Primary structure of allophycocyanin from the unicellular rhodophyte, Cyanidium caldarium. The complete amino acid sequences of the alpha and beta subunits

Molecular replacement studies on crystal structure of allophycocyanin from red algaePorphyra yezoensis

Using the crystal structure of allophycocyanin from cyanobacteriumSpirulina platensis (APC-SP) as a search model, the crystal structure of allophycocyanin from red algaePorphyra yezoensis (APC-PY) has been studied by molecular replacement methods. The APC-PY crystals (Form 3) belong to the space group of R32, cell dimensions a =b = 10.53 nm,c = 18.94 nm, alpha= beta = 90 degrees , gamma= 120 degrees ; there is one alphabeta monomer in each crystallographic asymmetric unit in the cell. The translation function search gave a unique peak with a correlation coefficient (Cc) of 67.0% and an R-factor of 36.1 % for reflection data from 1.0 to 0.4 nm. Using the results by molecular replacement, the initial model of APC-PY was built, and the coincidence of the chromophore in APC-PY initial model with its2F (o)- F(c) OMIT map further confirms the results by molecular replacement.

Localization of noncovalent complexes in MALDI-preparations by CLSM

The unambiguous detection of noncovalent complexes (NCCs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is still a far cry from being routine. For protein NCCs such as their quaternary structure it has been reported that signals of the intact complex are only obtained for the first or at most the first few laser exposures of a given sample area. This observation was called the first-shot phenomenon. In the present study, this first-shot phenomenon has been investigated for the hexameric protein complex allophycocyanine (APC) by two independent methods, MALDI-MS with a (nearly) pH-neutral matrix 6-aza-2-thiothymine (6-ATT) and by imaging the fluorescence of the complex in APC-6-ATT preparations by confocal laser scan microscopy (CLSM). The intact APC heterohexamer loses its visible fluorescence upon dissociation into its subunits. Both methods consistently show that intact APC complexes are precipitated at the matrix crystal surface, but dissociate upon incorporation into the matrix crystals.

Identification and characterization of a new class of bilin lyase: the cpcT gene encodes a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the beta-subunit of phycocyanin in Synechococcus sp. PCC 7002

Synechococcus sp. PCC 7002 and all other cyanobacteria that synthesize phycocyanin have a gene, cpcT, that is paralogous to cpeT, a gene of unknown function affecting phycoerythrin synthesis in Fremyella diplosiphon. A cpcT null mutant contains 40% less phycocyanin than wild type and produces smaller phycobilisomes with red-shifted absorbance and fluorescence emission maxima. Phycocyanin from the cpcT mutant has an absorbance maximum at 634 nm compared with 626 nm for the wild type. The phycocyanin beta-subunit from the cpcT mutant has slightly smaller apparent molecular weight on SDS-PAGE. Purified phycocyanins from the cpcT mutant and wild type were cleaved with formic acid, and the products were analyzed by SDS-PAGE. No phycocyanobilin chromophore was bound to the peptide containing Cys-153 derived from the phycocyanin beta-subunit of the cpcT mutant. Recombinant CpcT was used to perform in vitro bilin addition assays with apophycocyanin (CpcA/CpcB) and phycocyanobilin. Depending on the source of phycocyanobilin, reaction products with CpcT had absorbance maxima between 597 and 603 nm as compared with 638 nm for the control reactions, in which mesobiliverdin becomes covalently bound. After trypsin digestion and reverse phase high performance liquid chromatography, the CpcT reaction product produced one major phycocyanobilin-containing peptide. This peptide had a retention time identical to that of the tryptic peptide that includes phycocyanobilin-bound, cysteine 153 of wild-type phycocyanin. The results from characterization of the cpcT mutant as well as the in vitro biochemical assays demonstrate that CpcT is a new phycocyanobilin lyase that specifically attaches phycocyanobilin to Cys-153 of the phycocyanin beta-subunit.

Allophycocyanin and energy transfer

Allophycocyanin is a biliprotein located in the core of the phycobilisome. The biliprotein is isolated and purified as a trimer (alpha3beta3), where a monomer is an alphabeta structure. Each alpha and beta subunit has a single noncyclic tetrapyrrole chromophore, called phycocyanobilin. The trimer of allophycocyanin has an unusual absorption maximum at 650 nm with a shoulder at 620 nm, while the monomer has an absorption maximum at 615 nm. Two explanations have been proposed for the 650-nm maximum. In one, this maximum is produced by the interaction of a particular local protein environment for three of the chromophores, causing them to red shift, while the other three chromophores are at a higher energy. Energy is transferred from the high- to the low-energy chromophores by Förster resonance energy transfer, the donor-acceptor model. In the second proposal, there is strong exciton coupling between two chromophores of the trimer that closely approach across the monomer-monomer interface. The strong interaction causes exciton splitting and a red shift in the absorption. There are three of these strongly coupled chromophore pairs, and energy is transferred between the two-exciton states of a pair by internal conversion. A variety of biophysical methods have been used to examine this question. Although evidence supporting both models has been produced, sophisticated ultra fast fluorescence results from a plethora of approaches now firmly point to the latter strong coupling hypothesis as being more likely. Between the different strongly coupled pairs, Förster resonance energy transfer should occur. For monomers of allophycocyanin, Förster resonance energy transfer occurs between the two chromophores.

Allophycocyanin: trimers, monomers, subunits, and homodimers

Allophycocyanin is a photosynthetic light-harvesting pigment-protein complex located in the phycobilisomes of cyanobacteria and red algae. Using dynamic light scattering and circular dichroism, solutions of purified allophycocyanin were shown to consist of homogeneous trimers (alpha3beta3) with a nonspherical shape over a very wide range of protein concentrations at pH 6.0 and 20 degrees C. Deconvolutions of the visible circular dichroism spectrum of the trimer were carried out for the first determination of the individual spectra of all six-component chromophores. The chromophores were shown to be in different microenvironments that helped determine the spectrum of the trimer. Monomers (alpha beta) that were formed in either the presence of 0.50M NaSCN or at 45 degrees C were shown to be completely reversible to trimers. However, subunits (alpha and beta) that were formed in either the presence of 8M urea or at 60 degrees C, using spectroscopy and gel-filtration column chromatography, were observed to only partially reconstitute trimers. Homodimers (alpha2 and/or beta2) formed during the regeneration of trimers. The homodimer, which was detected for the first time when both subunits were present, was shown to be in equilibrium with its subunits. Unlike the trimer situation, subunits were found to fully reconstitute monomers in the presence of 0.50M NaSCN. These results suggest a route to trimer assembly from subunits with monomers serving as intermediaries and the homodimers forming in a nonproductive step that did not interfere with the overall assembly scheme.

Studies on C-phycocyanin from Cyanidium caldarium, a eukaryote at the extremes of habitat

C-Phycocyanin, a biliprotein, was purified from the red alga, Cyanidium caldarium. This alga grows at temperatures up to 57 degrees C, a very high temperature for a eukaryote, and at pH values down to 0.05. Using the chromophores on C-phycocyanin as naturally occurring reporter groups, the effects of temperature on the stability of the protein were studied by circular dichroism and absorption spectroscopy. The protein was unchanged from 10 to 50 degrees C, which indicates that higher temperatures are not required to cause the protein to be photosynthetically active. At 60 and 65 degrees C, which are above the temperatures at which the alga can survive, the protein undergoes irreversible denaturation. Gel-filtration column chromatography demonstrated that the irreversibility is caused by the dissociation of the trimeric protein to its constitutive polypeptides. Upon cooling, the alpha and beta polypeptides did not reassemble to the trimer. Unlike phycocyanins 645 and 612, the C-phycocyanin does not show a reversible conformational change at moderately high temperatures. At constant temperature, the C-phycocyanin was more stable than a mesophilic counterpart. It is designated a temperature-resistant protein.

Crystal structure of allophycocyanin from red algae Porphyra yezoensis at 2.2-A resolution

The crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) at 2.2-A resolution has been determined by the molecular replacement method. The crystal belongs to space group R32 with cell parameters a = b = 105.3 A, c = 189.4 A, alpha = beta = 90 degrees, gamma = 120 degrees. After several cycles of refinement using program X-PLOR and model building based on the electron density map, the crystallographic R-factor converged to 19.3% (R-free factor is 26.9%) in the range of 10.0 to 2.2 A. The r.m.s. deviations of bond length and angles are 0.015 A and 2.9 degrees, respectively. In the crystal, two APC-PY trimers associate face to face into a hexamer. The assembly of two trimers within the hexamer is similar to that of C-phycocyanin (C-PC) and R-phycoerythrin (R-PE) hexamers, but the assembly tightness of the two trimers to the hexamer is not so high as that in C-PC and R-PE hexamers. The chromophore-protein interactions and possible pathway of energy transfer were discussed. Phycocyanobilin 1alpha84 of APC-PY forms 5 hydrogen bonds with 3 residues in subunit 2beta of another monomer. In R-PE and C-PC, chromophore 1alpha84 only forms 1 hydrogen bond with 2beta77 residue in subunit 2beta. This result may support and explain great spectrum difference exists between APC trimer and monomer.

Cyanobacterial phycobilisomes

Cyanobacterial phycobilisomes harvest light and cause energy migration usually toward photosystem II reaction centers. Energy transfer from phycobilisomes directly to photosystem I may occur under certain light conditions. The phycobilisomes are highly organized complexes of various biliproteins and linker polypeptides. Phycobilisomes are composed of rods and a core. The biliproteins have their bilins (chromophores) arranged to produce rapid and directional energy migration through the phycobilisomes and to chlorophyll a in the thylakoid membrane. The modulation of the energy levels of the four chemically different bilins by a variety of influences produces more efficient light harvesting and energy migration. Acclimation of cyanobacterial phycobilisomes to growth light by complementary chromatic adaptation is a complex process that changes the ratio of phycocyanin to phycoerythrin in rods of certain phycobilisomes to improve light harvesting in changing habitats. The linkers govern the assembly of the biliproteins into phycobilisomes, and, even if colorless, in certain cases they have been shown to improve the energy migration process. The Lcm polypeptide has several functions, including the linker function of determining the organization of the phycobilisome cores. Details of how linkers perform their tasks are still topics of interest. The transfer of excitation energy from bilin to bilin is considered, particularly for monomers and trimers of C-phycocyanin, phycoerythrocyanin, and allophycocyanin. Phycobilisomes are one of the ways cyanobacteria thrive in varying and sometimes extreme habitats. Various biliprotein properties perhaps not related to photosynthesis are considered: the photoreversibility of phycoviolobilin, biophysical studies, and biliproteins in evolution. Copyright 1998 Academic Press.

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

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

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

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

Events in the phytochrome molecule after irradiation

The photoconversion of Pr to Pfr has been investigated by a large number of investigators. We have previously demonstrated that Z, E isomerization of the tetrapyrrole chromophore is involved in the photoconversion. It is the best candidate for the primary photoreaction. Conformation and configuration of the Pr chromophore will be compared with that of chromophores in phycocyanin. The crystal structure of phycocyanin had been elucidated by x-ray analysis. Proton transfer and/or Z, E isomerization of the tetrapyrrole are probably involved in different steps of the photoconversion in phytochrome and in photoreversible phycobiliproteins. Fluorescence decay kinetics of irradiated Pr and intermediate formation show heterogeneity. Possible reasons for this heterogeneity will be discussed.

Adaptive eradication of methionine and cysteine from cyanobacterial light-harvesting proteins

Sulphur is unique among the main elements of living cells in that it is covalently bound to biopolymers but does not occur in the biopolymer backbone. Indeed, most of the bacterial sulphur content resides in the methionine and cysteine side-chains of proteins. The growth yield of an organism under conditions of sulphur limitation could therefore be greatly enhanced by mutations that substitute Met and Cys in the organism's proteins for sulphur-free amino acids. Because the saving in sulphur would increase with such accumulating mutations, Met and Cys changes could be progressively selected. Abundant proteins should be the prime targets of such a selection. A few published observations give credence to this scenario. Sulphate permease, which is abundantly produced by sulphur-starved Salmonella typhimurium, lacks Met and Cys residues. Also, two species of marine purple bacteria synthesize more protein than can be expected from a limited sulphate supply. We now report that the cyanobacterium Calothrix sp. PCC 7601 (referred to here as Calothrix) encodes sulphur-depleted versions of its most abundant proteins--phycocyanin and its auxiliary polypeptides--which it specifically expresses under conditions of sulphur limitation. Although these proteins do not take part in the fixation of sulphur, their elevated synthesis affects the sulphur budget of cyanobacterial cells. Direct evidence is thus provided that the structure of macromolecules can be subject to metabolic optimization.

A novel and inexpensive source of allophycocyanin for multicolor flow cytometry

Allophycocyanin (APC) belongs to a family of phycobiliproteins that are well suited as fluorescent reagents for flow cytometric analysis, since they have a broad excitation spectrum, a large Stoke's shift and they fluoresce with a high quantum yield. The widespread use of APC has been limited by the availability of raw material and high cost of the purified phycobiliprotein. We have assessed the suitability of dry, powdered Spirulina platensis, available at health food stores, as an inexpensive source of APC. APC was extracted from Spirulina platensis by overnight treatment with lysozyme, followed by ammonium sulfate precipitation. APC was then separated from phycocyanin (the only other major phycobiliprotein in Spirulina) by elution of bound material from an hydroxylapatite column using an increasing continuous phosphate gradient. APC isolated in this manner retained its normal trimeric structure. The absorbance and fluorescence excitation and emission spectra of the purified phycobiliproteins were identical to those previously shown for C-PC and APC. APC can be stored concentrated at 4 degrees C, frozen at -70 degrees C, or as a saturated ammonium sulfate precipitate, with no subunit dissociation or change in spectral properties. Moreover, APC has been conjugated to monoclonal and polyclonal antibodies for use in multicolor FACS analysis, with the conjugated antibody activity remaining stable for at least 2 years. Thus, this procedure is a simple, cost-effective method for preparing reagents for multicolor immunofluorescence and flow cytometry.

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%).

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.

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.

Large scale preparation of pure phycobiliproteins

This paper describes simple procedures for the purification of large amounts of phycocyanin and allophycocyanin from the cyanobacterium Microcystis aeruginosa. A homogeneous natural bloom of this organism provided hundreds of kilograms of cells. Large samples of cells were broken by freezing and thawing. Repeated extraction of the broken cells with distilled water released phycocyanin first, then allophycocyanin, and provides supporting evidence for the current models of phycobilisome structure. The very low ionic strength of the aqueous extracts allowed allophycocyanin release in a particulate form so that this protein could be easily concentrated by centrifugation. Other proteins in the extract were enriched and concentrated by large scale membrane filtration. The biliproteins were purified to homogeneity by chromatography on DEAE cellulose. Purity was established by HPLC and by N-terminal amino acid sequence analysis. The proteins were examined for stability at various pHs and exposures to visible light.

Organization and nucleotide sequence of genes encoding core components of the phycobilisomes from Synechococcus 6301

Cyanobacteria possess specialized organelles, called phycobilisomes, which collect and transfer light energy to the reaction centres of photosystem II, in the photosynthetic membrane. Phycobilisomes consist of a central core, mainly composed of allophycocyanin, from which six rods radiate. We report here the isolation, for the first time, of three genes that encode core components of cyanobacterial phycobilisomes. The genes coding for the alpha- and beta-subunit apoproteins of allophycocyanin (apcA and apcB) were cloned from Synechococcus PCC 6301 and subjected to nucleotide sequence analysis. Dowstream of apcB, we found a third open reading frame (apcC) which, by comparison with known amino acid sequences, was assigned to L7.8c, a linker polypeptide associated with phycobiliproteins within the core of the phycobilisomes. Homologies between amino acid sequences deduced from the nucleotide sequence of the Synechococcus PCC 6301 apc genes and the amino acid sequences published for corresponding proteins either from cyanobacteria or chloroplast-like organelles of eukaryotic organisms, are 75% or more. The genetic organization of this photosynthetic gene cluster relative to that observed in the cyanelle genome of the flagellate Cyanophora paradoxa is discussed.

Crystal structure analysis and refinement at 2.5 A of hexameric C-phycocyanin from the cyanobacterium Agmenellum quadruplicatum. The molecular model and its implications for light-harvesting

The crystal structure of the light-harvesting protein-pigment complex C-phycocyanin from the cyanobacterium Agmenellum quadruplicatum has been determined by Patterson search techniques on the basis of the molecular model of C-phycocyanin from Mastigocladus laminosus. The crystal unit cell (space group P321) contains three (alpha beta)6 hexamers centred on the crystallographic triads. The hexamer at the origin of the unit cell exhibits crystallographic 32 point symmetry. The other two hexamers (independent of the former) show crystallographic 3-fold and local 2-fold symmetry. The 3-fold redundancy of the asymmetric unit of the crystal cell was used in the refinement process, which proceeded by cyclic averaging, model building and energy-restrained crystallographic refinement. Refinement was terminated with a conventional crystallographic R-value of 0.20 with data to 2.5 A resolution. The two independent hexamers of the unit cell are identical within the limits of error at all levels of aggregation. Two trimers, which closely resemble the M. laminosus C-phycocyanin, are aggregated head-to-head to form the hexamer. Both trimers fit complementarily and are held together by polar and ionic interactions. Conservation of the amino acid residues involved in protein-chromophore and intermonomer interactions suggests common structural features for all biliproteins. Most probably, the hexameric aggregation form present in the crystals is closely related to the discs of native phycobilisome rods. All tetrapyrrole chromophores are extended but with different geometries enforced by different protein surroundings. In particular, interactions of the propionic side-chains with arginine residues and of the pyrrole nitrogen atoms with aspartate residues define configuration and conformation of the chromophores. Relative chromophore distances and orientations have been determined and a preferential pathway for the energy transfer suggested. Accordingly, within a hexamer the absorbed energy is funneled to chromophore B84 and then transduced via B84 chromophores along the phycobilisome rods.

Phycobilisome structure and function

Phycobilisomes are aggregates of light-harvesting proteins attached to the stroma side of the thylakoid membranes of the cyanobacteria (blue-green algae) and red algae. The water-soluble phycobiliproteins, of which there are three major groups, tetrapyrrole chromophores covalently bound to apoprotein. Several additional protiens are found within the phycobilisome and serve to link the phycobiliproteins to each other in an ordered fashion and also to attach the phycobilisome to the thylakoid membrane. Excitation energy absorbed by phycoerythrin is transferred through phycocyanin to allophycocyanin with an efficiency approximating 100%. This pathway of excitation energy transfer, directly confirmed by time-resolved spectroscopic measurements, has been incorporated into models describing the ultrastructure of the phycobilisome. The model for the most typical type of phycobilisome describes an allophycocyanin-containing core composed of three cylinders arranged so that their longitudinal axes are parallel and their ends form a triangle. Attached to this core are six rod structures which contain phycocyanin proximal to the core and phycoerythrin distal to the core. The axes of these rods are perpendicular to the longitudinal axis of the core. This arrangement ensures a very efficient transfer of energy. The association of phycoerythrin and phycocyanin within the rods and the attachment of the rods to the core and the core to the thylakoid require the presence of several 'linker' polypeptides. It is recently possible to assemble functionally and structurally intact phycobilisomes in vitro from separated components as well as to reassociate phycobilisomes with stripped thylakoids. Understanding of the biosynthesis and in vivo assembly of phycobilisomes will be greatly aided by the current advances in molecular genetics, as exemplified by recent identification of several genes encoding phycobilisome components.Combined ultrastructural, biochemical and biophysical approaches to the study of cyanobacterial and red algal cells and isolated phycobilisome-thylakoid fractions are leading to a clearer understanding of the phycobilisome-thylakoid structural interactions, energy transfer to the reaction centers and regulation of excitation energy distribution. However, compared to our current knowledge concerning the structural and functional organization of the isolated phycobilisome, this research area is relatively unexplored.

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.