Phycobilins of cryptophycean algae. Structures of novel bilins with acryloyl substituents from phycoerythrin 566

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.

Uncovering Research Trends of Phycobiliproteins Using Bibliometric Approach

Phycobiliproteins are gaining popularity as long-term, high-value natural products which can be alternatives to synthetic products. This study analyzed research trends of phycobiliproteins from 1909 to 2020 using a bibliometric approach based on the Scopus database. The current findings showed that phycobiliprotein is a burgeoning field in terms of publications outputs with "biochemistry, genetics, and molecular biology" as the most related and focused subject. The Journal of Applied Phycology was the most productive journal in publishing articles on phycobiliproteins. Although the United States of America (U.S.A.) contributed the most publications on phycobiliproteins, the Chinese Academy of Sciences (China) is the institution with the largest number of publications. The most productive author on phycobiliproteins was Glazer, Alexander N. (U.S.A.). The U.S.A. and Germany were at the forefront of international collaboration in this field. According to the keyword analysis, the most explored theme was the optimization of microalgae culture parameters and phycobiliproteins extraction methods. The bioactivity properties and extraction of phycobiliproteins were identified as future research priorities. Synechococcus and Arthrospira were the most cited genera. This study serves as an initial step in fortifying the phycobiliproteins market, which is expected to exponentially expand in the future. Moreover, further research and global collaboration are necessary to commercialize phycobiliproteins and increase the consumer acceptability of the pigments and their products.

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.

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.

The 42.1 and 53.7 kDa bands in SDS-PAGE of R-phycoerythrin from Polysiphonia urceolata

In SDS-PAGE gels of three purified R-phycoerythrins (R-PEs) isolated from three species of red algae, two bands whose molecular weights were about 40 kDa and 50 kDa can stably be found when the sample loading amount was enough. It is important for structure study of R-PE to clarify what these bands represent and how they are formed. According to results of the second SDS-PAGE, as well as molecular weights, fluorescences under UV and abundance, the 42.1 kDa and 53.7 kDa bands in SDS-PAGE gels of R-PE from Polysiphonia urceolata were believed to be complexes of αβ and βγ1, respectively. Formation of these bands may be related to light and phycourobilins (PUB) in subunits; and appearance of these two bands provided some proofs on position of chromophores and directions of energy transfer in R-PE. R-PE containing γ1 subunit was obviously more stable than R-PE containing γ2 subunit when they were exposed to protein denaturants, so γ subunits of R-PE may play important roles in structural stability of R-PE aggregates and the main forces that maintain the stability of R-PE may be interactions between γ subunit and β subunits.

Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants

Heme-derived linear tetrapyrroles (phytobilins) in phycobiliproteins and phytochromes perform critical light-harvesting and light-sensing roles in oxygenic photosynthetic organisms. A key enzyme in their biogenesis, phycocyanobilin:ferredoxin oxidoreductase (PcyA), catalyzes the overall four-electron reduction of biliverdin IXalpha to phycocyanobilin--the common chromophore precursor for both classes of biliproteins. This interconversion occurs via semireduced bilin radical intermediates that are profoundly stabilized by selected mutations of two critical catalytic residues, Asp105 and His88. To understand the structural basis for this stabilization and to gain insight into the overall catalytic mechanism, we report the high-resolution crystal structures of substrate-loaded Asp105Asn and His88Gln mutants of Synechocystis sp. PCC 6803 PcyA in the initial oxidized and one-electron reduced radical states. Unlike wild-type PcyA, both mutants possess a bilin-interacting axial water molecule that is ejected from the active site upon formation of the enzyme-bound neutral radical complex. Structural studies of both mutants also show that the side chain of Glu76 is unfavorably located for D-ring vinyl reduction. On the basis of these structures and companion (15)N-(1)H long-range HMQC NMR analyses to assess the protonation state of histidine residues, we propose a new mechanistic scheme for PcyA-mediated reduction of both vinyl groups of biliverdin wherein an axial water molecule, which prematurely binds and ejects from both mutants upon one electron reduction, is required for catalytic turnover of the semireduced state.

A brief history of phytochromes

Photosensory proteins enable living things to detect the quantity and quality of the light environment and to transduce that physical signal into biochemical outputs which entrain their metabolism with the ambient light environment. Phytochromes, which photoconvert between red-absorbing P(r) and far-red-absorbing P(fr) states, are the most extensively studied of these interesting proteins. Critical regulators of a number of key adaptive processes in higher plants, including photomorphogenesis and shade avoidance, phytochromes are widespread in photosynthetic and nonphotosynthetic bacteria, and even in fungi. Cyanobacterial genomes also possess a plethora of more distant relatives of phytochromes known as cyanobacteriochromes (CBCRs). Biochemical characterization of representative CBCRs has demonstrated that this class of photosensors exhibits a broad range of wavelength sensitivities, spanning the entire visible spectrum. Distinct protein-bilin interactions are responsible for this astonishing array of wavelength sensitivities. Despite this spectral diversity, all members of the extended family of phytochrome photosensors appear to share a common photochemical mechanism for light sensing: photoisomerization of the 15/16 double bond of the bilin chromophore.

Phycocyanin sensitizes both photosystem I and photosystem II in cryptophyte Chroomonas CCMP270 cells

This article presents an investigation of the energy migration dynamics in intact cells of the unicellular photosynthetic cryptophyte Chroomonas CCMP270 by steady-state and time-resolved fluorescence measurements. By kinetic modeling of the fluorescence data on chlorophyll and phycocyanin 645 excitation (at 400 and 582 nm respectively), it has been possible to show the excited state energy distribution in the photosynthetic antenna of this alga. Excitation energy from phycocyanin 645 is distributed nearly equally between photosystem I and photosystem II with very high efficiency on a 100-ps timescale. The excitation energy trapping times for both photosystem I ( approximately 30 ps) and photosystem I (200 and approximately 540 ps) correspond well to those obtained from experiments on isolated photosystems. The results are compared with previous results for another cryptophyte species, Rhodomonas CS24, and suggest a similar membrane organization for the cryptophytes with the phycobiliproteins tightly packed in the thylakoid lumen around the periphery of the photosystems.

Biosynthesis of open-chain tetrapyrroles in plants, algae, and cyanobacteria

Phycobilins are open-chain tetrapyrroles of plants and algae which act as the chromophores of phycobiliproteins where they function as light energy-harvesting pigments. Phytochromobilin, another open-chain tetrapyrrole, is the chromophore of phytochrome, which functions as a light-sensing pigment in plant development. These open-chain tetrapyrroles are biosynthetically derived from protohaem. Enzyme reactions that convert protohaem to biliverdin IX alpha, and biliverdin IX alpha to phycocyanobilin, have been detected and characterized in extracts of the unicellular rhodophyte Cyanidium caldarium. Algal haem oxygenase and algal biliverdin-IX alpha reductase are both soluble enzymes that use electrons derived from reduced ferredoxin. Biochemical intermediates in the conversion of biliverdin IX alpha to (3E)-phycocyanobilin were identified as 15, 16-dihydrobiliverdin IX alpha, (3Z)-phycoerythrobilin and (3Z)-phycocyanobilin. Separate enzymes catalyse the two two-electron reduction steps in the conversion of biliverdin IX alpha to (3Z)-phycoerythrobilin. Z-to-E isomerization of the phycobilin ethylidine group is catalysed by an enzyme that requires glutathione for activity. Protein-bound phycoerythrobilin can be chemically converted to phytochromobilin which can then be released from the protein by methanolysis. This procedure was used to produce phytochromobilin in quantities sufficient to allow its chemical characterization and use in phytochrome reconstitution experiments. The results indicate that (2R,3E)-phytochromobilin spontaneously condenses with recombinant oat apophytochrome to form photoreversible holoprotein that is spectrally identical to native phytochrome.

Cryptomonad biliproteins: Bilin types and locations

Two crytophycean phycocyanins (Cr-PCs), Hemiselmis strain HP9001 Cr-PC 612 and Falcomonas daucoides Cr-PC 69 were purified and characterized with respect to bilin numbers, types and locations. Each biliprotein carried one bilin on the α subunit and three on the β subunit. Cr-PC 612 carried phycocyanobilin at α-Cys-18, β-Cys-82, and β-Cys-158, and a doubly-linked 15,16-dihydrobiliverdin at β-DiCys-50,61. Cr-PC 569 carried phycocyanobilin at α-Cys-18 and β-Cys-82, a singly-linked Bilin 584 at β-Cys-158, and a doubly-linked Bilin 584 at β-DiCys-50,61. This work, in conjunction with earlier studies on Cr-PE 545, Cr-PE 555, Cr-PE 566, and Cr-PC 645, shows that there is no conserved location for the bilin with longest wavelength visible absorption band among these proteins, and, consequently, that there is no conserved energy transfer pathway common to all native cryptophycean biliproteins. Only phycocyanobilin or phycoerythrobilin is found at β-Cys-82; there is greater bilin variability at the other three attachment sites.

Studies on the dissociation of cryptomonad biliproteins

The spectroscopic properties of two biliproteins, phycocyanin 645 and phycoerythrin 566, have been studied by treating the proteins with two different agents, NaSCN at pH 6.0, or pH 4.0 without NaSCN. For phycoerythrin 566, treatment with NaSCN revealed that the visible CD spectrum of its chromophores was separated into a pair of different spectra, and each of these spectra was observed as a negative and one or more positive bands. For phycocyanin 645, two negative CD bands have been observed previously, together with two or more positive bands, in the dimer (alpha 2 beta 2) state, and NaSCN treatment caused elimination of one of these negative bands. The dimer was stable at pH 6.0, but at pH 4.0 the spectra of phycocyanin 645 had one less negative band than those at pH 6.0. Chromatography demonstrated that phycocyanin 645 was a monomer (alpha beta) at pH 4.0. Monomers of cryptomonad biliproteins have never been observed before. Excitation at 514 nm, in picosecond time-resolved fluorescence studies, produced lifetimes of 11.0 and 45.2 ps for dimers and monomers, respectively. Excitation at 566 nm yielded times of 1.38 and 1.24 ps, for dimers and monomers, respectively. CD in the far UV showed that monomers and dimers had very similar secondary structures. These results have been used to test an hypothesis that proposed two types of exciton splitting among the chromophores of phycocyanin 645, and perhaps phycoerythrin 566 could also have this chromophore organization.

Cryptomonad biliproteins - an evolutionary perspective

Each cryptomonad strain contains only a single spectroscopic type of biliprotein. These biliproteins are isolated as ≈50000 kDa αα'β2 complexes which carry one bilin on the α and three on the β subunit. Six different bilins are present on the cryptomonad biliproteins, two of which (phycocyanobilin and phycoerythrobilin) also occur in cyanobacterial and rhodophytan biliproteins, while four are known only in the cryptomonads. The β subunit is encoded on the chloroplast genome, whereas the α subunits are encoded by a small nuclear multigene family. The β subunits of all cryptomonad biliproteins, regardless of spectroscopic type, have highly conserved amino acid sequences, which show > 80% identity with those of rhodophytan phycoerythrin β subunits. In contrast, cyanobacteria and red algal chloroplasts each contain several spectroscopically distinct biliproteins organized into macromolecular complexes (phycobilisomes). The data on biliproteins, as well as several other lines of evidence, indicate that the cryptomonad biliprotein antenna system is 'primitive' and antedates that of the cyanobacteria. It is proposed that the gene encoding the cryptomonad biliprotein β subunit is the ancestral gene of the gene family encoding cyanobacterial and rhodophytan biliprotein α and β subunits.