Cryptomonad biliproteins - an evolutionary perspective

Chirped Laser Pulse Control of Vibronic Wavepackets and Energy Transfer in Phycocyanin 645

Photosynthetic organisms use light-harvesting complexes to increase the spectrum of light that they absorb from solar photons. Recent ultrafast spectroscopic studies have revealed that efficient (sub-ps) energy transfer is mediated by vibronic coherence in the phycobiliprotein phycocyanin 645 (PC645). Here, we report studies that employ broadband pump-probe spectroscopy with linearly chirped excitation pulses to further investigate the relationship between vibronic state preparation and energy transfer dynamics in PC645. Negatively chirped pulse excitation is found to enhance wavepackets of a high-frequency mode (1580 cm-1) and increase the rate of downhill energy transfer, while on the other hand, positively chirped pulses suppress these oscillatory features and decrease this rate. Model calculations incorporating the influence of the chirped pump pulse are used to understand its effect on initial state preparation. These results provide mechanistic insight into how the overall nonequilibrium rate of energy transfer is influenced by initial state preparation.

Variability in spectral absorption within cryptophyte phycobiliprotein types

Cryptophytes are known to vary widely in coloration among species. These differences in color arise primarily from the presence of phycobiliprotein accessory pigments. There are nine defined cryptophyte phycobiliprotein (Cr-PBP) types, named for their wavelength of maximal absorbance. Because Cr-PBP type has traditionally been regarded as a categorical trait, there is a paucity of information about how spectral absorption characteristics of Cr-PBPs vary among species. We investigated variability in primary and secondary peak absorbance wavelengths and full width at half max (FWHM) values of spectra of Cr-PBPs extracted from 75 cryptophyte strains (55 species) grown under full spectrum irradiance. We show that there may be substantial differences in spectral shapes within Cr-PBP types, with Cr-Phycoerythrin (Cr-PE) 545 showing the greatest variability with two, possibly three, subtypes, while Cr-PE 566 spectra were the least variable, with only ±1 nm of variance around the mean absorbance maximum of 565 nm. We provide additional criteria for classification in cases where the wavelength of maximum absorbance alone is not definitive. Variations in spectral characteristics among strains containing the same presumed Cr-PBP type may indicate differing chromophore composition and/or the presence of more than one Cr-PBP in a single cryptophyte species.

Molecular and Supramolecular Materials: From Light-Harvesting to Quantum Information Science and Technology

The past two decades have witnessed immense advances in quantum information technology (QIT), benefited by advances in physics, chemistry, biology, and materials science and engineering. It is intriguing to consider whether these diverse molecular and supramolecular structures and materials, partially inspired by quantum effects as observed in sophisticated biological systems such as light-harvesting complexes in photosynthesis and the magnetic compass of migratory birds, might play a role in future QIT. If so, how? Herein, we review materials and specify the relationship between structures and quantum properties, and we identify the challenges and limitations that have restricted the intersection of QIT and chemical materials. Examples are broken down into two categories: materials for quantum sensing where nonclassical function is observed on the molecular scale and systems where nonclassical phenomena are present due to intermolecular interactions. We discuss challenges for materials chemistry and make comparisons to related systems found in nature. We conclude that if chemical materials become relevant for QIT, they will enable quite new kinds of properties and functions.

How can Phycobilisome, the unique light harvesting system in certain algae working highly efficiently: The connection in between structures and functions

Algae, which are ubiquitous in ecosystems, have evolved a variety of light-harvesting complexes to better adapt to diverse habitats. Phycobilisomes/phycobiliproteins, unique to cyanobacteria, red algae, and certain cryptomonads, compensate for the lack of chlorophyll absorption, allowing algae to capture and efficiently transfer light energy in aquatic environments. With the advancement of microscopy and spectroscopy, the structure and energy transfer processes of increasingly complex phycobilisomes have been elucidated, providing us with a vivid portrait of the dynamic adaptation of their structures to the light environment in which algae thrive: 1) Cyanobacteria living on the surface of the water use short, small phycobilisomes to absorb red-orange light and reduce the damage from blue-violet light via multiple methods; 2) Large red algae inhabiting the depths of the ocean have evolved long and dense phycobilisomes containing phycoerythrin to capture the feeble blue-green light; 3) In far-red light environments such as caves, algae use special allophycocyanin cores to optimally utilize the far-red light; 4) When the environment shifts, algae can adjust the length, composition and density of their rods to better adapt; 5) By carefully designing the position of the pigments, phycobilisomes can transfer light energy to the reaction center with nearly 100% efficiency via three energy transfer processes.

A three-genome ultraconserved element phylogeny of cryptophytes

Cryptophytes are single celled protists found in all aquatic environments. They are composed of a heterotrophic genus, Goniomonas, and a largely autotrophic group comprising many genera. Cryptophytes evolved through secondary endosymbiosis between a host eukaryotic heterotroph and a symbiont red alga. This merger resulted in a four-genome system that includes the nuclear and mitochondrial genomes from the host and a second nuclear genome (nucleomorph) and plastid genome inherited from the symbiont. Here, we make use of different genomes (with potentially distinct evolutionary histories) to perform a phylogenomic study of the early history of cryptophytes. Using ultraconserved elements from the host nuclear genome and symbiont nucleomorph and plastid genomes, we produce a three-genome phylogeny of 91 strains of cryptophytes. Our phylogenetic analyses find that that there are three major cryptophyte clades: Clade 1 comprises Chroomonas and Hemiselmis species, Clade 2, a taxonomically rich clade, comprises at least twelve genera, and Clade 3, comprises the heterotrophic Goniomonas species. Each of these major clades include both freshwater and marine species, but subclades within these clades differ in degrees of niche conservatism. Finally, we discuss priorities for taxonomic revision to Cryptophyceae based on previous studies and in light of these phylogenomic analyses.

Molecular dissection of the soluble photosynthetic antenna from the cryptophyte alga Hemiselmis andersenii

Cryptophyte algae have a unique phycobiliprotein light-harvesting antenna that fills a spectral gap in chlorophyll absorption from photosystems. However, it is unclear how the antenna transfers energy efficiently to these photosystems. We show that the cryptophyte Hemiselmis andersenii expresses an energetically complex antenna comprising three distinct spectrotypes of phycobiliprotein, each composed of two αβ protomers but with different quaternary structures arising from a diverse α subunit family. We report crystal structures of the major phycobiliprotein from each spectrotype. Two-thirds of the antenna consists of open quaternary form phycobiliproteins acting as primary photon acceptors. These are supplemented by a newly discovered open-braced form (~15%), where an insertion in the α subunit produces ~10 nm absorbance red-shift. The final components (~15%) are closed forms with a long wavelength spectral feature due to substitution of a single chromophore. This chromophore is present on only one β subunit where asymmetry is dictated by the corresponding α subunit. This chromophore creates spectral overlap with chlorophyll, thus bridging the energetic gap between the phycobiliprotein antenna and the photosystems. We propose that the macromolecular organization of the cryptophyte antenna consists of bulk open and open-braced forms that transfer excitations to photosystems via this bridging closed form phycobiliprotein.

Infrared Signatures of Phycobilins within the Phycocyanin 645 Complex

Aquatic photosynthetic organisms evolved to use a variety of light frequencies to perform photosynthesis. Phycobiliprotein phycocyanin 645 (PC645) is a light-harvesting complex in cryptophyte algae able to transfer the absorbed green solar light to other antennas with over 99% efficiency. The infrared signatures of the phycobilin pigments embedded in PC645 are difficult to access and could provide useful information to understand the mechanism behind the high efficiency of energy transfer in PC645. We use visible-pump IR-probe and two-dimensional electronic vibrational spectroscopy to study the dynamical evolution and assign the fingerprint mid-infrared signatures to each pigment in PC645. Here, we report the pigment-specific vibrational markers that enable us to track the spatial flow of excitation energy between the phycobilin pigment pairs. We speculate that two high-frequency modes (1588 and 1596 cm^-1) are involved in the vibronic coupling leading to fast (<ps) and direct energy transfer from the highest to lowest exciton, bypassing the intermediate excitons.

Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at least two decades. Although anoxygenic purple and green sulfur bacteria have been well studied, reports on oxygenic phytoplankton have remained sparse since their discovery in the 1920s. Nearly a century later, this study presents the first near-complete genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno, provisionally named Chlorella-like MAG. The 18.9 Mbp nuclear genome displays a high GC content (71.5%), and the phylogenetic placement suggests that it is a novel species of the genus Chlorella of Chlorophytes. Functional annotation of the Chlorella-like metagenome-assembled genome predicted 10,732 protein-coding genes, with an approximate 0.6% proportion potentially involved in carbon, sulfur, and nitrogen (C, N, and S) metabolism. In addition to C4 photosynthesis, this study detected genes for heat shock proteins (HSPs) in the Chlorella-like algae, consistent with the other Chlorella species. Altogether, the genomic insights in this study suggest the cooperation of photosynthetic algae with phototrophic sulfur bacteria via C, N, and S metabolism, which may aid their collective persistence in the Lake Cadagno chemocline. Furthermore, this work additionally presents the chloroplast genome of Cryptomonas-like species, which was likely to be presumed as cyanobacteria in previous studies because of the presence of phycobilisomes.

Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins

In addition to their membrane-bound chlorophyll a/c light-harvesting antenna, the cryptophyte algae have evolved a unique phycobiliprotein antenna system located in the thylakoid lumen. The basic unit of this antenna consists of two copies of an αβ protomer where the α and β subunits scaffold different combinations of a limited number of linear tetrapyrrole chromophores. While the β subunit is highly conserved, encoded by a single plastid gene, the nuclear-encoded α subunits have evolved diversified multigene families. It is still unclear how this sequence diversity results in the spectral diversity of the mature proteins. By careful examination of three newly determined crystal structures in comparison with three previously obtained, we show how the α subunit amino acid sequences control chromophore conformations and hence spectral properties even when the chromophores are identical. Previously we have shown that α subunits control the quaternary structure of the mature αβ.αβ complex (either open or closed), however, each species appeared to only harbor a single quaternary form. Here we show that species of the Hemiselmis genus contain expressed α subunit genes that encode both distinct quaternary structures. Finally, we have discovered a common single-copy gene (expressed into protein) consisting of tandem copies of a small α subunit that could potentially scaffold pairs of light harvesting units. Together, our results show how the diversity of the multigene α subunit family produces a range of mature cryptophyte antenna proteins with differing spectral properties, and the potential for minor forms that could contribute to acclimation to varying light regimes.

Phycobilisomes and Phycobiliproteins in the Pigment Apparatus of Oxygenic Photosynthetics: From Cyanobacteria to Tertiary Endosymbiosis

Eukaryotic photosynthesis originated in the course of evolution as a result of the uptake of some unstored cyanobacterium and its transformation to chloroplasts by an ancestral heterotrophic eukaryotic cell. The pigment apparatus of Archaeplastida and other algal phyla that emerged later turned out to be arranged in the same way. Pigment-protein complexes of photosystem I (PS I) and photosystem II (PS II) are characterized by uniform structures, while the light-harvesting antennae have undergone a series of changes. The phycobilisome (PBS) antenna present in cyanobacteria was replaced by Chl a/b- or Chl a/c-containing pigment-protein complexes in most groups of photosynthetics. In the form of PBS or phycobiliprotein aggregates, it was inherited by members of Cyanophyta, Cryptophyta, red algae, and photosynthetic amoebae. Supramolecular organization and architectural modifications of phycobiliprotein antennae in various algal phyla in line with the endosymbiotic theory of chloroplast origin are the subject of this review.

Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop

Lake Cadagno, a permanently stratified high-alpine lake with a persistent microbial bloom in its chemocline, has long been considered a model for the low-oxygen, high-sulfide Proterozoic ocean. Although the lake has been studied for over 25 years, the absence of concerted study of the bacteria, phytoplankton, and viruses, together with primary and secondary production, has hindered a comprehensive understanding of its microbial food web. Here, the identities, abundances, and productivity of microbes were evaluated in the context of Lake Cadagno biogeochemistry. Photosynthetic pigments together with 16S rRNA gene phylogenies suggest the prominence of eukaryotic phytoplankton chloroplasts, primarily chlorophytes. Chloroplasts closely related to those of high-alpine-adapted Ankyra judayi persisted with oxygen in the mixolimnion, where photosynthetic efficiency was high, while chloroplasts of Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. The anoxygenic phototrophic sulfur bacterium Chromatium dominated the chemocline along with Lentimicrobium, a genus of known fermenters. Secondary production peaked in the chemocline, which suggested that anoxygenic primary producers depended on heterotrophic nutrient remineralization. The virus-to-microbe ratio peaked with phytoplankton abundances in the mixolimnion and were at a minimum where Chromatium abundance was highest, trends that suggest that viruses may play a role in the modulation of primary production. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical spatial dynamics, we provide a comprehensive synthesis of the Lake Cadagno microbial loop. This study offers a new ecological perspective on how biological and geochemical connections may have occurred in the chemocline of the Proterozoic ocean, where eukaryotic microbial life is thought to have evolved.

Exchange of a single amino acid residue in the cryptophyte phycobiliprotein lyase GtCPES expands its substrate specificity

Cryptophytes are among the few eukaryotes employing phycobiliproteins (PBP) for light harvesting during oxygenic photosynthesis. In contrast to cyanobacterial PBP that are organized in membrane-associated phycobilisomes, those from cryptophytes are soluble within the chloroplast thylakoid lumen. Their light-harvesting capacity is due to covalent linkage of several open-chain tetrapyrrole chromophores (phycobilins). Guillardia theta utilizes the PBP phycoerythrin 545 with 15,16-dihydrobiliverdin (DHBV) in addition to phycoerythrobilin (PEB) as chromophores. The assembly of PBPs in cryptophytes involves the action of PBP-lyases as shown for cyanobacterial PBP. PBP-lyases facilitate the attachment of the chromophore in the right configuration and stereochemistry. Here we present the functional characterization of the eukaryotic S-type PBP lyase GtCPES. We show GtCPES-mediated transfer and covalent attachment of PEB to the conserved Cys82 of the acceptor PBP β-subunit (PmCpeB) of Prochlorococcus marinus MED4. On the basis of the previously solved crystal structure, the GtCPES binding pocket was investigated using site-directed mutagenesis. Thereby, amino acid residues involved in phycobilin binding and transfer were identified. Interestingly, exchange of a single amino acid residue Met67 to Ala extended the substrate specificity to phycocyanobilin (PCB), most likely by enlarging the substrate-binding pocket. Variant GtCPES_M67A binds both PEB and PCB forming a stable, colored complex in vitro and produced in Escherichia coli. GtCPES_M67A is able to mediate PCB transfer to Cys82 of PmCpeB. Based on these findings, we postulate that this single amino acid residue has a crucial role for bilin binding specificity of S-type phycoerythrin lyases but additional factors regulate handover to the target protein.

Hemiselmis aquamarina sp. nov. (Cryptomonadales, Cryptophyceae), A Cryptophyte with A Novel Phycobiliprotein Type (Cr-PC 564)

Cryptophytes are a small group of photosynthetic biflagellate organisms distributed worldwide in fresh, brackish and marine waters. Although members of this class are easily distinguished from other groups, species identification is difficult and studies concerning their diversity are scarce. Two strains of an undescribed Hemiselmis species were isolated from the marine waters off Brazil and Japan. Analyses of morphology, phycobiliprotein spectral characterization, molecular phylogeny and ITS2 secondary structure comparisons were performed to assist the identification. The morphological features of Hemiselmis aquamarina sp. nov. matches that of other species from the same genus, but it has a new type of phycocyanin. Molecular phylogeny and ITS2 secondary structure support H. aquamarina as a distinct species. Furthermore, phylogenetic inferences indicate H. aquamarina as closely related to H. tepida, H. andersenii and H. rufescens. Currently, all Hemiselmis species have been described from the Northern Hemisphere and most from the subtropical region. H. aquamarina is the first species of this genus described from the South Atlantic.

Estimation of the relative contributions to the electronic energy transfer rates based on Förster theory: The case of C-phycocyanin chromophores

In the present study, we provide a reformulation of the theory originally proposed by Förster which allows for simple and convenient formulas useful to estimate the relative contributions of transition dipole moments of a donor and acceptor (chemical factors), their orientation factors (intermolecular structural factors), intermolecular center-to-center distances (intermolecular structural factors), spectral overlaps of absorption and emission spectra (photophysical factors), and refractive index (material factor) to the excitation energy transfer (EET) rate constant. To benchmark their validity, we focused on the EET occurring in C-phycocyanin (C-PC) chromophores. To this aim, we resorted to quantum chemistry calculations to get optimized molecular structures of the C-PC chromophores within the density functional theory (DFT) framework. The absorption and emission spectra, as well as transition dipole moments, were computed by using the time-dependent DFT (TDDFT). Our method was applied to several types of C-PCs showing that the EET rates are determined by an interplay of their specific physical, chemical, and geometrical features. These results show that our formulas can become a useful tool for a reliable estimation of the relative contributions of the factors regulating the EET transfer rate.

Spectroscopic and Photophysical Investigation of Model Dipyrroles Common to Bilins: Exploring Natural Design for Steering Torsion to Divergent Functions

Biliproteins are a unique class of photosynthetic proteins in their diverse, and at times, divergent biophysical function. The two contexts of photosynthetic light harvesting and photoreception demonstrate characteristically opposite criteria for success, with light harvesting demanding structurally-rigid chromophores which minimize excitation quenching, and photoreception requiring structural flexibility to enable conformational isomerization. The functional plasticity borne out in these two biological contexts is a consequence of the structural plasticity of the pigments utilized by biliproteins―linear tetrapyrroles, or bilins. In this work, the intrinsic flexibility of the bilin framework is investigated in a bottom-up fashion by reducing the active nuclear degrees of freedom through model dipyrrole subunits of the bilin core and terminus free of external protein interactions. Steady-state spectroscopy was carried out on the dipyrrole (DPY) and dipyrrinone (DPN) subunits free in solution to characterize their intrinsic spectroscopic properties including absorption strengths and nonradiative activity. Transient absorption (TA) spectroscopy was utilized to determine the mechanism and kinetics of nonradiative decay of the dipyrrole subunits, revealing dynamics dominated by rapid internal conversion with some Z→E isomerization observable in DPY. Computational analysis of the ground state conformational landscapes indicates enhanced complexity in the asymmetric terminal subunit, and the prediction was confirmed by heterogeneity of species and kinetics observed in TA. Taken together, the large oscillator strengths (f ∼ 0.6) of the dipyrrolic derivatives and chemically-efficient spectral tunability seen through the ∼100 nm difference in absorption spectra, validate Nature's "selection" of multi-pyrrole pigments for light capture applications. However, the rapid deactivation of the excited state via their natural torsional activity when free in solution would limit their effective biological function. Comparison with phytochrome and phycocyanin 645 crystal structures reveals binding motifs within the in vivo bilin environment that help to facilitate or inhibit specific inter-pyrrole twisting vital for protein operation.

Phycoerythrin Association with Photosystem II in the Cryptophyte Alga Rhodomonas salina

# Deceased. Cryptophyte algae belong to a special group of oxygenic photosynthetic organisms containing pigment combination unique for plastids - phycobiliproteins and chlorophyll a/c-containing antenna. Despite the progress in investigation of morphological and ecological features, as well as genome-based systematics of cryptophytes, their photosynthetic apparatus remains poorly understood. The ratio of the photosystems (PS)s I and II is unknown and information on participation of the two antennal complexes in functions of the two photosystems is inconsistent. In the present work we demonstrated for the first time that the cryptophyte alga Rhodomonas salina had the PSI to PSII ratio in thylakoid membranes equal to 1 : 4, whereas this ratio in cyanobacteria and higher plants was known to be 3 : 1 and 1 : 1, respectively. Furthermore, it was established that contrary to the case of cyanobacteria the phycobiliprotein antenna represented by phycoerythrin-545 (PE-545) in R. salina was associated only with the PSII, which indicated specific spatial organization of these protein pigments within the thylakoids that did not facilitate interaction with the PSI.

Chloroplast history clarified by the criterion of light-harvesting complex

Bacterial essence of mitochondria and chloroplasts was initially proclaimed in general outline. Later, the remarkable insight gave way to an elaborate hypothesis. Finally, it took shape of a theory confirmed by molecular biology data. In particular, the rrn operon, which is the key phylogeny marker, locates chloroplasts on the tree of Cyanobacteria. Chloroplast ancestry and diversity can be also traced with the rpoС and psbA genes, rbc operon, and other molecular criteria of prime importance. Another criterion, also highly reliable, is light-harvesting complex (LHC). LHC pigment and protein moieties specify light acclimation strategies in evolutionary retrospect and modern biosphere. The onset of symbiosis between eukaryotic host and pre-chloroplast, as well as further mutual adjustment of partners depended on physiological competence of LHC. In this review, the criterion of LHC is applied to the origin and diversity of chloroplasts. In particular, ancient cyanobacterium possessing tandem antenna (encoded by the cbp genes and the pbp genes, correspondingly), and defined as a prochlorophyte, is argued to be chloroplast ancestor.

Potential Therapeutic Applications of C-Phycocyanin

BACKGROUND

Cancer and other disorders such as inflammation, autoimmune diseases and diabetes are the major health problems observed all over the world. Therefore, identifying a therapeutic target molecule for the treatment of these diseases is urgently needed to benefit public health. C-Phycocyanin (C-PC) is an important light yielding pigment intermittently systematized in the cyanobacterial species along with other algal species. It has numerous applications in the field of biotechnology and drug industry and also possesses antioxidant, anticancer, antiinflammatory, enhanced immune function, including liver and kidney protection properties. The molecular mechanism of action of C-PC for its anticancer activity could be the blockage of cell cycle progression, inducing apoptosis and autophagy in cancer cells.

OBJECTIVES

The current review summarizes an update on therapeutic applications of C-PC, its mechanism of action and mainly focuses on the recent development in the field of C-PC as a drug that exhibits beneficial effects against various human diseases including cancer and inflammation.

CONCLUSION

The data from various studies suggest the therapeutic applications of C-PC such as anti-cancer activity, anti-inflammation, anti-angiogenic activity and healing capacity of certain autoimmune disorders. Mechanism of action of C-PC for its anticancer activity is the blockage of cell cycle progression, inducing apoptosis and autophagy in cancer cells. The future perspective of C-PC is to identify and define the molecular mechanism of its anti-cancer, anti-inflammatory and antioxidant activities, which would shed light on our knowledge on therapeutic applications of C-PC and may contribute significant benefits to global public health.

Diversification of light capture ability was accompanied by the evolution of phycobiliproteins in cryptophyte algae

Evolutionary biologists have long sought to identify phenotypic traits whose evolution enhances an organism's performance in its environment. Diversification of traits related to resource acquisition can occur owing to spatial or temporal resource heterogeneity. We examined the ability to capture light in the Cryptophyta, a phylum of single-celled eukaryotic algae with diverse photosynthetic pigments, to better understand how acquisition of an abiotic resource may be associated with diversification. Cryptophytes originated through secondary endosymbiosis between an unknown eukaryotic host and a red algal symbiont. This merger resulted in distinctive pigment-protein complexes, the cryptophyte phycobiliproteins, which are the products of genes from both ancestors. These novel complexes may have facilitated diversification across environments where the spectrum of light available for photosynthesis varies widely. We measured light capture and pigments under controlled conditions in a phenotypically and phylogenetically diverse collection of cryptophytes. Using phylogenetic comparative methods, we found that phycobiliprotein characteristics were evolutionarily associated with diversification of light capture in cryptophytes, while non-phycobiliprotein pigments were not. Furthermore, phycobiliproteins were evolutionarily labile with repeated transitions and reversals. Thus, the endosymbiotic origin of cryptophyte phycobiliproteins provided an evolutionary spark that drove diversification of light capture, the resource that is the foundation of photosynthesis.

Photopigment, Absorption, and Growth Responses of Marine Cryptophytes to Varying Spectral Irradiance

The underwater light field of lakes, estuaries, and oceans may vary greatly in spectral composition. Phytoplankton in these environments must contain pigments that absorb the available colors of light. If spectral quality changes, acclimation to the new spectral environment would confer an ecological advantage in terms of photosynthesis and growth. Here, we explored the capacity of eight marine cryptophytes to adjust pigmentation in response to changes in spectral irradiance and related effects on light absorption, photosynthetically useable radiation (PUR), and growth rate. The pigment composition of all species changed in some way in response to shifts in spectral irradiance, but not all pigment changes could be considered advantageous in the context of chromatic acclimation. For most species, absorption by chl-a and chl-c₂ resulted in highest absorption in the blue region, highest PUR values for blue-light grown cells, and highest growth rates in blue light. The exception was Chroomonas mesostigmatica (CCMP 1168), which contains a high percentage of Cryptophyte-Phycocyanin (Cr-PC) 645, absorbs strongly in the orange-to-red region of the spectrum, and grew fastest under red light. The position and magnitude of the maximum and secondary absorption peak of Cr-PC 569, the phycobiliprotein pigment of Hemiselmis cryptochromatica, varied with spectral irradiance. The underlying cause remains unknown, but may represent a mechanism by which cryptophytes optimize photon capture.

Light capture and pigment diversity in marine and freshwater cryptophytes

Phenotypic traits associated with light capture and phylogenetic relationships were characterized in 34 strains of diversely pigmented marine and freshwater cryptophytes. Nuclear SSU and partial LSU rDNA sequence data from 33 of these strains plus an additional 66 strains produced a concatenated rooted maximum likelihood tree that classified the strains into 7 distinct clades. Molecular and phenotypic data together support: (i) the reclassification of Cryptomonas irregularis NIES 698 to the genus Rhodomonas, (ii) revision of phycobiliprotein (PBP) diversity within the genus Hemiselmis to include cryptophyte phycocyanin (Cr-PC) 569, (iii) the inclusion of previously unidentified strain CCMP 2293 into the genus Falcomonas, even though it contains cryptophyte phycoerythrin 545 (Cr-PE 545), and (iv) the inclusion of previously unidentified strain CCMP 3175, which contains Cr-PE 545, in a clade with PC-containing Chroomonas species. A discriminant analysis-based model of group membership correctly predicted 70.6% of the clades using three traits: PBP concentration · cell^-1 , the wavelength of PBP maximal absorption, and habitat. Non-PBP pigments (alloxanthin, chl-a, chl-c₂ , α-carotene) did not contribute significantly to group classification, indicating the potential plasticity of these pigments and the evolutionary conservation of the PBPs. Pigment data showed evidence of trade-offs in investments in PBPs vs. chlorophylls (a +c₂ ).

Proteomic analysis of the phycobiliprotein antenna of the cryptophyte alga Guillardia theta cultured under different light intensities

Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel soluble light-harvesting antenna utilizing phycobilin pigments to complement the membrane-intrinsic Chl a/c-binding LHC antenna. This new antenna consists of the plastid-encoded β-subunit, a relic of the ancestral phycobilisome, and a novel nuclear-encoded α-subunit unique to cryptophytes. Together, these proteins form the active α₁β·α₂β-tetramer. In all cryptophyte algae investigated so far, the α-subunits have duplicated and diversified into a large gene family. Although there is transcriptional evidence for expression of all these genes, the X-ray structures determined to date suggest that only two of the α-subunit genes might be significantly expressed at the protein level. Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light. The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied. GtcpeA10 seems to be a special member of the α-subunit family, because it consists of two similar N- and C-terminal domains, which likely are the result of a partial tandem gene duplication. The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.

Synthesis of chlorophyll-c derivatives by modifying natural chlorophyll-a

Chlorophyll-a (Chl-a) was extracted from cyanobacterial cells and modified to methyl pyropheophorbide-a. The 3-vinyl-chlorin was transformed to zinc complex of the corresponding 3-acetyl-porphyrin. The zinc porphyrin was oxidized to give cis-7,8- and 17,18-dihydroxy-chlorins as well cis-7,8-cis-17,18-tetrahydroxybacteriochlorin. After zinc-demetallation, the isolated cis-7,8- and 17,18-diols were reduced at the 3-acetyl group and triply dehydrated under acidic conditions to afford two regioisomeric 3-vinyl-porphyrins, methyl divinyl-pyroprotopheophorbide-a possessing the 8-vinyl group and 17-propionate residue (one of the divinyl-protoChl-a derivatives) and methyl pyropheophorbide-c 1 possessing the 8-ethyl group and 17-acrylate residue (one of the Chl-c 1 derivatives), respectively. The resulting 7,8,17,18-tetrol was reduced and then acidically treated, giving five-fold dehydrated free base porphyrin, methyl pyropheophorbide-c 2 possessing the 3,8-divinyl groups and 17-acrylate residue (one of the Chl-c 2 derivatives). The visible absorption and fluorescence emission spectra of the three semi-synthetic 3-vinyl-porphyrins in dichloromethane were compared with those of the corresponding 8-ethyl-porphyrin bearing the 17-propionate residue, methyl pyroprotopheophorbide-a (one of the protoChl-a derivatives). The Soret and Qy absorption maxima were shifted to longer wavelengths with an increase of π-conjugation in a molecule: protoChl-a (8-CH2CH3/17-CH2CH2COOCH3) < divinyl-protoChl-a (8-CH=CH2/17-CH2CH2COOCH3) < Chl-c 1 (8-CH2CH3/17-CH=CHCOOCH3) < Chl-c 2 derivatives (8-CH=CH2/17-CH=CHCOOCH3). The 17(1),17(2)-dehydrogenation broadened the absorption bands. The emission maxima were bathochromically shifted in the same order. The reaction mechanism of the present dehydration indicates that the biosynthetic pathway of Chls-c would include the hydroxylation of the 17-propionate reside at the 17(1)-position and successive dehydration to the 17-acrylate residue.

Chromophore composition of the phycobiliprotein Cr-PC577 from the cryptophyte Hemiselmis pacifica

The cryptophyte phycocyanin Cr-PC577 from Hemiselmis pacifica is a close relative of Cr-PC612 found in Hemiselmis virescens and Hemiselmis tepida. The two biliproteins differ in that Cr-PC577 lacks the major peak at around 612 nm in the absorption spectrum. Cr-PC577 was thus purified and characterized with respect to its bilin chromophore composition. Like other cryptophyte phycobiliproteins, Cr-PC577 is an (αβ)(α'β) heterodimer with phycocyanobilin (PCB) bound to the α-subunits. While one chromophore of the β-subunit is also PCB, mass spectrometry identified an additional chromophore with a mass of 585 Da at position β-Cys-158. This mass can be attributed to either a dihydrobiliverdin (DHBV), mesobiliverdin (MBV), or bilin584 chromophore. The doubly linked bilin at position β-Cys-50 and β-Cys-61 could not be identified unequivocally but shares spectral features with DHBV. We found that Cr-PC577 possesses a novel chromophore composition with at least two different chromophores bound to the β-subunit. Overall, our data contribute to a better understanding of cryptophyte phycobiliproteins and furthermore raise the question on the biosynthetic pathway of cryptophyte chromophores.

Insights into the biosynthesis and assembly of cryptophycean phycobiliproteins

Phycobiliproteins are employed by cyanobacteria, red algae, glaucophytes, and cryptophytes for light-harvesting and consist of apoproteins covalently associated with open-chain tetrapyrrole chromophores. Although the majority of organisms assemble the individual phycobiliproteins into larger aggregates called phycobilisomes, members of the cryptophytes use a single type of phycobiliprotein that is localized in the thylakoid lumen. The cryptophyte Guillardia theta (Gt) uses phycoerythrin PE545 utilizing the uncommon chromophore 15,16-dihydrobiliverdin (DHBV) in addition to phycoerythrobilin (PEB). Both the biosynthesis and the attachment of chromophores to the apophycobiliprotein have not yet been investigated for cryptophytes. In this study, we identified and characterized enzymes involved in PEB biosynthesis. In addition, we present the first in-depth biochemical characterization of a eukaryotic phycobiliprotein lyase (GtCPES). Plastid-encoded HO (GtHo) was shown to convert heme into biliverdin IXα providing the substrate with a putative nucleus-encoded DHBV:ferredoxin oxidoreductase (GtPEBA). A PEB:ferredoxin oxidoreductase (GtPEBB) was found to convert DHBV to PEB, which is the substrate for the phycobiliprotein lyase GtCPES. The x-ray structure of GtCPES was solved at 2.0 Å revealing a 10-stranded β-barrel with a modified lipocalin fold. GtCPES is an S-type lyase specific for binding of phycobilins with reduced C15=C16 double bonds (DHBV and PEB). Site-directed mutagenesis identified residues Glu-136 and Arg-146 involved in phycobilin binding. Based on the crystal structure, a model for the interaction of GtCPES with the apophycobiliprotein CpeB is proposed and discussed.

Involvement of mammalian bilitranslocase-like protein(s) in chlorophyll catabolism of Pisum sativum L. tissues

Putative pea bilin and cyclic tetrapyrrole transporter proteins were identified by means of an antibody raised against a bilirubin-interacting aminoacidic sequence of mammalian bilitranslocase (TC No. 2.A.65.1.1). The immunochemical approach showed the presence of several proteins mostly in leaf microsomal, chloroplast and tonoplast vesicles. In these membrane fractions, electrogenic bromosulfalein transport activity was also monitored, being specifically inhibited by anti-bilitranslocase sequence antibody. Moreover, the inhibition of transport activity in pea leaf chloroplast vesicles, by both the synthetic cyclic tetrapyrrole chlorophyllin and the heme catabolite biliverdin, supports the involvement of some of these proteins in the transport of linear/cyclic tetrapyrroles during chlorophyll metabolism. Immunochemical localization in chloroplast sub-compartments revealed that these putative bilitranslocase-like transporters are restricted to the thylakoids only, suggesting their preferential implication in the uptake of cyclic tetrapyrrolic intermediates from the stroma during chlorophyll biosynthesis. Finally, the presence of a conserved bilin-binding sequence in different proteins (enzymes and transporters) from divergent species is discussed in an evolutionary context.

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions

CyanoLyase (http://cyanolyase.genouest.org/) is a manually curated sequence and motif database of phycobilin lyases and related proteins. These enzymes catalyze the covalent ligation of chromophores (phycobilins) to specific binding sites of phycobiliproteins (PBPs). The latter constitute the building bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae. Phycobilin lyases sequences are poorly annotated in public databases. Sequences included in CyanoLyase were retrieved from all available genomes of these organisms and a few others by similarity searches using biochemically characterized enzyme sequences and then classified into 3 clans and 32 families. Amino acid motifs were computed for each family using Protomata learner. CyanoLyase also includes BLAST and a novel pattern matching tool (Protomatch) that allow users to rapidly retrieve and annotate lyases from any new genome. In addition, it provides phylogenetic analyses of all phycobilin lyases families, describes their function, their presence/absence in all genomes of the database (phyletic profiles) and predicts the chromophorylation of PBPs in each strain. The site also includes a thorough bibliography about phycobilin lyases and genomes included in the database. This resource should be useful to scientists and companies interested in natural or artificial PBPs, which have a number of biotechnological applications, notably as fluorescent markers.

Flow of excitation energy in the cryptophyte light-harvesting antenna phycocyanin 645

We report a detailed description of the energy migration dynamics in the phycocyanin 645 (PC645) antenna complex from the photosynthetic alga Chroomonas CCMP270. Many of the cryptophyceae are known to populate greater depths than most other algal families, having developed a 99.5% efficient light-harvesting system. In this study, we used femtosecond time-resolved spectroscopy and global analysis to characterize the excited-state dynamics of PC645. Several different pump colors were selected to excite different fractions of the four phycobiliprotein pairs present in the complex. Measurements were also performed at cryogenic temperature to enhance spectral resolution and selectively promote downhill energy transfers. Upon excitation of the highest-energy bilins (dihydrobiliverdins), energy is transferred from the core of the complex to the periphery within 0.82 ps. Four bilins (mesobiliverdin (MBV) A/B and phycocyanobilins (PCB) 158C/D), which are responsible for the central band of the absorption spectrum, show concerted spectral dynamics. These chromophores show a biphasic decay with lifetimes of 0.6 ps (MBV) and 5-7 ps (PCB 158) to the lowest bilin pair (PCB 82C/D) absorbing around 650-657 nm. Within this lifetime of several picoseconds, the excitations reach the PCB 82 bilins on the two poles at the smaller sides of PC645. A slow 44-46 ps energy transfer step to the lowest-energy PCB 82 bilin concludes the dynamics.

The supramolecular architecture, function, and regulation of thylakoid membranes in red algae: an overview

Red algae are a group of eukaryotic photosynthetic organisms. Phycobilisomes (PBSs), which are composed of various types of phycobiliproteins and linker polypeptides, are the main light-harvesting antennae in red algae, as in cyanobacteria. Two morphological types of PBSs, hemispherical- and hemidiscoidal-shaped, are found in different red algae species. PBSs harvest solar energy and efficiently transfer it to photosystem II (PS II) and finally to photosystem I (PS I). The PS I of red algae uses light-harvesting complex of PS I (LHC I) as a light-harvesting antennae, which is phylogenetically related to the LHC I found in higher plants. PBSs, PS II, and PS I are all distributed throughout the entire thylakoid membrane, a pattern that is different from the one found in higher plants. Photosynthesis processes, especially those of the light reactions, are carried out by the supramolecular complexes located in/on the thylakoid membranes. Here, the supramolecular architecture, function and regulation of thylakoid membranes in red algal are reviewed.

MICROSPECTROPHOTOMETRY AS A METHOD TO IDENTIFY KLEPTOPLASTIDS IN THE NAKED FRESHWATER DINOFLAGELLATE GYMNODINIUM ACIDOTUM(1)

A relatively small number of freshwater dinoflagellates are involved in symbiotic association with cryptophytes. The chloroplasts of the cryptophytes are retained by the dinoflagellate and give it the characteristic phycobilin pigmentation, either phycoerythrin or phycocyanin. The pigment characterization of the retained chloroplasts can give precise and accurate information about the type of cryptophyte preyed upon by the dinoflagellate. For this purpose, we performed microspectrophotometric evaluation of the pigments of Gymnodinium acidotum Nygaard and three different cryptophytes present in samples collected from a tributary of the river Arno, in Tuscany (Italy). The comparison of the different spectroscopic data allowed us to discriminate effectively among the cryptophytes preyed upon by the dinoflagellate.

Phylogenetic Relationships among the Cryptophyta: Analyses of Nuclear-Encoded SSU rRNA Sequences Support the Monophyly of Extant Plastid-Containing Lineages

The Cryptophyta comprise photoautotrophic protists with complex plastids which harbor a remnant eukaryotic nucleus (nucleomorph) and a few heterotrophic taxa which either lack a plastid (Goniomonas) or contain a complex plastid devoid of pigments (Ieucoplast; Chilomonas). To resolve the phylogenetic relationships between photosynthetic, leucoplast-containing and aplastidial taxa, we determined complete nuclear-encoded SSU rRNA-sequences from 12 cryptophyte taxa representing the genera Cryptomonas, Chilomonas, Rhodomonas, Chroomonas, Hemiselmis, Proteomonas and Teleaulax and, as an outgroup taxon, Cyanoptyche gloeocystis (Glaucocystophyta). Phylogenetic analyses of SSU rRNA sequences from a total of 24 cryptophyte taxa rooted with 4 glaucocystophyte taxa using distance, parsimony and likelihood methods as well as LogDet transformations invariably position the aplastidial genus Goniomonas as a sister taxon to a monophyletic lineage consisting of all plastid containing cryptophytes including Chilomonas. Among the plastid-containing taxa, we identify six major clades each supported by high bootstrap values: clade I (Cryptomonas and Chilomonas), clade II (Rhodomonas, Pyrenomonas, Rhinomonas and Storeatula), clade III (Guillardia and the 'unidentified cryptophyte' strain CCMP 325), clade IV (Teleaulax and Geminigera), clade V (Proteomonas) and clade VI (Hemiselmis, Chroomonas and Komma). Clade I (Cryptomonas and Chilomonas) represents a sister group to clades II-VI which together form a monophyletic lineage; the phylogenetic relationships between clades II-VI remain largely unresolved. Chilomonas is positioned within the Cryptomonas clade and thus presumably evolved from a photosynthetic taxon of this genus. In our analysis the characters blue and red pigmentation do not correspond with a basal subdivision of the phylum, thus rejecting this character for higher-level classification of cryptophytes. However, different spectroscopic subtypes of phycoerythrin (PE I-III) and phycocyanin (PC II-IV) represent informative characters at a lower taxonomic level. Phycocyanin types are confined to the later diverging clade VI and within Hemiselmis, a species with phycocyanin is monophyletic with two species containing phycoerythrin. This supports previous molecular studies which demonstrated that the β subunit of all cryptophyte biliproteins, regardless of spectroscopic type, is phylogenetically derived from the red algal β-phycoerythrin gene family, therefore the cryptophyte phycocyanins presumably originated by chromophore replacement from phycoerythrin. Our phylogenetic analysis does not support a previous suggestion that the aplastidial cryptophyte Goniomonas evolved from an ancestor containing a complex cryptomonadtype plastid by nucleomorph and plastid loss.

MOLECULAR PHYLOGENY OF PHYCOCYANIN-CONTAINING CRYPTOPHYTES: EVOLUTION OF BILIPROTEINS AND GEOGRAPHICAL DISTRIBUTION(1)

Of 34 strains assigned to the cryptophyte genera Chroomonas Hansg., Hemiselmis Parke, and Komma D. R. A. Hill, distribution patterns of biliproteins, habitats, and sampling sites across a phylogenetic tree have been examined. The combined data set assembled from nuclear SSU rDNA, partial nuclear LSU rDNA, and nucleomorph SSU rDNA sequences comprised 4,083 positions and yielded an almost completely resolved tree. Spectrophotometry of the biliproteins and mapping of the different types of biliproteins onto the phylogenetic tree unveiled a complex evolutionary history. Different from other cryptophyte clades, the types of biliproteins were not generally congruent with clades or subclades of the genera Chroomonas (paraphyletic, phycocyanins [PCs] 645 or 630), Hemiselmis (PCs 612, 630 or phycoerythrin [PE] 555), and Komma (PC 645). At least one putative character reversal took place in the genus Chroomonas. Several changes in biliproteins have been found in the genus Hemiselmis, including two new biliprotein variants that probably originated by slight modifications from PC 612 and PE 555, respectively (PC 577 and PE 545/555). Freshwater and marine/brackish taxa were intermingled across the tree without displaying a specific pattern. In four terminal clades, genetically identical strains have been found to occur both in Europe and in the USA. The Chroomonas/Hemiselmis/Komma clade proved to be the most diverse of all cryptophyte clades concerning types of biliproteins and distribution of clades across marine or freshwater habitats.

NEW MARINE MEMBERS OF THE GENUS HEMISELMIS (CRYPTOMONADALES, CRYPTOPHYCEAE)(1)

Cryptomonads are a ubiquitous and diverse assemblage of aquatic flagellates. The relatively obscure genus Hemiselmis includes some of the smallest of these cells. This genus contained only two species until 1967, when Butcher described seven new marine species mainly on the basis of observations with the light microscope. However, from these seven taxa, only H. amylifera and H. oculata were validly published. Additionally, the features Butcher used to distinguish species have since been questioned, and the taxonomy within Hemiselmis has remained clouded due to the difficulty in unambiguously applying his classification and validating many of his species. As a result, marine strains are often placed into one of three species-H. rufescens Parke, H. virescens Droop, or the invalid H. brunnescens Butcher-based on cell color alone. Here we applied microscopic and molecular tools to 13 publicly available Hemiselmis strains in an effort to clarify species boundaries. SEM failed to provide sufficient morphological variation to distinguish species of Hemiselmis, and results from LM did not correlate with clades found using both molecular phylogenetic and nucleomorph genome karyotype analysis, indicating a high degree of morphological plasticity within species. On the basis of molecular characters and collection geography we recognize four new marine species of Hemiselmis-H. cryptochromatica sp. nov., H. andersenii sp. nov., H. pacifica sp. nov., and H. tepida sp. nov.-from the waters around North America.

Distinctive organization of genes for light-harvesting proteins in the cryptophyte alga Rhodomonas

Cryptophyte algae contain two kinds of light-harvesting protein, phycobiliproteins and chlorophyll a,c-binding proteins. The beta subunit of the phycobiliprotein phycoerythrin (PE) is encoded in the chloroplast. Genes for the other PE polypeptides are located in the nucleus but little is known of their organization. We cloned and sequenced six cpeA genes encoding the phycoerythrin alpha subunit from a genomic library of the cryptophyte Rhodomonas CS24. Derived peptide sequences of the cpeA genes show that alpha subunits occur in at least two forms, a longer alpha1 form and a shorter alpha2 form. Remarkably, all six cpeA genes occur in divergent pairs encoding one alpha1 and one alpha2 subunit. Four cac genes encoding chlorophyll a,c-binding proteins were cloned and sequenced and also found to occur in divergent pairs comprising one cac1 and one cac2 gene. Inspection of the predicted targeting sequences of the alpha1 and alpha2 phycoerythrin polypeptides shows that only the alpha1 polypeptides have a thylakoid lumen targeting sequence, corresponding to the TAT pathway. Given the previously reported lack of a lumen-targeting sequence on the beta subunit, we propose a novel import mechanism in which the entire alpha1alpha2 betabeta phycoerythrin complex is assembled in the stroma and transported into the thylakoid under the direction of the single targeting sequence on the alpha1 protein. The FAP motif implicated in plastid targeting in diatoms appears to be conserved in this cryptophyte.

Multiple Independent Losses of Photosynthesis and Differing EvolutionaryRates in the Genus Cryptomonas (Cryptophyceae): Combined Phylogenetic Analyses of DNA Sequences of the Nuclear and the Nucleomorph Ribosomal Operons

In this study, evidence for at least three independent losses of photosynthesis in the freshwater cryptophyte genus Cryptomonas is presented. The phylogeny of the genus was inferred by molecular phylogenetic analyses of the nuclear internal transcribed spacer 2 (nuclear ITS2), partial nuclear large subunit ribosomal DNA (LSU rDNA), and nucleomorph small subunit ribosomal DNA (SSU rDNA, NM). Both concatenated and single data sets were used. In all data sets, the colorless Cryptomonas strains formed three different lineages, always supported by high bootstrap values (maximum parsimony, neighbor joining and maximum likelihood) and posterior probabilities (Bayesian analyses). The three leukoplast-bearing lineages displayed differing degrees of accelerated evolutionary rates in nuclear and nucleomorph rDNA. Also an increase in A + T-content in highly variable regions of the nucleomorph SSU rDNA was observed in one of the leukoplast-bearing lineages.

Finding important sites in protein sequences

By using sequence information from an aligned protein family, a procedure is exhibited for finding sites that may be functionally or structurally critical to the protein. Features based on sequence conservation within subfamilies in the alignment and associations between sites are used to select the sites. The sites are subject to statistical evaluation correcting for phylogenetic bias in the collection of sequences. This method is applied to two families: the phycobiliproteins, light-harvesting proteins in cyanobacteria, red algae, and cryptomonads, and the globins that function in oxygen storage and transport. The sites identified by the procedure are located in key structural positions and merit further experimental study.

The role of UV-B radiation in aquatic and terrestrial ecosystems--an experimental and functional analysis of the evolution of UV-absorbing compounds

We analysed and compared the functioning of UV-B screening pigments in plants from marine, fresh water and terrestrial ecosystems, along the evolutionary line of cyanobacteria, unicellular algae, primitive multicellular algae, charophycean algae, lichens, mosses and higher plants, including amphibious macrophytes. Lichens were also included in the study. We were interested in the following key aspects: (a) does the water column function effectively as an 'external UV-B filter'?; (b) do aquatic plants need less 'internal UV-B screening' than terrestrial plants?; (c) what role does UV screening play in protecting the various plant groups from UV-B damage, such as the formation of thymine dimers?; and (d) since early land 'plants' (such as the predecessors of present-day cyanobacteria, lichens and mosses) experienced higher UV-B fluxes than higher plants, which evolved later, are primitive aquatic and land organisms (cyanobacteria, algae, lichens, mosses) better adapted to present-day levels of UV-B than higher plants? Furthermore, polychromatic action spectra for the induction of UV screening pigments of aquatic organisms have been determined. This is relevant for translating 'physical' radiation measurements of solar UV-B into 'biological' and 'ecological' effects. From the action spectra, radiation amplification factors (RAFs) have been calculated. These action spectra allow us to determine any mitigating or antagonistic effects in the ecosystems and therefore qualify the damage prediction for the ecosystems under study. We summarize and discuss the main results based on three years of research of four European research groups. The central theme of the work was the investigation of the effectiveness of the various screening compounds from the different species studied in order to gain some perspective of the evolutionary adaptations from lower to higher plant forms. The induction of mycosporine-like amino acids (MAAs) was studied in the marine dinoflagellate Gyrodinium dorsum, the green algal species Prasiola stipitata and in the cyanobacterium Anabaena sp. While visible (400-700 nm) and long wavelength UV-A (315-400 nm) showed only a slight effect, MAAs were effectively induced by UV-B (280-315 nm). The growth of the lower land organisms studied, i.e. the lichens Cladina portentosa, Cladina foliacaea and Cladonia arbuscula, and the club moss Lycopodiumannotinum, was not significantly reduced when grown under elevated UV-B radiation (simulating 15% ozone depletion). The growth in length of the moss Tortula ruralis was reduced under elevated UV-B. Of the aquatic plants investigated the charophytes Chara aspera showed decreased longitudinal growth under elevated UV-B. In the 'aquatic higher plants' studied, Ceratophyllum demersum, Batrachium trichophyllum and Potamogeton alpinus, there was no such depressed growth with enhanced UV-B. In Chara aspera, neither MAAs nor flavonoids could be detected. Of the terrestrial higher plants studied, Fagopyrum esculentum, Deschampsia antarctica, Vicia faba, Calamagrostis epigejos and Carex arenaria, the growth of the first species was depressed with enhanced UV-B, in the second species length growth was decreased, but the shoot number was increased, and in the latter two species of a dune grassland there was no reduced growth with enhanced UV-B. In the dune grassland species studied outdoors, at least five different flavonoids appeared in shoot tissue. Some of the flavonoids in the monocot species, which were identified and quantified with HPLC, included orientin, luteolin, tricin and apigenin. A greenhouse study with Vicia faba showed that two flavonoids (aglycones) respond particularly to enhanced UV-B. Of these, quercetin is UV-B inducible and mainly located in epidermal cells, while kaempferol occurs constitutively. In addition to its UV-screening function, quercetin may also act as an antioxidant. Polychromatic action spectra were determined for induction of the UV-absorbing pigments in three photosynthetic organisms, representing very different taxonomic groups and different habitats. In ultraviolet photobiology, action spectra mainly serve two purposes: (1) identification of the molecular species involved in light absorption; and (2) calculation of radiation amplification factors for assessing the effect of ozone depletion. Radiation amplification factors (RAFs) were calculated from the action spectra. In a somewhat simplified way, RAF can be defined as the percent increase of radiation damage for a 1% depletion of the ozone layer. Central European summer conditions were used in the calculations, but it has been shown that RAF values are not critically dependent on latitude or season. If only the ultraviolet spectral region is considered, the RAF values obtained are 0.7 for the green alga Prasiola stipitata, 0.4 for the dinoflagellate Gyrodinium dorsum, and 1.0 for the cyanobacterium Anabaena sp. In the case of P. stipitata, however, the effect of visible light (PAR, photosynthetically active radiation, 400-700 nm) is sufficient to lower the RAF to about 0.4, while the PAR effect for G. dorsum is negligible. RAFs for some damage processes, such as for DNA damage (RAF=2.1 if protective effects or photorepair are not considered [1]), are higher than those above. Our interpretation of this is that if the ozone layer is depleted, increased damaging radiation could overrule increased synthesis of protective pigments. In addition to investigating the functional effectiveness of the different screening compounds, direct UV effects on a number of key processes were also studied in order to gain further insight into the ability of the organisms to withstand enhanced UV-B radiation. To this end, the temperature-dependent repair of cyclobutane dimers (CPD) and (6-4) photoproducts induced by enhanced UV-B was studied in Nicotiana tabacum, and the UV-B induction of CPD was studied in the lichen Cladonia arbuscula. Also, photosynthesis and motility were monitored and the response related to the potential function of the screening compounds of the specific organism.

Recovery of pure B-phycoerythrin from the microalga Porphyridium cruentum

Phycoerythrin is a major light-harvesting pigment of red algae and cyanobacteria that is widely used as a fluorescent probe and analytical reagent. In this paper, B-phycoerythrin and R-phycocyanin in native state, from the red alga Porphyridium cruentum were obtained by an inexpensive and simple process. The best results of this purification procedure were scaled up by a factor of 13 to a large preparative level using an anionic chromatographic column of DEAE cellulose. Gradient elution with acetic acid-sodium acetate buffer (pH 5.5) was used. In these conditions both 32% of B-phycoerythrin and 12% of R-phycocyanin contained in the biomass of the microalgae was recovered. B-phycoerythrin was homogeneous as determined by sodium dodecyl sulfate-poly-acrylamide gel electrophoresis (SDS-PAGE), yielding three migrating bands corresponding to its three subunits, consistent with the (alpha beta)(6)gamma subunit composition characteristic of this biliprotein and the spectroscopic characterization of B-PE (UV-visible absorption and emission spectroscopy; steady-state and polarization fluorescence), is accompanied. Finally, a preliminary cost analysis of the recovery process is presented.

Characterization of a phycoerythrin without alpha-subunits from a unicellular red alga

We describe here the spectral and biochemical properties of a novel biliprotein belonging to the phycoerythrin family, purified from the phycobilisome of a unicellular red alga, Rhodella reticulata strain R6. This biliprotein is assembled from a unique beta-type subunit, chloroplast-encoded, whose hexameric or dodecameric aggregates are stabilized by unusually large linkers (87 and 60 kDa) encoded by the nuclear genome. Although each beta-type subunit bears two phycoerythrobilins and one phycocyanobilin per chain, the linker polypeptides are non-chromophorylated. The apoprotein of the beta-subunit of the R. reticulata R6 phycoerythrin is specified by a monocistronic rpeB chloroplast gene that is split into three exons. We discuss the relationships between R6 beta-phycoerythrin and the previously published polypeptide sequences, the structural consequences due to the absence of an alpha-subunit, and its evolutionary implications.

The origin of red algae and cryptomonad nucleomorphs: A comparative phylogeny based on small and large subunit rRNA sequences of Palmaria palmata, Gracilaria verrucosa, and the Guillardia theta nucleomorph

The complete large subunit rRNA sequences from the red algae Palmaria palmata and Gracilaria verrucosa, and from the nucleomorph of the cryptomonad Guillardia theta, were determined in order to assess their phylogenetic relationships relative to each other and to other eukaryotes. Neighbor-joining, maximum-parsimony, and maximum-likelihood trees were constructed on the basis of small subunit rRNA, large subunit rRNA, and a combination of both molecules. Our results support the hypothesis that the cryptomonad plastid is derived from a primitive red alga, in that an ancient common ancestor of rhodophytes and cryptomonad nucleomorphs is indicated. This cluster shows some affinity with chlorobionts, which could point to a monophyletic origin of green and red plastids. However, the exact branching order of the crown eukaryotes remains uncertain and further research is required.

Crystallization of phycoerythrin 545 of Rhodomonas lens using detergents and unusual additives

Phycoerythrin 545 from the cryptomonad alga, Rhodomonas lens, has been crystallized under a wide variety of conditions. Although this type of photosynthetic light-harvesting protein is water soluble, detergents were always required for crystallization. The crystals were typically poorly ordered, or ordered in only two dimensions. However, crystals that were well-ordered in three dimensions could be obtained under two different conditions. Both used polyethylene glycol as precipitant and the detergent lauryldimethylaminoxide, but the additives that were critical for obtaining well-ordered crystals were propionamide in one case and Cs+/Br- in the other. Crystals obtained in the presence of propionamide have the space group P2(1)2(1)2(1), with cell constants of a = 85.6 angstroms, b = 108.2 angstroms, and c = 131.0 angstroms, and contain two dimers [i.e., 2 x (alpha2beta2)] in the asymmetric unit. They show diffraction to at least 3.0 angstroms resolution. The crystals grown with Cs+/Br- are nearly isomorphous. Both types of crystals show intense, strongly polarized fluorescence, suggesting that energy transfer in the crystals is highly efficient. This should provide a basis for quantitative investigation of the role of exciton interactions in energy transfer in cryptomonad phycobiliproteins.

Characterization of cyanobacterial biliverdin reductase. Conversion of biliverdin to bilirubin is important for normal phycobiliprotein biosynthesis

The Synechocystis sp. PCC 6803 gene (bvdR) encoding biliverdin reductase was amplified by the polymerase chain reaction, cloned, and overexpressed in Escherichia coli as the native form and as a 6-histidine-tagged amino-terminal fusion. The latter form of the enzyme was purified by affinity chromatography and shown to have the appropriate molecular weight by electrospray mass spectrometry. Both forms of the enzyme reduced biliverdin IXalpha using NADPH or NADH, with NADPH as the preferred reductant. The His-tagged enzyme has a Km for biliverdin of 1.3 microM. The pH optimum for the NADPH-dependent activity is 5.8, whereas that for rat biliverdin reductase is at pH 8.7. Absorbance spectra and high performance liquid chromatography retention times of the reaction product reaction match those of authentic bilirubin, the product of the reduction of biliverdin by the mammalian enzymes. These results provide the first evidence for the formation of bilirubin in bacteria. Fully segregated Synechocystis sp. PCC 6803 bvdR interposon mutants produce approximately 85% of the normal amount of phycobilisome cores containing allophycocyanin and other phycocyanobilin-bearing core polypeptides, but no detectable phycocyanin. Thus, surprisingly, the blockage of the conversion of biliverdin to bilirubin interferes with normal phycobiliprotein biosynthesis in cyanobacteria. Possible interpretations of this finding are presented.