Structural and functional diversification of the light-harvesting complexes in photosynthetic eukaryotes

Ecological diversification of a cyanobacterium through divergence of its novel chlorophyll d-based light-harvesting system

The evolution of novel traits can have important consequences for biological diversification. Novelties such as new structures are associated with changes in both genotype and phenotype that often lead to changes in ecological function.1,2 New ecological opportunities provided by a novel trait can trigger subsequent trait modification or niche partitioning3; however, the underlying mechanisms of novel trait diversification are still poorly understood. Here, we report that the innovation of a new chlorophyll (Chl) pigment, Chl d, by the cyanobacterium Acaryochloris marina was followed by the functional divergence of its light-harvesting complex. We identified three major photosynthetic spectral types based on Chl fluorescence properties for a collection of A. marina laboratory strains for which genome sequence data are available,4,5 with shorter- and longer-wavelength types more recently derived from an ancestral intermediate phenotype. Members of the different spectral types exhibited extensive variation in the Chl-binding proteins as well as the Chl energy levels of their photosynthetic complexes. This spectral-type divergence is associated with differences in the wavelength dependence of both growth rate and photosynthetic oxygen evolution. We conclude that the divergence of the light-harvesting apparatus has consequently impacted A. marina ecological diversification through specialization on different far-red photons for photosynthesis.

Structure and distinct supramolecular organization of a PSII-ACPII dimer from a cryptophyte alga Chroomonas placoidea

Cryptophyte algae are an evolutionarily distinct and ecologically important group of photosynthetic unicellular eukaryotes. Photosystem II (PSII) of cryptophyte algae associates with alloxanthin chlorophyll a/c-binding proteins (ACPs) to act as the peripheral light-harvesting system, whose supramolecular organization is unknown. Here, we purify the PSII-ACPII supercomplex from a cryptophyte alga Chroomonas placoidea (C. placoidea), and analyze its structure at a resolution of 2.47 Å using cryo-electron microscopy. This structure reveals a dimeric organization of PSII-ACPII containing two PSII core monomers flanked by six symmetrically arranged ACPII subunits. The PSII core is conserved whereas the organization of ACPII subunits exhibits a distinct pattern, different from those observed so far in PSII of other algae and higher plants. Furthermore, we find a Chl a-binding antenna subunit, CCPII-S, which mediates interaction of ACPII with the PSII core. These results provide a structural basis for the assembly of antennas within the supercomplex and possible excitation energy transfer pathways in cryptophyte algal PSII, shedding light on the diversity of supramolecular organization of photosynthetic machinery.

Radiocarbon Flux Measurements Provide Insight into Why a Pyroligneous Acid Product Stimulates Plant Growth

Agriculture in the 21st century faces many formidable challenges with the growing global population. Increasing demands on the planet's natural resources already tax existing agricultural practices. Today, many farmers are using biochemical treatments to improve their yields. Commercialized organic biostimulants exist in the form of pyroligneous acid generated by burning agricultural waste products. Recently, we examined the mechanisms through which a commercial pyroligneous acid product, Coriphol™, manufactured by Corigin Solutions, Inc., stimulates plant growth. During the 2023 growing season, outdoor studies were conducted in soybean to examine the effects of different Coriphol™ treatment concentrations on plant growth. Plant height, number of leaves, and leaf size were positively impacted in a dose-dependent manner with 2 gallon/acre soil treatments being optimal. At harvest, this level of treatment boosted crop yield by 40%. To gain an understanding of why Coriphol™ improves plant fitness, follow-up laboratory-based studies were conducted using radiocarbon flux analysis. Here, radioactive 11CO2 was administered to live plants and comparisons were made between untreated soybean plants and plants treated at an equivalent Coriphol™ dose of 2 gallons/acre. Leaf metabolites were analyzed using radio-high-performance liquid chromatography for [11C]-chlorophyll (Chl) a and b components, as well as [11C]-β-carotene (β-Car) where fractional yields were used to calculate metabolic rates of synthesis. Altogether, Coriphol™ treatment boosted rates of Chl a, Chl b, and β-Car biosynthesis 3-fold, 2.6-fold, and 4.7-fold, respectively, and also increased their metabolic turnover 2.2-fold, 2.1-fold, and 3.9-fold, respectively. Also, the Chl a/b ratio increased from 3.1 to 3.4 with treatment. Altogether, these effects contributed to a 13.8% increase in leaf carbon capture.

Integrating the multiple functions of CHLH into chloroplast-derived signaling fundamental to plant development and adaptation as well as fruit ripening

Chlorophyll (Chl)-mediated oxygenic photosynthesis sustains life on Earth. Greening leaves play fundamental roles in plant growth and crop yield, correlating with the idea that more Chls lead to better adaptation. However, they face significant challenges from various unfavorable environments. Chl biosynthesis hinges on the first committed step, which involves inserting Mg2+ into protoporphyrin. This step is facilitated by the H subunit of magnesium chelatase (CHLH) and features a conserved mechanism from cyanobacteria to plants. For better adaptation to fluctuating land environments, especially drought, CHLH evolves multiple biological functions, including Chl biosynthesis, retrograde signaling, and abscisic acid (ABA) responses. Additionally, it integrates into various chloroplast-derived signaling pathways, encompassing both retrograde signaling and hormonal signaling. The former comprises ROS (reactive oxygen species), heme, GUN (genomes uncoupled), MEcPP (methylerythritol cyclodiphosphate), β-CC (β-cyclocitral), and PAP (3'-phosphoadenosine-5'-phosphate). The latter involves phytohormones like ABA, ethylene, auxin, cytokinin, gibberellin, strigolactone, brassinolide, salicylic acid, and jasmonic acid. Together, these elements create a coordinated regulatory network tailored to plant development and adaptation. An intriguing example is how drought-mediated improvement of fruit quality provides insights into chloroplast-derived signaling, aiding the shift from vegetative to reproductive growth. In this context, we explore the integration of CHLH's multifaceted roles into chloroplast-derived signaling, which lays the foundation for plant development and adaptation, as well as fruit ripening and quality. In the future, manipulating chloroplast-derived signaling may offer a promising avenue to enhance crop yield and quality through the homeostasis, function, and regulation of Chls.

Acetyl-Proteomic Profiling of Sorghum bicolor Seedlings after Chitin Treatment Reveals the Involvement of Acetylated Chlorophyll a/b Binding Proteins in the Innate Immune Response

Plant pathogen-associated molecular pattern-triggered immunity (PTI) is affected by post-translational modifications, but the role of acetylation in the PTI responses of Sorghum bicolor remains unclear. In this study, a comprehensive acetyl-proteomic analysis was performed on sorghum seedlings treated with chitin based on label-free protein quantification. Chitin rapidly induced 15 PTI-related genes and 5 defense enzymes. Acetylation was upregulated in sorghum after the chitin treatment, and 579, 895, and 929 acetylated proteins, peptides, and sites, respectively, were identified using high-performance liquid chromatography-tandem mass spectrometry. Acetylation and expression of chlorophyll a/b binding proteins (Lhcs) were significantly upregulated, and they were localized in chloroplasts. Additionally, we found that the expression of Lhcs in vivo enhanced chitin-mediated acetylation. The findings of this study provide a comprehensive assessment of the lysine acetylome in sorghum and a foundation for future study into the regulatory mechanisms of acetylation during chlorophyll synthesis.

Comparative assessment of algaecide performance on freshwater phytoplankton: Understanding differential sensitivities to frame cyanobacteria management

Cyanobacterial bloom represent a growing threat to global water security. With fast proliferation, they raise great concern due to potential health and socioeconomic concerns. Algaecides are commonly employed as a mitigative measure to suppress and manage cyanobacteria. However, recent research on algaecides has a limited phycological focus, concentrated predominately on cyanobacteria and chlorophytes. Without considering phycological diversity, generalizations crafted from these algaecide comparisons present a biased perpective. To limit the collateral impacts of algaecide interventions on phytoplankton communities it is critical to understand differential phycological sensitivities for establishing optimal dosage and tolerance thresholds. This research attempts to fill this knowledge gap and provide effective guidelines to frame cyanobacterial management. We investigate the effect of two common algaecides, copper sulfate (CuSO₄) and hydrogen peroxide (H₂O₂), on four major phycological divisions (chlorophytes, cyanobacteria, diatoms, and mixotrophs). All phycological divisions exhibited greater sensitivity to copper sulfate, except chlorophytes. Mixotrophs and cyanobacteria displayed the highest sensitivity to both algaecides with the highest to lowest sensitivity being observed as follows: mixotrophs, cyanobacteria, diatoms, and chlorophytes. Our results suggest that H₂O₂ represents a comparable alternative to CuSO₄ for cyanobacterial control. However, some eukaryotic divisions such as mixotrophs and diatoms mirrored cyanobacteria sensitivity, challenging the assumption that H₂O₂ is a selective cyanocide. Our findings suggest that optimizing algaecide treatments to suppress cyanobacteria while minimizing potential adverse effects on other phycological members is unattainable. An apparent trade-off between effective cyanobacterial management and conserving non-targeted phycological divisions is expected and should be a prime consideration of lake management.

De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

BACKGROUND

The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies.

RESULTS

In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments.

CONCLUSIONS

Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.

Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus

Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome-wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long-day (LD) and short-day (SD) conditions. A time-series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock-associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis-related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non-model trees.

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.

Phylogenetic, Structural and Functional Evolution of the LHC Gene Family in Plant Species

Light-harvesting chlorophyll a/b-binding (LHC) superfamily proteins play a vital role in photosynthesis. Although the physiological and biochemical functions of LHC genes have been well-characterized, the structural evolution and functional differentiation of the products need to be further studied. In this paper, we report the genome-wide identification and phylogenetic analysis of LHC genes in photosynthetic organisms. A total of 1222 non-redundant members of the LHC family were identified from 42 species. According to the phylogenetic clustering of their homologues with Arabidopsis thaliana, they can be divided into four subfamilies. In the subsequent evolution of land plants, a whole-genome replication (WGD) event was the driving force for the evolution and expansion of the LHC superfamily, with its copy numbers rapidly increasing in angiosperms. The selection pressure of photosystem II sub-unit S (PsbS) and ferrochelatase (FCII) families were higher than other subfamilies. In addition, the transcriptional expression profiles of LHC gene family members in different tissues and their expression patterns under exogenous abiotic stress conditions significantly differed, and the LHC genes are highly expressed in mature leaves, which is consistent with the conclusion that LHC is mainly involved in the capture and transmission of light energy in photosynthesis. According to the expression pattern and copy number of LHC genes in land plants, we propose different evolutionary trajectories in this gene family. This study provides a basis for understanding the molecular evolutionary characteristics and evolution patterns of plant LHCs.

Transcriptomic analysis reveals distinct mechanisms of adaptation of a polar picophytoplankter under ocean acidification conditions

Human emissions of carbon dioxide are causing irreversible changes in our oceans and impacting marine phytoplankton, including a group of small green algae known as picochlorophytes. Picochlorophytes grown in natural phytoplankton communities under future predicted levels of carbon dioxide have been demonstrated to thrive, along with redistribution of the cellular metabolome that enhances growth rate and photosynthesis. Here, using next-generation sequencing technology, we measured levels of transcripts in a picochlorophyte Chlorella, isolated from the sub-Antarctic and acclimated under high and current ambient CO2 levels, to better understand the molecular mechanisms involved with its ability to acclimate to elevated CO2. Compared to other phytoplankton taxa that induce broad transcriptomic responses involving multiple parts of their cellular metabolism, the changes observed in Chlorella focused on activating gene regulation involved in different sets of pathways such as light harvesting complex binding proteins, amino acid synthesis and RNA modification, while carbon metabolism was largely unaffected. Triggering a specific set of genes could be a unique strategy of small green phytoplankton under high CO2 in polar oceans.

Nitrogen and Iron Availability Drive Metabolic Remodeling and Natural Selection of Diverse Phytoplankton during Experimental Upwelling

Nearly half of carbon fixation and primary production originates from marine phytoplankton, and much of it occurs in episodic blooms in upwelling regimes. Here, we simulated blooms limited by nitrogen and iron by incubating Monterey Bay surface waters with subnutricline waters and inorganic nutrients and measured the whole-community transcriptomic response during mid- and late-bloom conditions. Cell counts revealed that centric and pennate diatoms (largely Pseudo-nitzschia and Chaetoceros spp.) were the major blooming taxa, but dinoflagellates, prasinophytes, and prymnesiophytes also increased. Viral mRNA significantly increased in late bloom and likely played a role in the bloom's demise. We observed conserved shifts in the genetic similarity of phytoplankton populations to cultivated strains, indicating adaptive population-level changes in community composition. Additionally, the density of single nucleotide variants (SNVs) declined in late-bloom samples for most taxa, indicating a loss of intraspecific diversity as a result of competition and a selective sweep of adaptive alleles. We noted differences between mid- and late-bloom metabolism and differential regulation of light-harvesting complexes (LHCs) under nutrient stress. While most LHCs are diminished under nutrient stress, we showed that diverse taxa upregulated specialized, energy-dissipating LHCs in low iron. We also suggest the relative expression of NRT2 compared to the expression of GSII as a marker of cellular nitrogen status and the relative expression of iron starvation-induced protein genes (ISIP1, ISIP2, and ISIP3) compared to the expression of the thiamine biosynthesis gene (thiC) as a marker of iron status in natural diatom communities. IMPORTANCE Iron and nitrogen are the nutrients that most commonly limit phytoplankton growth in the world's oceans. The utilization of these resources by phytoplankton sets the biomass available to marine systems and is of particular interest in high-nutrient, low-chlorophyll (HNLC) coastal fisheries. Previous research has described the biogeography of phytoplankton in HNLC regions and the transcriptional responses of representative taxa to nutrient limitation. However, the differential transcriptional responses of whole phytoplankton communities to iron and nitrogen limitation has not been previously described, nor has the selective pressure that these competitive bloom environments exert on major players. In addition to describing changes in the physiology of diverse phytoplankton, we suggest practical indicators of cellular nitrogen and iron status for future monitoring.

Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment

The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the 'core chlorophytes'. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and Hi-C technologies, performed comparative analyses of genome and gene family evolution, and analyzed the transcriptome under various abiotic stresses. Although the genome is relatively small (55 Mb), it shares many traits with core chlorophytes including number of introns and protein-coding genes, messenger RNA (mRNA) lengths, and abundance of transposable elements. Pedinomonas minor is only bounded by the plasma membrane, thriving in temporary habitats that frequently dry out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Horizontal gene transfers from bacteria and fungi have possibly contributed to the evolution of some of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome, their spread enhanced by transposable elements, located at gene boundaries in several of the expanded gene families.

Carotenoids Biosynthesis, Accumulation, and Applications of a Model Microalga Euglenagracilis

The carotenoids, including lycopene, lutein, astaxanthin, and zeaxanthin belong to the isoprenoids, whose basic structure is made up of eight isoprene units, resulting in a C40 backbone, though some of them are only trace components in Euglena. They are essential to all photosynthetic organisms due to their superior photoprotective and antioxidant properties. Their dietary functions decrease the risk of breast, cervical, vaginal, and colorectal cancers and cardiovascular and eye diseases. Antioxidant functions of carotenoids are based on mechanisms such as quenching free radicals, mitigating damage from reactive oxidant species, and hindering lipid peroxidation. With the development of carotenoid studies, their distribution, functions, and composition have been identified in microalgae and higher plants. Although bleached or achlorophyllous mutants of Euglena were among the earliest carotenoid-related microalgae under investigation, current knowledge on the composition and biosynthesis of these compounds in Euglena is still elusive. This review aims to overview what is known about carotenoid metabolism in Euglena, focusing on the carotenoid distribution and structure, biosynthesis pathway, and accumulation in Euglena strains and mutants under environmental stresses and different culture conditions. Moreover, we also summarize the potential applications in therapy preventing carcinogenesis, cosmetic industries, food industries, and animal feed.

Strawberry Vein Banding Virus Movement Protein P1 Interacts With Light-Harvesting Complex II Type 1 Like of Fragaria vesca to Promote Viral Infection

Chlorophyll a/b-binding protein of light-harvesting complex II type 1 like (LHC II-1L) is an essential component of photosynthesis, which mainly maintains the stability of the electron transport chain. However, how the LHC II-1L protein of Fragaria vesca (FvLHC II-1L) affects viral infection remains unclear. In this study, we demonstrated that the movement protein P1 of strawberry vein banding virus (SVBV P1) interacted with FvLHC II-1L in vivo and in vitro by bimolecular fluorescence complementation and pull-down assays. SVBV P1 was co-localized with FvLHC II-1L at the edge of epidermal cells of Nicotiana benthamiana leaves, and FvLHC II-1L protein expression was upregulated in SVBV-infected F. vesca. We also found that FvLHC II-1L effectively promoted SVBV P1 to compensate for the intercellular movement of movement-deficient potato virus X (PVX^ΔP25) and the systemic movement of movement-deficient cucumber mosaic virus (CMV^ΔMP). Transient overexpression of FvLHC II-1L and inoculation of an infectious clone of SVBV showed that the course of SVBV infection in F. vesca was accelerated. Collectively, the results showed that SVBV P1 protein can interact with FvLHC II-1L protein, which in turn promotes F. vesca infection by SVBV.

Investigating the impact of light quality on macromolecular composition of Chaetoceros muelleri

Diatoms (Bacillariophyceae) are important to primary productivity of aquatic ecosystems. This algal group is also a valuable source of high value compounds that are utilised as aquaculture feed. The productivity of diatoms is strongly driven by light and CO2 availability, and macro- and micronutrient concentrations. The light dependency of biomass productivity and metabolite composition is well researched in diatoms, but information on the impact of light quality, particularly the productivity return on energy invested when using different monochromatic light sources, remains scarce. In this work, the productivity return on energy invested of improving growth rate, photosynthetic activity, and metabolite productivity of the diatom Chaetoceros muelleri under defined wavelengths (blue, red, and green) as well as while light is analysed. By adjusting the different light qualities to equal photosynthetically utilisable radiation, it was found that the growth rate and photosynthetic oxygen evolution was unchanged under white, blue, and green light, but it was lower under red light. Blue light improved the productivity return on energy invested for biomass, total protein, total lipid, total carbohydrate, and in fatty acids production, which would suggest that blue light should be used for aquaculture feed production.

Photoprotective energy quenching in the red alga Porphyridium purpureum occurs at the core antenna of the photosystem II but not at its reaction center

Photosynthetic organisms have evolved light-harvesting antennae over time. In cyanobacteria, external phycobilisomes (PBSs) are the dominant antennae, whereas in green algae and higher plants, PBSs have been replaced by proteins of the Lhc family that are integrated in the membrane. Red algae represent an evolutionary intermediate between these two systems, as they employ both PBSs and membrane LHCR proteins as light-harvesting units. Understanding how red algae cope with light is not only interesting for biotechnological applications, but is also of evolutionary interest. For example, energy-dependent quenching (qE) is an essential photoprotective mechanism widely used by species from cyanobacteria to higher plants to avoid light damage; however, the quenching mechanism in red algae remains largely unexplored. Here, we used both pulse amplitude-modulated (PAM) and time-resolved chlorophyll fluorescence to characterize qE kinetics in the red alga Porphyridium purpureum. PAM traces confirmed that qE in P. purpureum is activated by a decrease in the thylakoid lumen pH, whereas time-resolved fluorescence results further revealed the quenching site and ultrafast quenching kinetics. We found that quenching exclusively takes place in the photosystem II (PSII) complexes and preferentially occurs at PSII’s core antenna rather than at its reaction center, with an overall quenching rate of 17.6 ± 3.0 ns⁻¹. In conclusion, we propose that qE in red algae is not a reaction center type of quenching, and that there might be a membrane-bound protein that resembles PsbS of higher plants or LHCSR of green algae that senses low luminal pH and triggers qE in red algae.

The structure of the Physcomitrium patens photosystem I reveals a unique Lhca2 paralogue replacing Lhca4

The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary processes. The photosynthetic machinery of modern flowering plants is adapted to the high light conditions on land. Red-shifted Lhca4 antennae are present in the photosystem I light-harvesting complex of many green-lineage plants but absent in P. patens. The cryo-EM structure of the P. patens photosystem I light-harvesting complex I supercomplex (PSI-LHCI) at 2.8 Å reveals that Lhca4 is replaced by a unique Lhca2 paralogue in moss. This PSI-LHCI supercomplex also retains the PsaM subunit, present in Cyanobacteria and several algal species but lost in vascular plants, and the PsaO subunit responsible for binding light-harvesting complex II. The blue-shifted Lhca2 paralogue and chlorophyll b enrichment relative to flowering plants make the P. patens PSI-LHCI spectroscopically unique among other green-lineage supercomplexes. Overall, the structure represents an evolutionary intermediate PSI with the crescent-shaped LHCI common in vascular plants, and contains a unique Lhca2 paralogue that facilitates the moss's adaptation to low-light niches.

Size and Fluorescence Properties of Algal Photosynthetic Antenna Proteins Estimated by Microscopy

Antenna proteins play a major role in the regulation of light-harvesting in photosynthesis. However, less is known about a possible link between their sizes (oligomerization state) and fluorescence intensity (number of photons emitted). Here, we used a microscopy-based method, Fluorescence Correlation Spectroscopy (FCS), to analyze different antenna proteins at the particle level. The direct comparison indicated that Chromera Light Harvesting (CLH) antenna particles (isolated from Chromera velia) behaved as the monomeric Light Harvesting Complex II (LHCII) (from higher plants), in terms of their radius (based on the diffusion time) and fluorescence yields. FCS data thus indicated a monomeric oligomerization state of algal CLH antenna (at our experimental conditions) that was later confirmed also by biochemical experiments. Additionally, our data provide a proof of concept that the FCS method is well suited to measure proteins sizes (oligomerization state) and fluorescence intensities (photon counts) of antenna proteins per single particle (monomers and oligomers). We proved that antenna monomers (CLH and LHCIIm) are more "quenched" than the corresponding trimers. The FCS measurement thus represents a useful experimental approach that allows studying the role of antenna oligomerization in the mechanism of photoprotection.

Acclimation of photosynthetic apparatus in the mesophilic red alga Dixoniella giordanoi

Eukaryotic algae are photosynthetic organisms capable of exploiting sunlight to fix carbon dioxide into biomass with highly variable genetic and metabolic features. Information on algae metabolism from different species is inhomogeneous and, while green algae are, in general, more characterized, information on red algae is relatively scarce despite their relevant position in eukaryotic algae diversity. Within red algae, the best-known species are extremophiles or multicellular, while information on mesophilic unicellular organisms is still lacunose. Here, we investigate the photosynthetic properties of a recently isolated seawater unicellular mesophilic red alga, Dixoniella giordanoi. Upon exposure to different illuminations, D. giordanoi shows the ability to acclimate, modulate chlorophyll content, and re-organize thylakoid membranes. Phycobilisome content is also largely regulated, leading to almost complete disassembly of this antenna system in cells grown under intense illumination. Despite the absence of a light-induced xanthophyll cycle, cells accumulate zeaxanthin upon prolonged exposure to strong light, likely contributing to photoprotection. D. giordanoi cells show the ability to perform cyclic electron transport that is enhanced under strong illumination, likely contributing to the protection of Photosystem I from over-reduction and enabling cells to survive PSII photoinhibition without negative impact on growth.

Unique Peripheral Antennas in the Photosystems of the Streptophyte Alga Mesostigma viride

Land plants evolved from a single group of streptophyte algae. One of the key factors needed for adaptation to a land environment is the modification in the peripheral antenna systems of photosystems (PSs). Here, the PSs of Mesostigma viride, one of the earliest-branching streptophyte algae, were analyzed to gain insight into their evolution. Isoform sequencing and phylogenetic analyses of light-harvesting complexes (LHCs) revealed that M. viride possesses three algae-specific LHCs, including algae-type LHCA2, LHCA9 and LHCP, while the streptophyte-specific LHCB6 was not identified. These data suggest that the acquisition of LHCB6 and the loss of algae-type LHCs occurred after the M. viride lineage branched off from other streptophytes. Clear-native (CN)-polyacrylamide gel electrophoresis (PAGE) resolved the photosynthetic complexes, including the PSI-PSII megacomplex, PSII-LHCII, two PSI-LHCI-LHCIIs, PSI-LHCI and the LHCII trimer. Results indicated that the higher-molecular weight PSI-LHCI-LHCII likely had more LHCII than the lower-molecular weight one, a unique feature of M. viride PSs. CN-PAGE coupled with mass spectrometry strongly suggested that the LHCP was bound to PSII-LHCII, while the algae-type LHCA2 and LHCA9 were bound to PSI-LHCI, both of which are different from those in land plants. Results of the present study strongly suggest that M. viride PSs possess unique features that were inherited from a common ancestor of streptophyte and chlorophyte algae.

Light Harvesting in Fluctuating Environments: Evolution and Function of Antenna Proteins across Photosynthetic Lineage

Photosynthesis is the major natural process that can harvest and harness solar energy into chemical energy. Photosynthesis is performed by a vast number of organisms from single cellular bacteria to higher plants and to make the process efficient, all photosynthetic organisms possess a special type of pigment protein complex(es) that is (are) capable of trapping light energy, known as photosynthetic light-harvesting antennae. From an evolutionary point of view, simpler (unicellular) organisms typically have a simple antenna, whereas higher plants possess complex antenna systems. The higher complexity of the antenna systems provides efficient fine tuning of photosynthesis. This relationship between the complexity of the antenna and the increasing complexity of the organism is mainly related to the remarkable acclimation capability of complex organisms under fluctuating environmental conditions. These antenna complexes not only harvest light, but also provide photoprotection under fluctuating light conditions. In this review, the evolution, structure, and function of different antenna complexes, from single cellular organisms to higher plants, are discussed in the context of the ability to acclimate and adapt to cope under fluctuating environmental conditions.

Substitution of Deoxycholate with the Amphiphilic Polymer Amphipol A8-35 Improves the Stability of Large Protein Complexes during Native Electrophoresis

Native polyacrylamide gel electrophoresis (PAGE) is a powerful technique for protein complex separation that retains both their activity and structure. In photosynthetic research, native-PAGE is particularly useful given that photosynthetic complexes are generally large in size, ranging from 200 kD to 1 MD or more. Recently, it has been reported that the addition of amphipol A8-35 to solubilized protein samples improved protein complex stability. In a previous study, we found that amphipol A8-35 could substitute sodium deoxycholate (DOC), a conventional electrophoretic carrier, in clear-native (CN)-PAGE. In this study, we present the optimization of amphipol-based CN-PAGE. We found that the ratio of amphipol A8-35 to α-dodecyl maltoside, a detergent commonly used to solubilize photosynthetic complexes, was critical for resolving photosynthetic machinery in CN-PAGE. In addition, LHCII dissociation from PSII-LHCII was effectively prevented by amphipol-based CN-PAGE compared with that of DOC-based CN-PAGE. Our data strongly suggest that majority of the PSII-LHCII in vivo forms C2S2M2 at least in Arabidopsis and Physcomitrella. The other forms might appear owing to the dissociation of LHCII from PSII during sample preparation and electrophoresis, which could be prevented by the addition of amphipol A8-35 after solubilization from thylakoid membranes. These results suggest that amphipol-based CN-PAGE may be a better alternative to DOC-based CN-PAGE for the study of labile protein complexes.

Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium

The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O₂ availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium's adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a diverse set of fermentation pathways allows it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral samples and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching, and recovery.

Exploring Core Response Mechanisms to Multiple Environmental Stressors Via A Genome-Wide Study in the Brown Alga Saccharina japonica (Laminariales, Phaeophyceae)

Saccharina japonica is an important large brown alga and a major component of productive beds on the northwest coast of the Pacific Ocean. Abiotic stress response mechanisms are receiving considerable attention because global climate change is increasing their abiotic stress levels. However, our knowledge of how S. japonica broadly responds to stress is limited. In this study, we investigated the S. japonica responsive genes underlying acclimation to diverse stressors of acidification, high light, high temperature, hypersalinity, and hyposalinity and identified 408 core genes constantly and differentially expressed in response to all stressors. Our results confirm that stressors had strong effects on genes participating in photosynthesis, amino acid metabolism, carbohydrate metabolism, halogen metabolism, and reactive oxygen species defense. These findings will improve our understanding of brown algal response mechanisms linked to environmental stress and provide a list of candidate genes for improving algal stress tolerance in light of environmental stress in future studies.

Adaptation of light-harvesting and energy-transfer processes of a diatom Chaetoceros gracilis to different light qualities

Diatoms are a major group of microalgae in marine and freshwater environments. To utilize the light energy in blue to green region, diatoms possess unique antenna pigment-protein complexes, fucoxanthin chlorophyll a/c-binding proteins (FCPs). Depending on light qualities and quantities, diatoms form FCPs with different energies: normal-type and red-shifted FCPs. In the present study, we examined changes in light-harvesting and energy-transfer processes of a diatom Chaetoceros gracilis cells grown using white- and single-colored light-emitting diodes (LEDs), by means of time-resolved fluorescence spectroscopy. The blue LED, which is harvested by FCPs, modified energy transfer involving CP47, and suppressed energy transfer to PSI. Under the red-LED conditions, which is absorbed by both FCPs and PSs, energy transfer to PSI was enhanced, and the red-shifted FCP appeared. The red-shifted FCP was also recognized under the green- and yellow-LEDs, suggesting that lack of the shorter-wavelength light induces the red-shifted FCP. Functions of the red-shifted FCPs are discussed.

Adaptation of light-harvesting and energy-transfer processes of a diatom Phaeodactylum tricornutum to different light qualities

Fucoxanthin-chlorophyll (Chl) a/c-binding proteins (FCPs) are light-harvesting pigment-protein complexes found in diatoms and brown algae. Due to the characteristic pigments, such as fucoxanthin and Chl c, FCPs can capture light energy in blue-to green regions. A pennate diatom Phaeodactylum tricornutum synthesizes a red-shifted form of FCP under weak or red light, extending a light-absorption ability to longer wavelengths. In the present study, we examined changes in light-harvesting and energy-transfer processes of P. tricornutum cells grown under white- and single-colored light-emitting diodes (LEDs). The red-shifted FCP appears in the cells grown under the green, yellow, and red LEDs, and exhibited a fluorescence peak around 714 nm. Additional energy-transfer pathways are established in the red-shifted FCP; two forms (F713 and F718) of low-energy Chl a work as energy traps at 77 K. Averaged fluorescence lifetimes are prolonged in the cells grown under the yellow and red LEDs, whereas they are shortened in the blue-LED-grown cells. Based on these results, we discussed the light-adaptation machinery of P. tricornutum cells involved in the red-shifted FCP.

Photoconversion Fluoropolymer Films for the Cultivation of Agricultural Plants Under Conditions of Insufficient Insolation

Plants are capable of using mainly the quanta of the red and blue parts of a spectrum for the reception of energy during photosynthesis. However, for many crops grown indoors in high latitudes or under conditions of insufficient insolation, the average daily intensity of the red and blue parts of the spectrum is usually sufficient only on clear summer days. A technology has been proposed to produce a photoconversion fluoropolymer film for greenhouses, which is based on the modification of fluoropolymer by nanoparticles with fluorescence in the blue or red part of the spectrum (quantum dots). The films are capable of converting UV and violet radiation into the blue and red region of the visible spectrum, the most important for plants. It has been shown that the use of photoconversion fluoropolymer films promotes biomass growth. The area of cucumber leaves grown under photoconversion films increases by 20%, pumpkins by 25%, pepper by 30%, and tomatoes by 55%. The use of photoconversion fluoropolymer films for greenhouses also allows obtaining 15% more fruit biomass from one bush. In general, the use of photoconversion fluoropolymer films may be in great demand for greenhouses lying in high latitudes and located in areas with insufficient insolation.

Development and application of photoconversion fluoropolymer films for greenhouses located at high or polar latitudes

To convert and store energy in the process of photosynthesis, plants primarily use quanta of the red and blue parts of the spectrum. At high latitudes, the average daily intensity of red and blue parts of the spectrum is not very high; for many crops cultivated under greenhouse conditions, it reaches the sufficient level only on clear summer days. The problem of insufficient illumination in greenhouses is usually solved with artificial light sources. This article describes a technology for the manufacture of photoconversion fluoropolymer films for greenhouses. The fluoropolymer films described in the paper make use of original gold nanoparticles and nanoparticles with fluorescence in the blue or red region of the spectrum. In the polymer film, nanoparticles aggregate in the form of "beads", which enhances the field of the optical wave. The film photoconverts UV and violet light into blue and red light. Gold nanoparticles also partially convert energy in the green region of the spectrum (not used by plants) into heat, which is also important for agriculture at high latitudes. In addition, impregnation of gold nanoparticles into fluoropolymer significantly increases the lifetime of the film. The films described in the paper can significantly increase the productivity of greenhouses located at high latitudes. Plants cultivated under the films have more chlorophyll and a higher intensity of photosynthesis - although their system of distance stress signals is, to a certain degree, suppressed.

Genome-wide analysis of the light-harvesting chlorophyll a/b-binding gene family in apple (Malus domestica) and functional characterization of MdLhcb4.3, which confers tolerance to drought and osmotic stress

In higher plants, the light-harvesting chlorophyll a/b-binding (Lhc) proteins function in multiple processes that are critical to plant growth, development, and abiotic stress response. However, the Lhc gene family has not been well characterized in the important fruit crop, apple (Malus × domestica Borkh.). In this study, we identified 27 Lhc genes in the apple genome. Phylogenetic analysis showed that the Lhc gene family could be classified into three major subfamilies, each of whose members shared similar conserved motifs. Evolutionary analysis indicated that duplicated MdLhc genes were primarily under purifying selection. MdLhcs were expressed at varying levels in all tissues examined and showed different expression patterns under drought stress. The overexpression of MdLhcb4.3 in transgenic Arabidopsis and apple callus enhanced their tolerance to drought and osmotic stress. Taken together, these results demonstrate the important role of Lhc proteins in the regulation of plant resistance to drought and osmotic stress and provide valuable information for further study of Lhc functions in apple.

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.

From algal cells to autofluorescent ghost plasma membrane vesicles

Plasma membrane vesicles can be effective, non-toxic carriers for microscale material transport, provide a convenient model for probing membrane-related processes, since intracellular biochemical processes are eliminated. We describe here a fine-tuned protocol for isolating ghost plasma membrane vesicles from the unicellular alga Dunaliella tertiolecta, and preliminary characterization of their structural features and permeability properties, with comparisons to giant unilamellar phospholipid vesicles. The complexity of the algal ghost membrane vesicles reconstructed from the native membrane material released after hypoosmotic stress lies between that of phospholipid vesicles and cells. AFM structural characterization of reconstructed vesicles shows a thick envelope and a nearly empty vesicle interior. The surface of the envelope contains a heterogeneous distribution of densely packed, nanometer-scale globules and pore-like structures which may be derived from surface coat proteins. Confocal fluorescence imaging reveals the highly pigmented photosynthetic apparatus located within the thylakoid membrane and retained in the vesicle membrane. Transport of the fluorescent dye calcein into ghost and giant unilamellar vesicles reveals significant differences in permeability. Expanded knowledge of this unique membrane system will contribute to the design of marine bio-inspired carriers for advanced biotechnological applications.

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.

Structural analysis and comparison of light-harvesting complexes I and II

Photosynthesis is a fundamental biological process involving the conversion of solar energy into chemical energy. The initial photochemical and photophysical events of photosynthesis are mediated by photosystem II (PSII) and photosystem I (PSI). Both PSII and PSI are multi-subunit supramolecular machineries composed of a core complex and a peripheral antenna system. The antenna system serves to capture light energy and transfer it to the core efficiently. Both PSII and PSI in the green lineage (plants and green algae) and PSI in red algae have an antenna system comprising a series of chlorophyll- and carotenoid-binding membrane proteins belonging to the light-harvesting complex (LHC) superfamily, including LHCII and LHCI. However, the antenna size and subunit composition vary considerably in the two photosystems from diverse organisms. On the basis of the plant and algal LHCII and LHCI structures that have been solved by X-ray crystallography and single-particle cryo-electron microscopy we review the detailed structural features and characteristic pigment properties of these LHCs in PSII and PSI. This article is part of a Special Issue entitled Light harvesting, edited by Dr. Roberta Croce.

Light harvesting complexes in chlorophyll c-containing algae

Besides the so-called 'green lineage' of eukaryotic photosynthetic organisms that include vascular plants, a huge variety of different algal groups exist that also harvest light by means of membrane intrinsic light harvesting proteins (Lhc). The main taxa of these algae are the Cryptophytes, Haptophytes, Dinophytes, Chromeridae and the Heterokonts, the latter including diatoms, brown algae, Xanthophyceae and Eustigmatophyceae amongst others. Despite the similarity in Lhc proteins between vascular plants and these algae, pigmentation is significantly different since no Chl b is bound, but often replaced by Chl c, and a large diversity in carotenoids functioning in light harvesting and/or photoprotection is present. Due to the presence of Chl c in most of the taxa the name 'Chl c-containing organisms' has become common, however, Chl b-less is more precise since some harbour Lhc proteins that only bind one type of Chl, Chl a. In recent years huge progress has been made about the occurrence and function of Lhc in diatoms, so-called fucoxanthin chlorophyll proteins (FCP), where also the first molecular structure became available recently. In addition, especially energy transfer amongst the unusual pigments bound was intensively studied in many of these groups. This review summarises the present knowledge about the molecular structure, the arrangement of the different Lhc in complexes, the excitation energy transfer abilities and the involvement in photoprotection of the different Lhc systems in the so-called Chl c-containing organisms. This article is part of a Special Issue entitled Light harvesting, edited by Dr. Roberta Croce.

Structural and functional differentiation of the light-harvesting protein Lhcb4 during land plant diversification

About 475 million years ago, plants originated from an ancestral green alga and evolved first as non-vascular and later as vascular plants, becoming the primary producers of biomass on lands. During that time, the light-harvesting complex II (LHCII), responsible for sunlight absorption and excitation energy transfer to the photosystem II (PSII) core, underwent extensive differentiation. Lhcb4 is an ancestral LHCII that, in flowering plants, differentiated into up to three isoforms, Lhcb4.1, Lhcb4.2 and Lhcb4.3. The pivotal position of Lhcb4 in the PSII-LHCII supercomplex (PSII-LHCIIsc) allows functioning as linker for either S- or M-trimers of LHCII to the PSII core. The increased accumulation of Lhcb4.3 observed in PSII-LHCIIsc of plants acclimated to moderate and high light intensities induced us to investigate, whether this isoform has a preferential localization in a specific PSII-LHCIIsc conformation that might explain its light-dependent accumulation. In this work, by combining an improved method for separation of different forms of PSII-LHCIIsc from thylakoids of Pisum sativum L. grown at increasing irradiances with quantitative proteomics, we assessed that Lhcb4.3 is abundant in PSII-LHCIIsc of type C₂ S₂ , and, interestingly, similar results were found for the PsbR subunit. Phylogenetic comparative analysis on different taxa of the Viridiplantae lineage and structural modeling further pointed out to an effect of the evolution of different Lhcb4 isoforms on the light-dependent modulation of the PSII-LHCIIsc organization. This information provides new insight on the properties of the Lhcb4 and its isoforms and their role on the structure, function and regulation of PSII.

Antenna arrangement and energy transfer pathways of a green algal photosystem-I-LHCI supercomplex

During oxygenic photosynthesis, photosystems I and II (PSI and PSII) are essential for light-driven electron transport. Excitation energy transfer in PSI occurs extremely quickly, making it an efficient energy converter. In the alga Chlamydomonas reinhardtii (Cr), multiple units of light-harvesting complex I (LHCI) bind to the PSI core and function as peripheral antennae, forming a PSI-LHCI supercomplex. CrPSI-LHCI shows significantly larger antennae compared with plant PSI-LHCI while maintaining highly efficient energy transfer from LHCI to PSI. Here, we report structures of CrPSI-LHCI, solved by cryo-electron microscopy, revealing that up to ten LHCIs are associated with the PSI core. The structures provide detailed information about antenna organization and pigment arrangement within the supercomplexes. Highly populated and closely associated chlorophylls in the antennae explain the high efficiency of light harvesting and excitation energy transfer in CrPSI-LHCI.

Pigment configuration in the light-harvesting protein of the xanthophyte alga Xanthonema debile

The soil chromophyte alga Xanthonema (X.) debile contains only non-carbonyl carotenoids and Chl-a. X. debile has an antenna system denoted Xanthophyte light-harvesting complex (XLH) that contains the carotenoids diadinoxanthin, heteroxanthin, and vaucheriaxanthin. The XLH pigment stoichiometry was calculated by chromatographic techniques and the pigment-binding structure studied by resonance Raman spectroscopy. The pigment ratio obtained by HPLC was found to be close to 8:1:2:1 Chl-a:heteroxanthin:diadinoxanthin:vaucheriaxanthin. The resonance Raman spectra suggest the presence of 8-10 Chl-a, all of which are 5-coordinated to the central Mg, with 1-3 Chl-a possessing a macrocycle distorted from the relaxed conformation. The three populations of carotenoids are in the all-trans configuration. Vaucheriaxanthin absorbs around 500-530 nm, diadinoxanthin at 494 nm and heteroxanthin at 487 nm at 4.5 K. The effective conjugation length of heteroxanthin and diadinoxanthin has been determined as 9.4 in both cases; the environment polarizability of the heteroxanthin and diadinoxanthin binding pockets is 0.270 and 0.305, respectively.

A unique supramolecular organization of photosystem I in the moss Physcomitrella patens

The photosynthesis machinery in chloroplast thylakoid membranes is comprised of multiple protein complexes and supercomplexes^1,2. Here, we show a novel supramolecular organization of photosystem I (PSI) in the moss Physcomitrella patens by single-particle cryo-electron microscopy. The moss-specific light-harvesting complex (LHC) protein Lhcb9 is involved in this PSI supercomplex, which has been shown to have a molecular density similar to that of the green alga Chlamydomonas reinhardtii³. Our results show that the structural organization is unexpectedly different-two rows of the LHCI belt exist as in C. reinhardtii⁴, but the outer one is shifted toward the PsaK side. Furthermore, one trimeric LHC protein and one monomeric LHC protein position alongside PsaL/K, filling the gap between these subunits and the outer LHCI belt. We provide evidence showing that Lhcb9 is a key factor, acting as a linkage between the PSI core and the outer LHCI belt to form the unique supramolecular organization of the PSI supercomplex in P. patens.

Coherent phenomena in photosynthetic light harvesting: part two-observations in biological systems

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or "quantum beats" via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.

Binding of pigments to the cyanobacterial high-light-inducible protein HliC

Cyanobacteria possess a family of one-helix high-light-inducible proteins (HLIPs) that are widely viewed as ancestors of the light-harvesting antenna of plants and algae. HLIPs are essential for viability under various stress conditions, although their exact role is not fully understood. The unicellular cyanobacterium Synechocystis sp. PCC 6803 contains four HLIPs named HliA-D, and HliD has recently been isolated in a small protein complex and shown to bind chlorophyll and β-carotene. However, no HLIP has been isolated and characterized in a pure form up to now. We have developed a protocol to purify large quantities of His-tagged HliC from an engineered Synechocystis strain. Purified His-HliC is a pigmented homo-oligomer and is associated with chlorophyll and β-carotene with a 2:1 ratio. This differs from the 3:1 ratio reported for HliD. Comparison of these two HLIPs by resonance Raman spectroscopy revealed a similar conformation for their bound β-carotenes, but clear differences in their chlorophylls. We present and discuss a structural model of HliC, in which a dimeric protein binds four chlorophyll molecules and two β-carotenes.

Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga

Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga Cyanidioschyzon merolae in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls a and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls a and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.

Photoprotective, excited-state quenching mechanisms in diverse photosynthetic organisms

Light-harvesting complexes (LHCs) serve a dual role in photosynthesis, depending on the prevailing light conditions. In low light, they ensure photosynthetic efficiency by maximizing the light absorption cross-section and subsequent energy storage. Under excess light conditions, LHCs perform photoprotective quenching functions to prevent harmful chemical species such as triplet chlorophyll and singlet oxygen from forming and damaging the photosynthetic apparatus. In this Minireview, various photoprotective quenching mechanisms that have been identified in different photosynthetic organisms are surveyed and summarized, and implications for improving photosynthetic productivity are briefly discussed.

Algal light sensing and photoacclimation in aquatic environments

Anoxygenic photosynthetic prokaryotes arose in ancient oceans ~3.5 billion years ago. The evolution of oxygenic photosynthesis by cyanobacteria followed soon after, enabling eukaryogenesis and the evolution of complex life. The Archaeplastida lineage dates back ~1.5 billion years to the domestication of a cyanobacterium. Eukaryotic algae have subsequently radiated throughout oceanic/freshwater/terrestrial environments, adopting distinctive morphological and developmental strategies for adaptation to diverse light environments. Descendants of the ancestral photosynthetic alga remain challenged by a typical diurnally fluctuating light supply ranging from ~0 to ~2000 μE m^-2  s^-1 . Such extreme changes in light intensity and variations in light quality have driven the evolution of novel photoreceptors, light-harvesting complexes and photoprotective mechanisms in photosynthetic eukaryotes. This minireview focuses on algal light sensors, highlighting the unexpected roles for linear tetrapyrroles (bilins) in the maintenance of functional chloroplasts in chlorophytes, sister species to streptophyte algae and land plants.