide occurred in ammonium-grown cells, while these macromolecules were not detected in cells grown with nitrate. In contrast, glycogen reserves displayed a dynamic pattern of accumulation and disappearance during cell growth which varied only slightly with the nitrogen source. The observed changes in cell pigmentation are reminiscent of the phenomenon of complementary chromatic adaptation, in which green and red wavelengths promote the syntheses of phycoerythrin and phycocyanin-2, respectively. As in complementary chromatic adaptation, the regulation of synthesis of phycoerythrin and phycocyanin-2 by the nitrogen source occurred mainly at the mRNA level. Moreover, the transcriptional start sites for the expression of the cpeBA and the cpc2 operons, which respectively encode the two subunits of phycoerythrin and phycocyanin-2, were the same in cells grown in nitrate or ammonium, and identical to those in green- and red-light-grown cells. The results of this study suggest that acclimation to the spectral light quality and to the nitrogen source share some common regulatory elements.

Specific binding of Synechococcus sp. strain PCC 7942 proteins to the enhancer element of psbAII required for high-light-induced expression

The psbAII gene of the cyanobacterium Synechococcus sp. strain PCC 7942 is a member of a three-gene family that encodes the D1 protein of the photosystem II reaction center. Transcription of psbAII is rapidly induced when the light intensity reaching the culture increases from 125 microE.m-2.s-1 (low light) to 750 microE.m-2.s-1 (high light). The DNA segment upstream of psbAII that corresponds to the untranslated leader of its major transcript has enhancer activity and confers high-light induction. We show that one or more soluble proteins from PCC 7942 specifically bind to this region of psbAII (designated the enhancer element). In vivo footprinting showed protein binding to the enhancer element in high-light-exposed cell samples but not in those maintained at low light, even though in vitro mobility shifts were detectable with extracts from low- or high-light-grown cells. When 12 bp were deleted from the psbAII enhancer element, protein binding was impaired and high-light induction of both transcriptional and translational psbAII-lacZ reporters was significantly reduced. This finding indicates that protein binding to this region is required for high-light induction of psbAII. The mutant element also showed impaired enhancer activity when combined with a heterologous promoter.