Effects of CO2 and temperature on photosynthetic performance in the diatom Chaetoceros gracilis

The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs

Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

Isolation and characterization of trimeric and monomeric PSI cores from Acaryochloris marina MBIC11017

Photosystem I (PSI) catalyzes light-induced electron-transfer reactions and has been observed to exhibit various oligomeric states and different energy levels of chlorophylls (Chls) in response to oligomerization. However, the biochemical and spectroscopic properties of a PSI monomer containing Chls d are not well understood. In this study, we successfully isolated and characterized PSI monomers from the cyanobacterium Acaryochloris marina MBIC11017, and compared their properties with those of the A. marina PSI trimer. The PSI trimers and monomers were prepared using trehalose density gradient centrifugation after anion-exchange and hydrophobic interaction chromatography. The polypeptide composition of the PSI monomer was found to be consistent with that of the PSI trimer. The absorption spectrum of the PSI monomer showed the Qy band of Chl d at 704 nm, which was blue-shifted from the peak at 707 nm observed in the PSI-trimer spectrum. The fluorescence-emission spectrum of the PSI monomer measured at 77 K exhibited a peak at 730 nm without a broad shoulder in the range of 745-780 nm, which was clearly observed in the PSI-trimer spectrum. These spectroscopic properties of the A. marina PSI trimer and monomer suggest different formations of low-energy Chls d between the two types of PSI cores. Based on these findings, we discuss the location of low-energy Chls d in A. marina PSIs.

Biochemical and spectroscopic characterization of PSI-LHCI from the red alga Cyanidium caldarium

Light-harvesting complexes (LHCs) have been diversified in oxygenic photosynthetic organisms, and play an essential role in capturing light energy which is transferred to two types of photosystem cores to promote charge-separation reactions. Red algae are one of the groups of photosynthetic eukaryotes, and their chlorophyll (Chl) a-binding LHCs are specifically associated with photosystem I (PSI). In this study, we purified three types of preparations, PSI-LHCI supercomplexes, PSI cores, and isolated LHCIs, from the red alga Cyanidium caldarium, and examined their properties. The polypeptide bands of PSI-LHCI showed characteristic PSI and LHCI components without contamination by other proteins. The carotenoid composition of LHCI displayed zeaxanthins, β-cryptoxanthins, and β-carotenes. Among the carotenoids, zeaxanthins were enriched in LHCI. On the contrary, both zeaxanthins and β-cryptoxanthins could not be detected from PSI, suggesting that zeaxanthins and β-cryptoxanthins are bound to LHCI but not PSI. A Qy peak of Chl a in the absorption spectrum of LHCI was shifted to a shorter wavelength than those in PSI and PSI-LHCI. This tendency is in line with the result of fluorescence-emission spectra, in which the emission maxima of PSI-LHCI, PSI, and LHCI appeared at 727, 719, and 677 nm, respectively. Time-resolved fluorescence spectra of LHCI represented no 719 and 727-nm fluorescence bands from picoseconds to nanoseconds. These results indicate that energy levels of Chls around/within LHCIs and within PSI are changed by binding LHCIs to PSI. Based on these findings, we discuss the expression, function, and structure of red algal PSI-LHCI supercomplexes.

Photoacclimation impacts the molecular features of photosystem supercomplexes in the centric diatom Thalassiosira pseudonana

In diatoms, light-harvesting processes take place in a specific group of proteins, called fucoxanthin chlorophyll a/c proteins (FCP). This group includes many members and represents the major characteristic of the diatom photosynthetic apparatus, with specific pigments bound (chlorophyll c, fucoxanthin, diadino- and diatoxanthin besides chlorophyll a). In thylakoids, FCP and photosystems (PS) form multimeric supercomplexes. In this study, we compared the biochemical properties of PS supercomplexes isolated from Thalassiosira pseudonana cells grown under low light or high light conditions, respectively. High light acclimation changed the molecular features of the PS and their ratio in thylakoids. In PSII, no obvious changes in polypeptide composition were observed, whereas for PSI changes in one specific group of FCP proteins were detected. As reported before, the amount of xanthophyll cycle pigments and their de-epoxidation ratio was increased in PSI under HL. In PSII, however, no additional xanthophyll cycle pigments occurred, but the de-epoxidation ratio was increased as well. This comparison suggests how mechanisms of photoprotection might take place within and in the proximity of the PS, which gives new insights into the capacity of diatoms to adapt to different conditions and in different environments.

The Differential Responses of Coastal Diatoms to Ocean Acidification and Warming: A Comparison Between Thalassiosira sp. and Nitzschia closterium f.minutissima

Marine diatoms are one of the marine phytoplankton functional groups, with high species diversity, playing important roles in the marine food web and carbon sequestration. In order to evaluate the species-specific responses of coastal diatoms to the combined effects of future ocean acidification (OA) and warming on the coastal diatoms, we conducted a semi-continuous incubation on the large centric diatom Thalassiosira sp. (~30 μm) and small pennate diatom Nitzschia closterium f.minutissima (~15 μm). A full factorial combination of two temperature levels (15 and 20°C) and pCO2 (400 and 1,000 ppm) was examined. The results suggest that changes in temperature played a more important role in regulating the physiology of Thalassiosira sp. and N. closterium f.minutissima than CO2. For Thalassiosira sp., elevated temperature significantly reduced the cellular particulate organic carbon (POC), particulate organic nitrogen (PON), particulate organic phosphate (POP), biogenic silica (BSi), chlorophyll a (Chl a), and protein contents, and the C:N ratio. CO2 only had significant effects on the growth rate and the protein content. However, for the smaller pennate diatom N. closterium f.minutissima, the growth rate, POC production rate, and the C:P ratio significantly increased with an elevated temperature, whereas the cellular POP and BSi contents significantly decreased. CO2 had significant effects on the POC production rate, cellular BSi, POC, and PON contents, the C:P, Si:C, N:P, and Si:P ratios, and sinking rate. The interaction between OA and warming showed mostly antagonistic effects on the physiology of both species. Overall, by comparison between the two species, CO2 played a more significant role in regulating the growth rate and sinking rate of the large centric diatom Thalassiosira sp., whereas had more significant effects on the elemental compositions of the smaller pennate diatom N. closterium f.minutissima. These results suggest differential sensitivities of different diatom species with different sizes and morphology to the changes in CO2/temperature regimes and their interactions.

Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex

Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) function as light harvesters in diatoms. The structure of a diatom photosystem II-FCPII (PSII-FCPII) supercomplex have been solved by cryo-electron microscopy (cryo-EM) previously; however, the FCPII subunits that constitute the FCPII tetramers and monomers are not identified individually due to their low resolutions. Here, we report a 2.5 Å resolution structure of the PSII-FCPII supercomplex using cryo-EM. Two types of tetrameric FCPs, S-tetramer, and M-tetramer, are identified as different types of hetero-tetrameric complexes. In addition, three FCP monomers, m1, m2, and m3, are assigned to different gene products of FCP. The present structure also identifies the positions of most Chls c and diadinoxanthins, which form a complicated pigment network. Excitation-energy transfer from FCPII to PSII is revealed by time-resolved fluorescence spectroscopy. These structural and spectroscopic findings provide insights into an assembly model of FCPII and its excitation-energy transfer and quenching processes.

Fucoxanthin chlorophyll a/c-binding proteins (FCPs) harvest light energy in diatoms. The authors analyzed a structure of PSII-FCPII supercomplex at high resolution by cryo-EM, which identified each FCP subunit and pigment network in the supercomplex.

Structure, Function, and Variations of the Photosystem I-Antenna Supercomplex from Different Photosynthetic Organisms

Photosystem I (PSI) is a protein complex functioning in light-induced charge separation, electron transfer, and reduction reactions of ferredoxin in photosynthesis, which finally results in the reduction of NAD(P)^- to NAD(P)H required for the fixation of carbon dioxide. In eukaryotic algae, PSI is associated with light-harvesting complex I (LHCI) subunits, forming a PSI-LHCI supercomplex. LHCI harvests and transfers light energy to the PSI core, where charge separation and electron transfer reactions occur. During the course of evolution, the number and sequences of protein subunits and the pigments they bind in LHCI change dramatically depending on the species of organisms, which is a result of adaptation of organisms to various light environments. In this chapter, I will describe the structure of various PSI-LHCI supercomplexes from different organisms solved so far either by X-ray crystallography or by cryo-electron microscopy, with emphasis on the differences in the number, structures, and association patterns of LHCI subunits associated with the PSI core found in different organisms.

Characterization of chloroplast genome of the marine diatom Chaetoceros gracilis

In the present study, the chloroplast genome of Chaetoceros gracilis was sequenced using the PacBio sequencing platform and phylogenetic analysis was conducted using 38 other complete chloroplast genomes of the Bacillariophyta. The chloroplast genome of C. gracilis was 116,421 bp in length with the typical quadripartite structure, including a large single copy (LSC) region of 61,904 bp, a small single copy (SSC) region of 39,367 bp, and a pair of inverted repeats (IR) regions of 7575 bp. The overall GC content of C. gracilis chloroplast genome was 30.79%. This genome encoded 131 genes incuding 93 protein-coding genes, 30 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. Phylogenetic results exhibited that three Chaetoceros species were clustered together. Chaetoceros gracilis was closely related with Chaetoceros muelleri, and then formed a clade with Chaetoceros simplex with 100% bootstrap value This study will facilitate species identification and study of evolutionary in the family Chaetoceroceae.

Revealing the architecture of the photosynthetic apparatus in the diatom Thalassiosira pseudonana

Diatoms are a large group of marine algae that are responsible for about one-quarter of global carbon fixation. Light-harvesting complexes of diatoms are formed by the fucoxanthin chlorophyll a/c proteins and their overall organization around core complexes of photosystems (PSs) I and II is unique in the plant kingdom. Using cryo-electron tomography, we have elucidated the structural organization of PSII and PSI supercomplexes and their spatial segregation in the thylakoid membrane of the model diatom species Thalassiosira pseudonana. 3D sub-volume averaging revealed that the PSII supercomplex of T. pseudonana incorporates a trimeric form of light-harvesting antenna, which differs from the tetrameric antenna observed previously in another diatom, Chaetoceros gracilis. Surprisingly, the organization of the PSI supercomplex is conserved in both diatom species. These results strongly suggest that different diatom classes have various architectures of PSII as an adaptation strategy, whilst a convergent evolution occurred concerning PSI and the overall plastid structure.

Production of lipids by Chaetoceros affinis in media based on palm oil mill effluent

Biomass and lipid production by the marine diatom Chaetoceros affinis were characterized under continuous light with aeration. Media based on palm oil mill effluent (POME; 10, 20 and 30 % v/v in distilled water) were used together with a standard control medium. The maximum biomass concentration on day 12 of batch cultures in control medium was 821 ± 71 mg L^-1. Under identical conditions, in the best POME medium (20 % POME v/v in distilled water with other inorganic components), the biomass concentration was reduced by ∼11 % to 734 ± 66 mg L^-1. The lipid content of the biomass grown in the control medium was 50.8 ± 4.5 % by dry weight, but was a little lower (48.9 ± 4.1 % by dry wt) in the above specified best POME medium. In the best POME medium, oleic acid was the major fatty acid (72.3 ± 5.2 % by weight) in the total lipids extracted from the biomass and monounsaturated fatty acids were the main type of fatty acids (74.6 ± 5.2 %). POME levels of >20 % in the medium suppressed both biomass and lipid production relative to the medium with 20 % POME.

Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex

Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of fucoxanthin-chlorophyll a/c proteins (FCPIs). We report the structure of PSI-FCPI from a diatom Chaetoceros gracilis at 2.38 Å resolution by single-particle cryo-electron microscopy. PSI-FCPI is a monomeric supercomplex consisting of 12 core and 24 antenna subunits (FCPIs), and 326 chlorophylls a, 34 chlorophylls c, 102 fucoxanthins, 35 diadinoxanthins, 18 β-carotenes and some electron transfer cofactors. Two subunits designated PsaR and PsaS were found in the core, whereas several subunits were lost. The large number of pigments constitute a unique and huge network ensuring efficient energy harvesting, transfer and dissipation. These results provide a firm structural basis for unraveling the mechanisms of light-energy harvesting, transfer and quenching in the diatom PSI-FCPI, and also important clues to evolutionary changes of PSI-LHCI.

Diatoms are marine algae with an important role in global photosynthetic carbon fixation. Here, the authors present the 2.38 Å cryo-EM structure of photosystem I (PSI) in complex with its 24 fucoxanthin chlorophyll a/c-binding (FCPI) antenna proteins from the diatom Chaetoceros gracilis, which provides mechanistic insights into light-energy harvesting, transfer and quenching of the PSI-FCPI supercomplex.

Basic pH-induced modification of excitation-energy dynamics in fucoxanthin chlorophyll a/c-binding proteins isolated from a pinguiophyte, Glossomastix chrysoplasta

Photosynthetic organisms have diversified light-harvesting complexes (LHCs) to collect solar energy efficiently, leading to an acquisition of their ecological niches. Herein we report on biochemical and spectroscopic characterizations of fucoxanthin chlorophyll a/c-binding protein (FCP) complexes isolated from a marine pinguiophyte Glossomastix chrysoplasta. The pinguiophyte FCP showed one subunit band in SDS-PAGE and one protein-complex band with a molecular weight at around 66 kDa in clear-native PAGE. By HPLC analysis, the FCP possesses chlorophylls a and c, fucoxanthin, and violaxanthin. To clarify excitation-energy-relaxation processes in the FCP, we measured time-resolved fluorescence spectra at 77 K of the FCP adapted to pH 5.0, 6.5, and 8.0. Fluorescence curves measured at pH 5.0 and 8.0 showed shorter lifetime components compared with those at pH 6.5. The rapid decay components at pH 5.0 and 8.0 are unveiled by fluorescence decay-associated (FDA) spectra; fluorescence decays occur in the 270 and 160-ps FDA spectra only at pH 5.0 and 8.0, respectively. In addition, energy-transfer pathways with time constants of tens of picoseconds are altered under the basic pH condition but not the acidic pH condition. These findings provide novel insights into pH-dependent energy-transfer and energy-quenching machinery in not only FCP family but also photosynthetic LHCs.

Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex

Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-Å resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs.