Structure and molecular organization of the photosynthetic accessory pigments of cyanobacteria and red algae

Secondary structure analysis of proteins within the same topology group

The native conformation of a protein plays a decisive role in ensuring its functionality. It is established that the spatial structure of proteins may exhibit a greater degree of conservation than the corresponding amino acid sequences. This study aims to clarify structural distinctions between homologous and non-homologous proteins with identical topology. The analysis focuses on secondary structures with special emphasis on their fraction, distribution along the polypeptide chain, and chirality. Three different groups of proteins with identical topology were considered according to the CATH database: a homologous group of Globins, a group of Phycocyanins, which is often considered as a potential relative of globins, and a diverse assembly of other globin-like proteins. Some structural patterns in the distribution of secondary structure have been identified within Globins. A similar profile was observed in Phycocyanins, in contrast to the third group. In addition, a distinguishable structural motif, including structures such as 310-helix and irregular structure, has been found in both Globins and Phycocyanins, which can be proposed as an evolutionary imprint.

Chromatic acclimation in cyanobacteria renders robust photosynthesis and fitness in dynamic light environment: Recent advances and future perspectives

Cyanobacteria are photoautotrophic organisms that use light and water as a source of energy and electrons, respectively, to fix atmospheric carbon dioxide and release oxygen as a by-product during photosynthesis. However, photosynthesis and fitness of organisms are challenged by seasonal and diurnal fluctuations in light environments. Also, the distribution of cyanobacteria in a water column is subject to changes in the light regime. The quality and quantity of light change significantly in low and bright light environments that either limit photochemistry or result in photoinhibition due to an excess amount of light reaching reaction centers. Therefore, cyanobacteria have to adjust their light-harvesting machinery and cell morphology for the optimal harvesting of light. This adjustment of light-harvesting involves remodeling of the light-harvesting complex called phycobilisome or incorporation of chlorophyll molecules such as chlorophyll d and f into their light-harvesting machinery. Thus, photoacclimation responses of cyanobacteria at the level of pigment composition and cell morphology maximize their photosynthetic ability and fitness under a dynamic light environment. Cyanobacteria exhibit different types of photoacclimation responses that are commonly known as chromatic acclimation (CA). In this work, we discuss different types of CA reported in cyanobacteria and present a molecular mechanism of well-known type 3 CA where phycoerythrin and phycocyanin of phycobilisome changes according to light signals. We also include other aspects of type 3 CA that have been recently studied at a molecular level and highlight the importance of morphogenes, cytoskeleton, and carboxysome proteins. In summary, CA gives a unique competitive benefit to cyanobacteria by increasing their resource utilization ability and fitness.

Consequences of light spectra for pigment composition and gene expression in the cryptophyte Rhodomonas salina

Algae with a more diverse suite of pigments can, in principle, exploit a broader swath of the light spectrum through chromatic acclimation, the ability to maximize light capture via plasticity of pigment composition. We grew Rhodomonas salina in wide-spectrum, red, green, and blue environments and measured how pigment composition differed. We also measured expression of key light-capture and photosynthesis-related genes and performed a transcriptome-wide expression analysis. We observed the highest concentration of phycoerythrin in green light, consistent with chromatic acclimation. Other pigments showed trends inconsistent with chromatic acclimation, possibly due to feedback loops among pigments or high-energy light acclimation. Expression of some photosynthesis-related genes was sensitive to spectrum, although expression of most was not. The phycoerythrin α-subunit was expressed two-orders of magnitude greater than the β-subunit even though the peptides are needed in an equimolar ratio. Expression of genes related to chlorophyll-binding and phycoerythrin concentration were correlated, indicating a potential synthesis relationship. Pigment concentrations and expression of related genes were generally uncorrelated, implying post-transcriptional regulation of pigments. Overall, most differentially expressed genes were not related to photosynthesis; thus, examining associations between light spectrum and other organismal functions, including sexual reproduction and glycolysis, may be important.

The structural basis for light acclimation in phycobilisome light harvesting systems systems in Porphyridium purpureum

Photosynthetic organisms adapt to changing light conditions by manipulating their light harvesting complexes. Biophysical, biochemical, physiological and genetic aspects of these processes are studied extensively. The structural basis for these studies is lacking. In this study we address this gap in knowledge by focusing on phycobilisomes (PBS), which are large structures found in cyanobacteria and red algae. In this study we focus on the phycobilisomes (PBS), which are large structures found in cyanobacteria and red algae. Specifically, we examine red algae (Porphyridium purpureum) grown under a low light intensity (LL) and a medium light intensity (ML). Using cryo-electron microscopy, we resolve the structure of ML-PBS and compare it to the LL-PBS structure. The ML-PBS is 13.6 MDa, while the LL-PBS is larger (14.7 MDa). The LL-PBS structure have a higher number of closely coupled chromophore pairs, potentially the source of the red shifted fluorescence emission from LL-PBS. Interestingly, these differences do not significantly affect fluorescence kinetics parameters. This indicates that PBS systems can maintain similar fluorescence quantum yields despite an increase in LL-PBS chromophore numbers. These findings provide a structural basis to the processes by which photosynthetic organisms adapt to changing light conditions.

Maximization of red pigment production from Streptomyces sp. LS1 structure elucidation and application as antimicrobial/antifouling against human pathogens and marine microbes

BACKGROUND

Natural dyes are present in living organisms such as animals and plants and microorganisms such as fungi, bacteria, algae, and yeast. Pigments are fast and easy growth by using cheap components and do not effect by environmental conditions because they required some physical factors like heat, light, and pH and also they have many biotechnological applications such as medical and industrial needs. The natural pigments can act as antimicrobial agents and are used in drug manufacturing. Also, it can be used in the food industry as natural colorants instead of the synthetic colorants due to their safety on human health and low toxicity when emitted into the environment.

RESULTS

A pigmented actinomycetes LS1 strain isolated from El Mahmoudia canal (sediment soil) located in Egypt was microscopically examined and identified as Streptomyces sp. by molecular approach. Extraction, purification, and characterization of produced red pigment metabolite like carotenoids related were established based on spectroscopic studies and comparing the data from the literature. Factors (nutritional and physical) influencing red pigmentation by this isolate were investigated through One Variable At Time (OVAT), and then, the optimal levels of the significant key variables were recorded. Also, the productivity yield reached 30 mg of dried purified pigment/gram dry weight. The biological activity of the red product was tested against Gram-positive and Gram-negative marine bacterial pathogens; the recorded antimicrobial activity is more prominent against (P. aeruginosa ATCC 9027, K. pneumoniae ATCC 13883, S. aureus ATCC 6538, B. subtilis ATCC 6633 and E. coli ATCC 10418) at nearly 0.07 mg mL^-1 concentration. Also, the tested red pigment showed a positive antifouling activity (AF) against marine microbes; the activity increased by increasing the pigment concentrations from 1 to 3 mg mL^-1.

CONCLUSION

The present work focused on the optimization of culture conditions for the production of red pigment by Streptomyces sp. LS1; then, the antibacterial activity and antifouling activity of the produced pigments were tested.

An Insight into the Algal Evolution and Genomics

With the increase in biotechnological, environmental, and nutraceutical importance of algae, about 100 whole genomic sequences of algae have been published, and this figure is expected to double in the coming years. The phenotypic and ecological diversity among algae hints at the range of functional capabilities encoded by algal genomes. In order to explore the biodiversity of algae and fully exploit their commercial potential, understanding their evolutionary, structural, functional, and developmental aspects at genomic level is a pre-requisite. So forth, the algal genomic analysis revealed us that algae evolved through endosymbiotic gene transfer, giving rise to around eight phyla. Amongst the diverse algal species, the unicellular green algae Chlamydomonas reinhardtii has attained the status of model organism as it is an ideal organism to elucidate the biological processes critical to plants and animals, as well as commercialized to produce range of bio-products. For this review, an overview of evolutionary process of algae through endosymbiosis in the light of genomics, as well as the phylogenomic, studies supporting the evolutionary process of algae was reviewed. Algal genomics not only helped us to understand the evolutionary history of algae but also may have an impact on our future by helping to create algae-based products and future biotechnological approaches.

Global distribution of a chlorophyll f cyanobacterial marker

Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype’s distribution.

Crystal structure of the first eukaryotic bilin reductase GtPEBB reveals a flipped binding mode of dihydrobiliverdin

Phycobilins are light-harvesting pigments of cyanobacteria, red algae, and cryptophytes. The biosynthesis of phycoerythrobilin (PEB) is catalyzed by the subsequent action of two ferredoxin-dependent bilin reductases (FDBRs). Although 15,16-dihydrobiliverdin (DHBV):ferredoxin oxidoreductase (PebA) catalyzes the two-electron reduction of biliverdin IXα to 15,16-DHBV, PEB:ferredoxin oxidoreductase (PebB) reduces this intermediate further to PEB. Interestingly, marine viruses encode the FDBR PebS combining both activities within one enzyme. Although PebA and PebS share a canonical fold with similar substrate-binding pockets, the structural determinants for the stereo- and regiospecific modification of their tetrapyrrole substrates are incompletely understood, also because of the lack of a PebB structure. Here, we solved the X-ray crystal structures of both substrate-free and -bound PEBB from the cryptophyte Guillardia theta at 1.90 and 1.65 Å, respectively. The structures of PEBB exhibit the typical α/β/α-sandwich fold. Interestingly, the open-chain tetrapyrrole substrate DHBV is bound in an unexpected flipped orientation within the canonical FDBR active site. Biochemical analyses of the WT enzyme and active site variants identified two central aspartate residues Asp-99 and Asp-219 as essential for catalytic activity. In addition, the conserved Arg-215 plays a critical role in substrate specificity, binding orientation, and active site integrity. Because these critical residues are conserved within certain FDBRs displaying A-ring reduction activity, we propose that they present a conserved mechanism for this reaction. The flipped substrate-binding mode indicates that two-electron reducing FDBRs utilize the same primary site within the binding pocket and that substrate orientation is the determinant for A- or D-ring regiospecificity.

Loss of carotenoids from membranes of Pantoea sp. YR343 results in altered lipid composition and changes in membrane biophysical properties

Bacterial membranes are complex mixtures of lipids and proteins, the combination of which confers biophysical properties that allows cells to respond to environmental conditions. Carotenoids are sterol analogs that are important for regulating membrane dynamics. The membrane of Pantoea sp. YR343 is characterized by the presence of the carotenoid zeaxanthin, and a carotenoid-deficient mutant, ΔcrtB, displays defects in root colonization, reduced secretion of indole-3-acetic acid, and defects in biofilm formation. Here we demonstrate that the loss of carotenoids results in changes to the membrane lipid composition in Pantoea sp. YR343, including increased amounts of unsaturated fatty acids in the ΔcrtB mutant membranes. These mutant cells displayed less fluid membranes in comparison to wild type cells as measured by fluorescence anisotropy of whole cells. Studies with artificial systems, however, have shown that carotenoids impart membrane rigidifying properties. Thus, we examined membrane fluidity using spheroplasts and vesicles composed of lipids extracted from either wild type or mutant cells. Interestingly, with the removal of the cell wall and membrane proteins, ΔcrtB vesicles were more fluid than vesicles made from lipids extracted from wild type cells. In addition, carotenoids appeared to stabilize membrane fluidity during rapidly changing temperatures. Taken together, these results suggest that Pantoea sp. YR343 compensates for the loss of carotenoids by changing lipid composition, which together with membrane proteins, results in reduced membrane fluidity. These changes may influence the abundance or function of membrane proteins that are responsible for the physiological changes observed in the ΔcrtB mutant cells.

Fluorescence enhancement of a ligand-activated fluorescent protein induced by collective noncovalent interactions

Fluorescent proteins contain an internal chromophore constituted of amino acids or an external chromophore covalently bonded to the protein. To increase their fluorescence intensities, many research groups have attempted to mutate amino acids within or near the chromophore. Recently, a new type of fluorescent protein, called UnaG, in which the ligand binds to the protein through many noncovalent interactions was discovered. Later, a series of mutants of the UnaG protein were introduced, which include eUnaG with valine 2 mutated to leucine emitting significantly stronger fluorescence than the wild type and V2T mutant, in which valine 2 is mutated to threonine, emitting weaker fluorescence than the wild type. Interestingly, the single mutation sites of both eUnaG and V2T mutants are distant from the fluorophore, bilirubin, which renders the mechanism of such fluorescence enhancement or reduction unclear. To elucidate the origin of fluorescence intensity changes induced by the single mutations, we carried out extensive analyses on MD simulations for the original UnaG, eUnaG and V2T, and found that the bilirubin ligand bound to eUnaG is conformationally more rigid than the wild-type, particularly in the skeletal dihedral angles, possibly resulting in the increase of quantum yield through a reduction of non-radiative decay. On the other hand, the bilirubin bound to the V2T appears to be flexible than that in the UnaG. Furthermore, examining the structural correlations between the ligand and proteins, we found evidence that the bilirubin ligand is encapsulated in different environments composed of protein residues and water molecules that increase or decrease the stability of the ligand. The changed protein stability affects the mobility and confinement of water molecules captured between bilirubin and the protein. Since the flexible ligand contains multiple hydrogen bond (H-bond) donors and acceptors, the H-bonding structure and dynamics of bound water molecules are highly correlated with the rigidity of the bound ligand. Our results suggest that, to understand the fluorescence properties of protein mutants, especially the ones with noncovalently bound fluorophores with internal rotations, the interaction network among protein residues, ligand, and water molecules within the binding cavity should be investigated rather than focusing on the local structure near the fluorescing moiety. Our in-depth simulation study may offer a foundation for the design principles for engineering this new class of fluorescent proteins.

Analysis of the light intensity dependence of the growth of Synechocystis and of the light distribution in a photobioreactor energized by 635 nm light

Synechocystis gathered momentum in modelling studies and biotechnological applications owing to multiple factors like fast growth, ability to fix carbon dioxide into valuable products, and the relative ease of genetic manipulation. Synechocystis physiology and metabolism, and consequently, the productivity of Synechocystis-based photobioreactors (PBRs), are heavily light modulated. Here, we set up a turbidostat-controlled lab-scale cultivation system in order to study the influence of varying orange–red light intensities on Synechocystis growth characteristics and photosynthetic activity. Synechocystis growth and photosynthetic activity were found to raise as supplied light intensity increased up to 500 μmol photons m⁻² s⁻¹ and to enter the photoinhibition state only at 800 μmol photons m⁻² s⁻¹. Interestingly, reverting the light to a non-photo-inhibiting intensity unveiled Synechocystis to be able to promptly recover. Furthermore, our characterization displayed a clear correlation between variations in growth rate and cell size, extending a phenomenon previously observed in other cyanobacteria. Further, we applied a modelling approach to simulate the effects produced by varying the incident light intensity on its local distribution within the PBR vessel. Our model simulations suggested that the photosynthetic activity of Synechocystis could be enhanced by finely regulating the intensity of the light incident on the PBR in order to prevent cells from experiencing light-induced stress and induce their exploitation of areas of different local light intensity formed in the vessel. In the latter case, the heterogeneous distribution of the local light intensity would allow Synechocystis for an optimized usage of light.

Evolution and molecular mechanism of four-electron reducing ferredoxin-dependent bilin reductases from oceanic phages

Ferredoxin-dependent bilin reductases (FDBRs) are a class of enzymes reducing the heme metabolite biliverdin IXα (BV) to form open-chain tetrapyrroles used for light-perception and light-harvesting in photosynthetic organisms. Thus far, seven FDBR families have been identified, each catalysing a distinct reaction and either transferring two or four electrons from ferredoxin onto the substrate. The newest addition to the family is PcyX, originally identified from metagenomics data derived from phage. Phylogenetically, PcyA is the closest relative catalysing the reduction of BV to phycocyanobilin. PcyX, however, converts the same substrate to phycoerythrobilin, resembling the reaction catalysed by cyanophage PebS. Within this study, we aimed at understanding the evolution of catalytic activities within FDBRs using PcyX as an example. Additional members of the PcyX clade and a remote member of the PcyA family were investigated to gain insights into catalysis. Biochemical data in combination with the PcyX crystal structure revealed that a conserved aspartate-histidine pair is critical for activity. Interestingly, the same residues are part of a catalytic Asp-His-Glu triad in PcyA, including an additional Glu. While this Glu residue is replaced by Asp in PcyX, it is not involved in catalysis. Substitution back to a Glu failed to convert PcyX to a PcyA. Therefore, the change in regiospecificity is not only caused by individual catalytic amino acid residues. Rather the combination of the architecture of the active site with the positioning of the substrate triggers specific proton transfer yielding the individual phycobilin products.

ENZYMES

Suggested EC number for PcyX: 1.3.7.6 DATABASES: The PcyX X-ray structure was deposited in the PDB with the accession code 5OWG.

Direct single-molecule measurements of phycocyanobilin photophysics in monomeric C-phycocyanin

Phycobilisomes are highly organized pigment-protein antenna complexes found in the photosynthetic apparatus of cyanobacteria and rhodophyta that harvest solar energy and transport it to the reaction center. A detailed bottom-up model of pigment organization and energy transfer in phycobilisomes is essential to understanding photosynthesis in these organisms and informing rational design of artificial light-harvesting systems. In particular, heterogeneous photophysical behaviors of these proteins, which cannot be predicted de novo, may play an essential role in rapid light adaptation and photoprotection. Furthermore, the delicate architecture of these pigment-protein scaffolds sensitizes them to external perturbations, for example, surface attachment, which can be avoided by study in free solution or in vivo. Here, we present single-molecule characterization of C-phycocyanin (C-PC), a three-pigment biliprotein that self-assembles to form the midantenna rods of cyanobacterial phycobilisomes. Using the Anti-Brownian Electrokinetic (ABEL) trap to counteract Brownian motion of single particles in real time, we directly monitor the changing photophysical states of individual C-PC monomers from Spirulina platensis in free solution by simultaneous readout of their brightness, fluorescence anisotropy, fluorescence lifetime, and emission spectra. These include single-chromophore emission states for each of the three covalently bound phycocyanobilins, providing direct measurements of the spectra and photophysics of these chemically identical molecules in their native protein environment. We further show that a simple Förster resonant energy transfer (FRET) network model accurately predicts the observed photophysical states of C-PC and suggests highly variable quenching behavior of one of the chromophores, which should inform future studies of higher-order complexes.

Supramolecular architecture of photosynthetic membrane in red algae in response to nitrogen starvation

The availability of nitrogen is one of the most important determinants that can limit the growth of photosynthetic organisms including plants and algae; however, direct observations on the supramolecular architecture of photosynthetic membranes in response to nitrogen stress are still lacking. Red algae are an important evolutionary group of algae which contain phycobilisomes (PBSs) on their thylakoid membranes, as do cyanobacteria. PBSs function not only as light-harvesting antennae but also as nitrogen storage. In this report, alterations of the supramolecular architecture of thylakoid membranes from red alga Porphyridium cruentum during nitrogen starvation were characterized. The morphology of the intact thylakoid membrane was observed to be round vesicles. Thylakoid membranes were reduced in content and PBSs were degraded during nitrogen starvation. The size and density of PBSs were both found to be reduced. PBS size decreased by less than one-half after 20days of nitrogen starvation, but their hemispherical morphology was retained. The density of PBSs on thylakoid membranes was more seriously affected as time proceeded. Upon re-addition of nitrogen led to increasing of PBSs on thylakoid membranes. This work reports the first direct observation on alterations in the supramolecular architecture of thylakoid membranes from a photosynthetic organism in response to nitrogen stress.

The phycobilisomes: an early requisite for efficient photosynthesis in cyanobacteria

Cyanobacteria trap light energy by arrays of pigment molecules termed “phycobilisomes (PBSs)”, organized proximal to "reaction centers" at which chlorophyll perform the energy transduction steps with highest quantum efficiency. PBSs, composed of sequential assembly of various chromophorylated phycobiliproteins (PBPs), as well as nonchromophoric, basic and hydrophobic polypeptides called linkers. Atomic resolution structure of PBP is a heterodimer of two structurally related polypeptides but distinct specialised polypeptides- a and ß, made up of seven alpha-helices each which played a crucial step in evolution of PBPs. PBPs carry out various light dependent responses such as complementary chromatic adaptation. The aim of this review is to summarize and discuss the recent progress in this field and to highlight the new and the questions that remain unresolved.

Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731) for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. All reactions are elementally and charge balanced and localized into four different intracellular compartments (i.e., periplasm, cytosol, carboxysome and thylakoid lumen) and biomass descriptions are derived based on experimental measurements. Newly added reactions absent in earlier models (266 and 322, respectively) span most metabolic pathways with an emphasis on lipid biosynthesis. All thermodynamically infeasible loops are identified and eliminated from both models. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100) and a sensitivity of 1 (19/19) for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark) biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models.

Different phycobilin antenna organisations affect the balance between light use and growth rate in the cyanobacterium Microcystis aeruginosa and in the cryptophyte Cryptomonas ovata

During the recent years, wide varieties of methodologies have been developed up to the level of commercial use to measure photosynthetic electron transport by modulated chlorophyll a-in vivo fluorescence. It is now widely accepted that the ratio between electron transport rates and new biomass (P (Fl)/B (C)) is not fixed and depends on many factors that are also taxonomically variable. In this study, the balance between photon absorption and biomass production has been measured in two phycobilin-containing phototrophs, namely, a cyanobacterium and a cryptophyte, which differ in their antenna organization. It is demonstrated that the different antenna organization exerts influence on the regulation of the primary photosynthetic reaction and the dissipation of excessively absorbed radiation. Although, growth rates and the quantum efficiency of biomass production of both phototrophs were comparable, the ratio P (Fl)/B (C) was twice as high in the cryptophyte in comparison to the cyanobacterium. It is assumed that this discrepancy is because of differences in the metabolic regulation of cell growth. In the cryptophyte, absorbed photosynthetic energy is used to convert assimilated carbon directly into proteins and lipids, whereas in the cyanobacterium, the photosynthetic energy is preferentially stored as carbohydrates.

Morphology of a novel cyanobacterium and characterization of light-harvesting complexes from it: Implications for phycobiliprotein evolution

The morphology of the marine cyanobacterium DC-2 and two light-harvesting complexes from it have been characterized. DC-2 has an outer cell wall sheath not previously observed, the purified phycoerythrin shows many unusual properties that distinguish it from all phycoerythrins characterized to date, and isolated phycobilisomes have a single absorption band at 640 nm in the phycocyanin-allophycocyanin region of the spectrum. On the basis of these observations we suggest that DC-2, rather than being a member of the Synechococcus group, should be placed in its own taxonomic group. In addition, the particular properties of the isolated phycoerythrin suggest that it may be representative of an early stage in the evolution of the phycoerythrins. These observations are of special interest in light of the contribution DC-2 and related cyanobacteria may make to global primary productivity.

Isolation and characterization of a gene for a major light-harvesting polypeptide from Cyanophora paradoxa

Antibodies raised against mixtures of phycobilisome polypeptides from the eukaryotic alga Cyanidium caldarium were used in an immunological screen to detect expression of phycobiliprotein genes in an Escherichia coli library containing segments of plastid (chloroplast, cyanelle) DNA from another eukaryotic alga, Cyanophora paradoxa. The four candidate clones obtained were mapped by restriction analysis and found to be overlapping. The clone with the smallest insert (1.4 kilobases) was partially sequenced and a coding region similar to the carboxyl terminus of the phycobiliprotein subunit beta-phycocyanin was found. The coding region for the beta-phycocyanin gene in C. paradoxa has been mapped to the small single copy region on the cyanelle genome, and its orientation has been determined. A short probe unique to a conserved chromophore binding site shared by at least two phycobiliprotein subunits has now been generated from the carboxyl terminus of the beta-phycocyanin gene. This probe may be useful in identifying specific phycobiliprotein subunit genes, beta-phycocyanin, beta-phycoerythrocyanin, and possibly beta-phycoerythrin, in other eukaryotic algae and in prokaryotic cyanobacteria.

Cytoplasmic and chloroplast synthesis of phycobilisome polypeptides

In vivo labeling of eukaryotic phycobilisomes in the presence of inhibitors of translation on 70S and 80S ribosomes demonstrates that some of the polypeptides of this light-harvesting complex are synthesized in the cytoplasm while others are synthesized in the chloroplast. The major pigmented polypeptides, the alpha and beta subunits of the biliproteins (molecular weights between 15,000 and 20,000) and the anchor protein (molecular weight about 90,000) are translated on 70S ribosomes. This suggests that these polypeptides are made within the algal chloroplast. Because the alpha and beta subunits comprise a group of closely related polypeptides, the genes encoding these polypeptides may reside in the plastid genome as a multigene family. Other prominent phycobilisome polypeptides, including a nonpigmented polypeptide that may be involved in maintaining the structural integrity of the complex, are synthesized on cytoplasmic ribosomes. Because the synthesis of phycobilisomes appears to require the expression of genes in two subcellular compartments, this system may be an excellent model for: (i) examining interaction between nuclear and plastid genomes: (ii) elucidating the molecular processes involved in the evolution of plastid genes: (iii) clarifying the events in the synthesis and assembly of macromolecular complexes in the chloroplast.

A systems-level analysis of the effects of light quality on the metabolism of a cyanobacterium

Photosynthetic organisms experience changes in light quantity and light quality in their natural habitat. In response to changes in light quality, these organisms redistribute excitation energy and adjust photosystem stoichiometry to maximize the utilization of available light energy. However, the response of other cellular processes to changes in light quality is mostly unknown. Here, we report a systematic investigation into the adaptation of cellular processes in Synechocystis species PCC 6803 to light that preferentially excites either photosystem II or photosystem I. We find that preferential excitation of photosystem II and photosystem I induces massive reprogramming of the Synechocystis transcriptome. The rewiring of cellular processes begins as soon as Synechocystis senses the imbalance in the excitation of reaction centers. We find that Synechocystis utilizes the cyclic photosynthetic electron transport chain for ATP generation and a major part of the respiratory pathway to generate reducing equivalents and carbon skeletons during preferential excitation of photosystem I. In contrast, cytochrome c oxidase and photosystem I act as terminal components of the photosynthetic electron transport chain to produce sufficient ATP and limited amounts of NADPH and reduced ferredoxin during preferential excitation of photosystem II. To overcome the shortage of NADPH and reduced ferredoxin, Synechocystis preferentially activates transporters and acquisition pathways to assimilate ammonia, urea, and arginine over nitrate as a nitrogen source. This study provides a systematic analysis of cellular processes in cyanobacteria in response to preferential excitation and shows that the cyanobacterial cell undergoes significant adjustment of cellular processes, many of which were previously unknown.

Identification and characterization of thermophilicSynechococcusspp. isolates from Asian geothermal springs

Two thermophilic cyanobacterial strains, Ts and Bs, collected from Asian geothermal springs were identified morphologically and phylogenetically as Synechococcus in the order Chroococcales and were isolated into axenic cultures. In addition to the high similarities between their full 16S rRNA gene sequences, both strains also shared similar pigment profiles and fatty acid compositions but with varied ratios. Strain Ts had elevated levels of photoprotective pigments such as carotenoid and scytonemin even after prolonged culture under identical laboratory conditions, whereas strain Bs produced more chlorophyll a per unit cell volume, perhaps resulting from UV adaptation in the natural habitats. In addition, strain Ts had more content than strain Bs in terms of the total fatty acids and the proportion of unsaturated fatty acids. Neither isolate was able to fix nitrogen, and they had zero susceptibility to ampicillin and streptomycin.

Two novel phycoerythrin-associated linker proteins in the marine cyanobacterium Synechococcus sp. strain WH8102

The recent availability of the whole genome of Synechococcus sp. strain WH8102 allows us to have a global view of the complex structure of the phycobilisomes of this marine picocyanobacterium. Genomic analyses revealed several new characteristics of these phycobilisomes, consisting of an allophycocyanin core and rods made of one type of phycocyanin and two types of phycoerythrins (I and II). Although the allophycocyanin appears to be similar to that found commonly in freshwater cyanobacteria, the phycocyanin is simpler since it possesses only one complete set of alpha and beta subunits and two rod-core linkers (CpcG1 and CpcG2). It is therefore probably made of a single hexameric disk per rod. In contrast, we have found two novel putative phycoerythrin-associated linker polypeptides that appear to be specific for marine Synechococcus spp. The first one (SYNW2000) is unusually long (548 residues) and apparently results from the fusion of a paralog of MpeC, a phycoerythrin II linker, and of CpeD, a phycoerythrin-I linker. The second one (SYNW1989) has a more classical size (300 residues) and is also an MpeC paralog. A biochemical analysis revealed that, like MpeC, these two novel linkers were both chromophorylated with phycourobilin. Our data suggest that they are both associated (partly or totally) with phycoerythrin II, and we propose to name SYNW2000 and SYNW1989 MpeD and MpeE, respectively. We further show that acclimation of phycobilisomes to high light leads to a dramatic reduction of MpeC, whereas the two novel linkers are not significantly affected. Models for the organization of the rods are proposed.

Genes of the R-phycocyanin II locus of marine Synechococcus spp., and comparison of protein-chromophore interactions in phycocyanins differing in bilin composition

R-phycocyanin II (RPCII) is a recently discovered member of the phycocyanin family of photosynthetic light-harvesting proteins. Genes encoding the alpha and beta subunits of RPCII were cloned and sequenced from marine Synechococcus sp. strains WH8020 and WH8103. The deduced amino acid sequences of RPCII were compared to two other types of phycocyanin, C-phycocyanin (CPC) and phycoerythrocyanin (PEC). These three types vary in the composition of their covalently bound bilin prosthetic groups. In terms of amino acid sequence identity RPCII is highly homologous to CPC and PEC, suggesting that the known three-dimensional structures of the latter two are representative of RPCII. Thus the amino acid residues contacting the three bilins of RPCII could be inferred and compared to those in CPC and PEC. Certain residues were identified among the three phycocyanins as possibly correlating with specific bilin isomers. In overall sequence RPCII and CPC are more homologous to one another than either is to PEC. This probably reflects functional homology in the roles of RPCII and CPC in the transfer of light energy to the core of the phycobilisome, a function not attributed to PEC. The genomes of Synechococcus sp. strains WH8020, WH8103 and WH7803 share homologous open reading frames in the vicinity of RPCII genes. The nucleotide sequence extending 3' from RPCII genes in strain WH8020 revealed two open reading frames homologous to components of an alpha CPC phycocyanobilin lyase. These open reading frames may encode a lyase specific for the attachment of phycoerythrobilin to alpha RPCII.

Effects of green light on biological systems

Green light (510-565 nm) constitutes a significant portion of the visible spectrum impinging on biological systems. It plays many different roles in the biochemistry, physiology and structure of plants and animals. In only a relatively small number of responses to green light is the photoreceptor known with certainty or even provisionally and in even fewer systems has the chain of events leading from perception to response been examined experimentally. This review provides a detailed view of those biological systems shown to respond to green light, an evaluation of possible photoreceptors and a review of the known and postulated mechanisms leading to the responses.

Algal phycocyanins promote growth of human cells in culture

The growth-promoting substances in a non-dialyzable extract of Synechococcus elongatus var. on RPMI 8226 cells (a human myeloma cell line) were separated by gel filtration and ion exchange chromatography. By gel filtration with Sepharose 4B, the dialyzate was separated into two fractions. One fraction was green-colored (P-1) and the other was blue-colored (P-2). The P-2 fraction had a higher growth-promoting activity than P-1. By ion exchange chromatography, the P-2 fraction was separated into two blue-colored fractions of phycocyanin and allophycocyanin. Both biliproteins promoted the growth of RPMI 8226 cells; however, allophycocyanin was more active than phycocyanin.

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.

Photosynthetic action spectra and adaptation to spectral light distribution in a benthic cyanobacterial mat

We studied adaptation to spectral light distribution in undisturbed benthic communities of cyanobacterial mats growing in hypersaline ponds at Guerrero Negro, Baja California, Mexico. Microscale measurements of oxygen photosynthesis and action spectra were performed with microelectrodes; spectral radiance was measured with fiber-optic microprobes. The spatial resolution of all measurements was 0.1 mm, and the spectral resolution was 10 to 15 nm. Light attenuation spectra showed absorption predominantly by chlorophyll a (Chl a) (430 and 670 nm), phycocyanin (620 nm), and carotenoids (440 to 500 nm). Blue light (450 nm) was attenuated 10-fold more strongly than red light (600 nm). The action spectra of the surface film of diatoms accordingly showed activity over the whole spectrum, with maxima for Chl a and carotenoids. The underlying dense Microcoleus population showed almost exclusively activity dependent upon light harvesting by phycobilins at 550 to 660 nm. Maximum activity was at 580 and 650 nm, indicating absorption by phycoerythrin and phycocyanin as well as by allophycocyanin. Very little Chl a-dependent activity could be detected in the cyanobacterial action spectrum, even with additional 600-nm light to excite photosystem II. The depth distribution of photosynthesis showed detectable activity down to a depth of 0.8 to 2.5 mm, where the downwelling radiant flux at 600 nm was reduced to 0.2 to 0.6% of the surface flux.

Genes encoding major light-harvesting polypeptides are clustered on the genome of the cyanobacterium Fremyella diplosiphon

The polypeptide composition of the phycobilisome, the major light-harvesting complex of prokaryotic cyanobacteria and certain eukaryotic algae, can be modulated by different light qualities in cyanobacteria exhibiting chromatic adaptation. We have identified genomic fragments encoding a cluster of phycobilisome polypeptides (phycobiliproteins) from the chromatically adapting cyanobacterium Fremyella diplosiphon using previously characterized DNA fragments of phycobiliprotein genes from the eukaryotic alga Cyanophora paradoxa and from F. diplosiphon. Characterization of two lambda-EMBL3 clones containing overlapping genomic fragments indicates that three sets of phycobiliprotein genes--the alpha- and beta-allophycocyanin genes plus two sets of alpha- and beta-phycocyanin genes--are clustered within 13 kilobases on the cyanobacterial genome and transcribed off the same strand. The gene order (alpha-allophycocyanin followed by beta-allophycocyanin and beta-phycocyanin followed by alpha-phycocyanin) appears to be a conserved arrangement found previously in a eukaryotic alga and another cyanobacterium. We have reported that one set of phycocyanin genes is transcribed as two abundant red light-induced mRNAs (1600 and 3800 bases). We now present data showing that the allophycocyanin genes and a second set of phycocyanin genes are transcribed into major mRNAs of 1400 and 1600 bases, respectively. These transcripts are present in RNA isolated from cultures grown in red and green light, although lower levels of the 1600-base phycocyanin transcript are present in cells grown in green light. Furthermore, a larger transcript of 1750 bases hybridizes to the allophycocyanin genes and may be a precursor to the 1400-base species.

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

The major light-harvesting complex in cyanobacteria and red algae, the phycobilisome, is composed of chromophoric and nonchromophoric polypeptides. Two linked genes encoding major chromophoric components, the polypeptide subunits of phycocyanin, were isolated from the cyanobacterium Fremyella diplosiphon. Transcripts from this phycocyanin subunit gene cluster were present as major species in the cyanobacterium grown in red light, but not in cultures maintained in green light. The genes for the subunits of the red light-induced phycocyanin were transcribed together (beta-phycocyanin followed by alpha-phycocyanin) on two messenger RNA species; one contained 1600 bases while the other had 3800 bases. The latter, which encompassed the smaller transcript, contained additional sequences extending from the 3' end of the coding region of the alpha-phycocyanin gene. It may encode other light-induced components of the phycobilisome. Since phycocyanin, which effectively absorbs red light, becomes a dominant constituent of the phycobilisome in red light, these different levels may reflect an important adaptive mechanism of these organisms to their environment.

Fluorescent phycobiliprotein conjugates for analyses of cells and molecules

The synthesis of a novel class of reagents for fluorescence analyses of molecules and cells is reported. These compounds consist of a highly fluorescent phycobiliprotein conjugated to a molecule having biological specificity. Phycoerythrin-immunoglobulin, phycoerythrin-protein A, and phycoerythrin-avidin conjugates were prepared. These conjugates bind specifically to beads containing a covalently attached target molecule and render them highly fluorescent. Femtomole (10(-15) mole) quantities of phycoerythrin conjugates can be detected because of the high extinction coefficient (epsilon M = 2.4 x 10(6) cm-1 M-1 for 2.4 x 10(5) daltons) and high fluorescence quantum yield (Q = 0.8) of the phycobiliprotein moiety. An important feature of these conjugates is that they emit in the orange-red spectral region, where background fluorescence is less than at shorter wavelengths. Phycoerythrin conjugates are well-suited for two-color flow cytofluorimetric analyses employing a single excitation line. The distributions of Leu antigens (also called OKT antigens) on the surface of T-lymphocytes were analyzed using fluoresceinated antibody as the green-fluorescent stain and biotinylated antibody counter-stained with phycoerythrin-avidin as the red one. This one-laser two-color analysis showed that cells express Leu-3a and Leu-3b or neither antigen. In contrast, the distributions of Leu-2a (a marker of suppressor and cytotoxic T-cells) and Leu-3a (a marker of helper and inducer T-cells) are mutually exclusive. These studies show that phycobiliprotein conjugates can be applied to fluorescence-activated cell sorting and analysis, fluorescence microscopy, and fluorescence immunoassay.