Phycobilisome model with novel skeleton-like structures in a glaucocystophyte Cyanophora paradoxa

Assembly of CpcL-phycobilisomes

CpcL-phycobilisomes (CpcL-PBSs) are a reduced type of phycobilisome (PBS) found in several cyanobacteria. They lack the traditional PBS terminal energy emitters, but still show the characteristic red-shifted fluorescence at ~670 nm. We established a method of assembling in vitro a rod-membrane linker protein, CpcL, with phycocyanin, generating complexes with the red-shifted spectral features of CpcL-PBSs. The red-shift arises from the interaction of a conserved key glutamine, Q57 of CpcL in Synechocystis sp. PCC 6803, with a single phycocyanobilin chromophore of trimeric phycocyanin at one of the three β82-sites. This chromophore is the terminal energy acceptor of CpcL-PBSs and donor to the photosystem(s). This mechanism also operates in PBSs from Acaryochloris marina MBIC11017. We then generated multichromic complexes harvesting light over nearly the complete visible range via the replacement of phycocyanobilin chromophores at sites α84 and β153 of phycocyanins by phycoerythrobilin and/or phycourobilin. The results demonstrate the rational design of biliprotein-based light-harvesting elements by engineering CpcL and phycocyanins, which broadens the light-harvesting range and accordingly improves the light-harvesting capacity and may be potentially applied in solar energy harvesting.

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.

GUN4 appeared early in cyanobacterial evolution

Photosynthesis relies on chlorophylls, which are synthesized via a common tetrapyrrole trunk pathway also leading to heme, vitamin B12, and other pigmented cofactors. The first committed step for chlorophyll biosynthesis is insertion of magnesium into protoporphyrin IX by magnesium chelatase. Magnesium chelatase is composed of H-, I-, and D-subunits, with the tetrapyrrole substrate binding to the H-subunit. This subunit is rapidly inactivated in the presence of substrate, light, and oxygen, so oxygenic photosynthetic organisms require mechanisms to protect magnesium chelatase from similar loss of function. An additional protein, GUN4, binds to the H-subunit and to tetrapyrroles. GUN4 has been proposed to serve this protective role via its ability to bind linear tetrapyrroles (bilins). In the current work, we probe the origins of bilin binding by GUN4 via comparative phylogenetic analysis and biochemical validation of a conserved bilin-binding motif. Based on our results, we propose that bilin-binding GUN4 proteins arose early in cyanobacterial evolution and that this early acquisition represents an ancient adaptation for maintaining chlorophyll biosynthesis in the presence of light and oxygen.

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.

A hybrid type of chromatic acclimation regulated by the dual green/red photosensory systems in cyanobacteria

Cyanobacteria are phototrophic bacteria that perform oxygenic photosynthesis. They use a supermolecular light-harvesting antenna complex, the phycobilisome (PBS), to capture and transfer light energy to photosynthetic reaction centers. Certain cyanobacteria alter the absorption maxima and/or overall structure of their PBSs in response to the ambient light wavelength-a process called chromatic acclimation (CA). One of the most well-known CA types is the response to green and red light, which is controlled by either the RcaEFC or CcaSR photosensory system. Here, we characterized a hybrid type of CA in the cyanobacterium Pleurocapsa sp. Pasteur Culture Collection (PCC) 7319 that uses both RcaEFC and CcaSR systems. In vivo spectroscopy suggested that strain PCC 7319 alters the relative composition of green-absorbing phycoerythrin and red-absorbing phycocyanin in the PBS. RNA sequencing and promoter motif analyses suggested that the RcaEFC system induces a gene operon for phycocyanin under red light, whereas the CcaSR system induces a rod-membrane linker gene under green light. Induction of the phycoerythrin genes under green light may be regulated through a yet unidentified photosensory system called the Cgi system. Spectroscopy analyses of the isolated PBSs suggested that hemidiscoidal and rod-shaped PBSs enriched with phycoerythrin were produced under green light, whereas only hemidiscoidal PBSs enriched with phycocyanin were produced under red light. PCC 7319 uses the RcaEFC and CcaSR systems to regulate absorption of green or red light (CA3) and the amount of rod-shaped PBSs (CA1), respectively. Cyanobacteria can thus flexibly combine diverse CA types to acclimate to different light environments.

High Sequence Divergence but Limited Architectural Rearrangements in Organelle Genomes of Cyanophora (Glaucophyta) Species

Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3-fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups.

Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants

The glaucophyte Cyanophora paradoxa represents the most basal member of the kingdom Archaeplastida, but the function and expression of most of its genes are unknown. This information is needed to uncover how functional gene modules, that is groups of genes performing a given function, evolved in the plant kingdom. We have generated a gene expression atlas capturing responses of Cyanophora to various abiotic stresses. The data were included in the CoNekT-Plants database, enabling comparative transcriptomic analyses across two algae and six land plants. We demonstrate how the database can be used to study gene expression, co-expression networks and gene function in Cyanophora, and how conserved transcriptional programs can be identified. We identified gene modules involved in phycobilisome biosynthesis, response to high light and cell division. While we observed no correlation between the number of differentially expressed genes and the impact on growth of Cyanophora, we found that the response to stress involves a conserved, kingdom-wide transcriptional reprogramming, which is activated upon most stresses in algae and land plants. The Cyanophora stress gene expression atlas and the tools found in the https://conekt.plant.tools/ database thus provide a useful resource to reveal functionally related genes and stress responses in the plant kingdom.

What Happened to the Phycobilisome?

The phycobilisome (PBS) is the major light-harvesting complex of photosynthesis in cyanobacteria, red algae, and glaucophyte algae. In spite of the fact that it is very well structured to absorb light and transfer it efficiently to photosynthetic reaction centers, it has been completely lost in the green algae and plants. It is difficult to see how selection alone could account for such a major loss. An alternative scenario takes into account the role of chance, enabled by (contingent on) the evolution of an alternative antenna system early in the diversification of the three lineages from the first photosynthetic eukaryote.

Expansion of phycobilisome linker gene families in mesophilic red algae

The common ancestor of red algae (Rhodophyta) has undergone massive genome reduction, whereby 25% of the gene inventory has been lost, followed by its split into the species-poor extremophilic Cyanidiophytina and the broadly distributed mesophilic red algae. Success of the mesophile radiation is surprising given their highly reduced gene inventory. To address this latter issue, we combine an improved genome assembly from the unicellular red alga Porphyridium purpureum with a diverse collection of other algal genomes to reconstruct ancient endosymbiotic gene transfers (EGTs) and gene duplications. We find EGTs associated with the core photosynthetic machinery that may have played important roles in plastid establishment. More significant are the extensive duplications and diversification of nuclear gene families encoding phycobilisome linker proteins that stabilize light-harvesting functions. We speculate that the origin of these complex families in mesophilic red algae may have contributed to their adaptation to a diversity of light environments.

Widely distributed red algae have experienced massive genome reduction during evolution. Here, using an improved genome assembly of Porphyridium purpureum, Lee et al. show the role of endosymbiotic gene transfer in plastid evolution and the correlation between phycobilisome linker diversification and the red algal radiation.

Ultra-high voltage electron microscopy of primitive algae illuminates 3D ultrastructures of the first photosynthetic eukaryote

A heterotrophic organism 1–2 billion years ago enslaved a cyanobacterium to become the first photosynthetic eukaryote, and has diverged globally. The primary phototrophs, glaucophytes, are thought to retain ancestral features of the first photosynthetic eukaryote, but examining the protoplast ultrastructure has previously been problematic in the coccoid glaucophyte Glaucocystis due to its thick cell wall. Here, we examined the three-dimensional (3D) ultrastructure in two divergent species of Glaucocystis using ultra-high voltage electron microscopy. Three-dimensional modelling of Glaucocystis cells using electron tomography clearly showed that numerous, leaflet-like flattened vesicles are distributed throughout the protoplast periphery just underneath a single-layered plasma membrane. This 3D feature is essentially identical to that of another glaucophyte genus Cyanophora, as well as the secondary phototrophs in Alveolata. Thus, the common ancestor of glaucophytes and/or the first photosynthetic eukaryote may have shown similar 3D structures.

Five Cyanophora (Cyanophorales, Glaucophyta) species delineated based on morphological and molecular data

Cyanophora is an important glaucophyte genus of unicellular biflagellates that may have retained ancestral features of photosynthetic eukaryotes. The nuclear genome of Cyanophora was recently sequenced, but taxonomic studies of more than two strains are lacking for this genus. Furthermore, no study has used molecular methods to taxonomically delineate Cyanophora species. Here, we delimited the species of Cyanophora using light and electron microscopy, combined with molecular data from several globally distributed strains, including one newly established. Using a light microscope, we identified two distinct morphological groups: one with ovoid to ellipsoidal vegetative cells and another with dorsoventrally flattened or broad, bean-shaped vegetative cells containing duplicated plastids. Our light and scanning electron microscopy clearly distinguished three species with ovoid to ellipsoidal cells (C. paradoxa Korshikov, C. cuspidata Tos.Takah. & Nozaki sp. nov., and C. kugrensii Tos.Takah. & Nozaki sp. nov.) and two species with broad, bean-shaped cells (C. biloba Kugrens, B.L.Clay, C.J.Mey. & R.E.Lee and C. sudae Tos.Takah. & Nozaki sp. nov.) based on differences in cell shape and surface ornamentations of the vegetative cells under the field-emission scanning electron microscope. Molecular phylogenetic analyses of P700 chl a apoprotein A2 (psaB) genes and internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (rDNA), as well as a comparison of secondary structures of nuclear rDNA ITS-2 and genetic distances of psaB genes, supported the delineation of five morphological species of Cyanophora.

Phycobilisome: architecture of a light-harvesting supercomplex

The phycobilisome (PBS) is an extra-membrane supramolecular complex composed of many chromophore (bilin)-binding proteins (phycobiliproteins) and linker proteins, which generally are colorless. PBS collects light energy of a wide range of wavelengths, funnels it to the central core, and then transfers it to photosystems. Although phycobiliproteins are evolutionarily related to each other, the binding of different bilin pigments ensures the ability to collect energy over a wide range of wavelengths. Spatial arrangement and functional tuning of the different phycobiliproteins, which are mediated primarily by linker proteins, yield PBS that is efficient and versatile light-harvesting systems. In this review, we discuss the functional and spatial tuning of phycobiliproteins with a focus on linker proteins.