Biology subjects

Ifuku, K.

Publications and source records attributed to Ifuku, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Development of a Wearable Sensor-PAM for Continuous Monitoring of Photosynthetic Dynamics

Continuous monitoring of photosynthetic performance is essential for understanding plant responses to fluctuating environments and has important applications in plant physiology, field phenotyping, and digital agriculture. However, conventional pulse-amplitude modulation (PAM) fluorometers are primarily designed for point measurements and are not suitable for long-term monitoring while attached to intact leaves. Here, we developed Sensor-PAM, a wearable chlorophyll fluorescence measurement system capable of continuously monitoring photosynthetic dynamics from the abaxial side of a leaf. The system combines a commercially available color sensor with blue LEDs in a compact, low-cost optical design to perform PAM measurements. Chlorophyll fluorescence measured from the abaxial leaf surface showed a strong correlation with conventional adaxial measurements and accurately reflected changes in photosynthetic performance induced by chilling and high-light stress. Measurements obtained using Sensor-PAM also showed good agreement with those from a commercial PAM fluorometer across diverse plant species. Furthermore, the wearable system enabled continuous monitoring of the effective quantum yield of photosystem II [Y(II)] from the same position on the same strawberry leaf for three days under both greenhouse and outdoor conditions, successfully capturing photosynthetic responses to changing irradiance and temperature in real time. These findings establish Sensor-PAM as a wearable platform for continuous chlorophyll fluorescence monitoring, extending conventional PAM fluorometry from point-based measurements to long-term monitoring of photosynthetic dynamics under natural environmental conditions.

plant biology↗

bioRxiv2026

Tissue-resolved photosynthetic responses in living leaves revealed by microscopic imaging-pulse-amplitude-modulation

Leaves of terrestrial plants possess heterogeneous anatomical structures composed of multiple cell layers. Although biochemical differences among leaf tissues have been inferred from protein analyses and anatomical studies, direct comparisons of dynamic photochemical responses among tissues while preserving their spatial context remain challenging. Leaves experience intrinsically heterogeneous environments because incident light enters primarily from above and propagates through complex internal leaf structures. Therefore, analyzing photosynthetic activity at the tissue and cellular levels is essential for understanding how photosynthesis operates within structurally heterogeneous leaves. Here, we combined live leaf-section imaging with microscopic Imaging-PAM chlorophyll fluorescence measurements to analyze photochemical responses at the tissue level in living leaf sections. In dorsiventral dicot leaves, palisade tissues exhibited a higher effective PSII quantum yield [Y(II)] and more rapid induction of regulated energy dissipation [Y(NPQ)] than spongy tissues, indicating higher photosynthetic capacity and photoprotective activity. In contrast, rice leaves, which lack palisade-spongy differentiation, showed uniform photochemical responses along the adaxial-abaxial axis. In the C4 plant finger millet, mesophyll and bundle sheath cells displayed distinct photochemical responses consistent with their functional differentiation in C4 photosynthesis. These results demonstrate that photosynthetic responses are spatially organized according to leaf anatomical structure. Although section-based measurements do not reproduce the native optical and gas environments of intact leaves, they enable the comparison of intrinsic tissue-specific photochemical properties under approximately equivalent illumination. The present approach enables tissue-resolved chlorophyll fluorescence analysis in living leaves, providing a new framework for investigating how leaf architecture shapes the spatial organization of photosynthetic activity.

plant biology↗

bioRxiv2026

Structure–activity relationship of antimycin A-like compounds as photosystem II inhibitors

Antimycin A (AA) is widely used as an inhibitor of the mitochondrial respiratory chain, targeting the Qi site of cytochrome bc1 (complex III). In photosynthetic organisms, AA is also well known to inhibit the photosynthetic PROTON GRADIENT REGULATION 5 (PGR5)-dependent cyclic electron flow around photosystem I (CEF-PSI). Although AA is frequently used as a specific inhibitor of PGR5-dependent CEF-PSI in photosynthetic reactions, we recently clarified that some of the major components of AA, which is typically a mixture of closely related compounds, also exert direct inhibitory effects on photosystem II (PSII). Nevertheless, the binding site and binding mode of AA in PSII remain largely unexplored. Structurally, AA consists of a salicylic acid moiety connected via an amide bond to a hydrophobic dilactone ring moiety. To identify important structural factors of AA for exhibiting inhibitory effects on PSII (assessed by QA- reoxidation measurements), we here investigated the relationship between structure and inhibitory potency using 38 AA-like compounds (AALCs), including commercial compounds and a series of synthetic AA analogs. Some AALCs exhibited substantially stronger impacts on PSII than natural AA. High acidity of the phenolic OH and the presence of a free amide NH of the salicylamide moiety were critical for the effects on PSII. In contrast, while the dilactone ring moiety also affected the inhibitory activity, this was replaceable with certain hydrophobic structures. Based on our results, together with the known structure-activity relationship and binding mode of AA in complex III, we propose tentative binding models for AA in PSII. HighlightsO_LIStructure-activity relationship of AA-like compounds on PSII is examined C_LIO_LISeveral AA-like compounds more potent than AA against PSII are identified C_LIO_LIPhenolic OH acidity and free amide NH of salicylamide moiety are key for AA effects C_LIO_LIThe dilactone ring moiety is replaceable with certain hydrophobic structures C_LIO_LITentative binding models for AA in PSII are proposed C_LI

Plant Biology↗

bioRxiv2026

The PSI-NDH supercomplex prevents chilling-induced PSI photoinhibition

Chilling stress induces photosystem I (PSI) photoinhibition in chilling-sensitive cucumber, in which insufficient activity of the chloroplast NADH dehydrogenase-like complex (NDH) leads to PSI over-reduction and damage. However, it is not yet clear whether these findings can be generalized to other species or what the molecular mechanism underlying impaired NDH function is. In this study, we first examined whether NDH is essential for PSI protection under chilling stress using an NDH-deficient rice mutant. Compared with wild-type plants, the NDH-deficient mutant exhibited enhanced PSI over-reduction and pronounced PSI photoinhibition under chilling stress. In contrast, rice plants expressing flavodiiron protein (FLV), which functions as an alternative electron acceptor downstream of PSI, did not exhibit PSI photoinhibition under chilling stress, demonstrating that electron sink capacity of NDH is important for PSI protection under chilling stress. Furthermore, analysis of the factors responsible for NDH dysfunction under chilling stress in cucumber revealed that chilling stress destabilizes the PSI-NDH supercomplex, leading to NDH monomerization and a consequent loss of NDH activity. This NDH monomerization is likely attributable to chilling-induced damage to the light-harvesting complex Lhca, which mediates the association between PSI and NDH. Together, these results indicate that NDH is essential for protecting PSI from photoinhibition under chilling stress in both rice and cucumber, and that chilling-induced destabilization of the PSI-NDH supercomplex represents a key molecular mechanism underlying PSI over-reduction and photoinhibition.

plant biology↗

bioRxiv2026

PIFI Stabilizes Chloroplast NDH-PSI Supercomplex to Maintain Plastoquinone Redox Balance and PSII Efficiency

Photosynthetic electron transport is mediated by several protein supercomplexes that are spatially arranged in the thylakoid membranes of chloroplasts. The chloroplast NADH dehydrogenase-like (NDH) complex is part of the photosynthetic alternative electron transport (AET) chain, which reduces the plastoquinone (PQ) pool using reduced ferredoxin as a substrate. This NDH complex is associated with photosystem I (PSI) and mediates a portion of AET in stroma lamellae, whereas photosystem II (PSII) is concentrated in grana stacks. This study presents the findings regarding post-illumination chlorophyll fluorescence increase (PIFI), a protein crucial for regulating AET via the NDH pathway. A marked increase in NDH activity and a reduction in the PQ pool in the dark were observed in PIFI-deficient mutant strains (g-pifi) generated by genome editing. Blue native PAGE analysis indicated that PIFI was associated with the NDH-PSI supercomplex in the wild type, and the NDH complex was dissociated from PSI in the g-pifi mutants. Additionally, the g-pifi mutants exhibited a decrease in the maximum quantum yield of PSII (Fv/Fm). Notably, Fv/Fm was restored in a double mutant harboring both g-pifi and NDH-deficient pnsl1 mutations, demonstrating that deregulated NDH activity in g-pifi causes downregulation of PSII efficiency. However, the lower Fv/Fm was not observed in a mutant lacking thioredoxin m4 (trxm4), which showed deregulated NDH activity but maintained the NDH-PSI supercomplex. These data suggest that PIFI stabilizes the NDH-PSI supercomplex and maintains the spatial localization of PQ reduction via AET in thylakoid membranes, which is essential for the proper functioning of PSII.

plant biology↗

bioRxiv2026

Lhcf9 is a novel negative regulator of non-photochemical quenching in the diatom Chaetoceros gracilis

Photosynthetic organisms in aquatic environments experience rapid fluctuations in light intensity, light quality, and carbon availability, requiring tight regulation of photosynthetic energy conversion. In marine diatoms, non-photochemical quenching (NPQ), particularly energy-dependent quenching (qE), plays a central role in dissipating excess excitation energy as heat. However, excessive NPQ can reduce photosynthetic efficiency under light-limiting or carbon-rich conditions, and how this trade-off is regulated remains poorly understood. Here, we identify CgLhcf9, a previously uncharacterized light-harvesting complex (LHC) protein, as a negative regulator of qE-type NPQ in the centric diatom Chaetoceros gracilis. Expression of CgLhcf9 is induced under low red-light and high CO2 conditions and strongly suppressed by blue light, indicating regulation by both light quality and carbon availability. Functional analyses using CgLhcf9 knockout and overexpression lines reveal that CgLhcf9 suppresses qE: NPQ induction is enhanced in the absence of CgLhcf9, whereas its accumulation downregulates NPQ without affecting other established qE effectors, including Lhcx1 or xanthophyll cycle pigments. Notably, CgLhcf9 accumulation improves cellular growth under light-limiting conditions. These results identify CgLhcf9 as a novel LHC-type regulator that fine-tunes photosynthetic energy dissipation in response to environmental signals. Our findings establish a regulatory mechanism that balances photoprotection, electron transport, and carbon fixation, advancing our understanding of how marine diatoms optimize photosynthesis under fluctuating light and CO2 conditions. Significance statementPhotosynthetic microalgae must balance light-driven electron transport with carbon fixation to maximize growth under fluctuating light and CO2 conditions. While non-photochemical quenching (NPQ) protects photosystems from excess light, excessive NPQ can limit photosynthetic efficiency when light or carbon is limiting. Here, we identify the antenna protein CgLhcf9 as a negative regulator of energy-dependent NPQ in the marine diatom Chaetoceros gracilis. CgLhcf9 integrates light-quality and CO2 signals to suppress NPQ without altering canonical quenching effectors, thereby improving growth under light-limiting conditions. This study reveals a regulatory role for a light-harvesting complex protein in tuning the balance between photoprotection and photosynthetic efficiency, providing insight into how marine diatoms coordinate electron transport and carbon fixation in dynamic environments.

plant biology↗

bioRxiv2026

Lhcf2 in the peripheral antenna is essential for non-photochemical quenching and Lhcx1 accumulation in the diatom Chaetoceros gracilis

Photosynthetic organisms must continuously balance efficient light harvesting with protection against excess excitation energy, a challenge met by nonphotochemical quenching (NPQ). Although the molecular components involved in NPQ have been extensively studied, how the essential energy-quenching site is assembled remains poorly understood, particularly in marine diatoms. Here, we show that in the centric diatom Chaetoceros gracilis, which belongs to one of the most abundant and diverse genera in marine phytoplankton, the light-harvesting complex protein Lhcf2 is required for energy-dependent NPQ (qE). Targeted knockout of Lhcf2 abolished qE by preventing the stable accumulation of Lhcx1, the canonical NPQ effector in this species. Lhcf2 localizes to the peripheral antenna system and associates with Lhcx1 in a higher-order complex suggested by biochemical and functional analyses. In contrast, other established NPQ-related factors, including the trans-thylakoid proton gradient and the accumulation of diatoxanthin, were not affected by the loss of Lhcf2. These results identify a non-Lhcx-type light-harvesting complex protein as an essential structural component for qE-NPQ and establish a general design principle for the cooperative assembly of photoprotective energy-quenching sites in eukaryotic photosynthesis, with implications for marine carbon fixation. Significance StatementPhotosynthetic organisms must balance efficient light harvesting with protection against excess excitation energy. Nonphotochemical quenching (NPQ) is a conserved photoprotective mechanism, yet how the essential energy-quenching site is assembled remains unclear. Here, we show that in the marine diatom Chaetoceros gracilis, the peripheral light-harvesting complex protein Lhcf2 is strictly required for energy-dependent NPQ by enabling the stable accumulation and functional organization of the canonical NPQ effector Lhcx1. Our results reveal that photoprotective energy dissipation depends on cooperative interactions between distinct classes of light-harvesting complex proteins rather than on a single specialized factor. This study establishes a general design principle for NPQ machinery in eukaryotic photosynthesis, with implications for marine carbon fixation under fluctuating light environments.

plant biology↗

bioRxiv2025

Redistribution of excitation energy between two photosystems during light-shade adaptation in marine diatoms: State conversion of light-harvesting complexes

Marine diatoms effectively photosynthesize by acclimating to the wide range of growth irradiance in the ocean. Using a pennate diatom Phaeodactylum tricornutum and a centric diatom Chaetoceros gracilis, we evaluated differences in the photosynthetic machinery under a wide range of growth irradiances. The chlorophyll a-specific amounts of the major accessory pigments remained relatively constant irrespective of growth irradiance in both diatoms. However, fluorescence spectra at 77K differed drastically depending on the growth irradiance: In P. tricornutum, fluorescence from photosystem II was dominant in high-light-grown cells and negligible in low-light-grown cells, while in C. gracilis, the opposite trend was observed. These drastic changes in fluorescence spectra were slow processes. The amounts of the two reaction centers, as assessed by specific antibodies and absorption changes in P700, remained almost constant under different irradiances. These results indicate that under dim growth irradiance, more excitation energy is diverted to photosystem I in the pennate diatom, and to photosystem II in the centric diatom. Therefore, the light-harvesting antennas balance excitation energy distribution by changing their association between photosystems I and II in different manners between P. tricornutum and C. gracilis, depending on irradiance. This phenomenon is similar to state transitions, but differs in its magnitude and duration. Differences in the preference of energy distribution in the two diatoms suggest that the dynamic state conversion--an antenna rearrangement during the long-term acclimation process in diatoms--is the species-specific strategy to achieve effective photosynthesis under the wide range of growth irradiances in the ocean.

plant biology↗

bioRxiv2025

Antimycin A, but not antimycin A3 or myxothiazol, directly suppresses photosystem II activity

Antimycin A (AA) is a widely used inhibitor to study photosynthesis and respiration. In photosynthesis, it is commonly used to inhibit a cyclic electron flow (CEF) pathway but has also been reported to affect photosystem II (PSII), which is not involved in CEF. Although concerns have been raised about AAs specificity, its impact on PSII activity remains unclear. AA3 was recently proposed as a more specific inhibitor of the same CEF pathway. In the mitochondrial respiratory chain, AA inhibits complex III, similar to myxothiazol. Here, we investigated the direct effects of AA, AA3, and myxothiazol on PSII activity and linear photosynthetic electron transport using isolated plant PSII and thylakoid membranes. AA, but neither AA3 nor myxothiazol, directly suppressed PSII activity and linear electron transport. Furthermore, the extent of AAs effects was batch-dependent. Thus, we propose using AA3 to inhibit CEF and myxothiazol to inhibit complex III, instead of AA. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/675326v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@a61461org.highwire.dtl.DTLVardef@1841ac5org.highwire.dtl.DTLVardef@1f9a345org.highwire.dtl.DTLVardef@4e155c_HPS_FORMAT_FIGEXP M_FIG C_FIG Antimycin A inhibits at least three sites. Antimycin A3 has higher specificity for CEF-PSI, while myxothiazol is preferred to inhibit complex III.

plant biology↗

bioRxiv2025

Evolutionary origin and functional mechanism of Lhcx in the diatom photoprotection

Diatoms are red-lineage algae that utilize the light-harvesting complex (LHC) subfamily Lhcx for photoprotection via non-photochemical quenching (NPQ); however, its evolutionary origin and molecular mechanism remain poorly understood. Through molecular phylogenetic analysis, we show that diatom Lhcxs and green algal Lhcsrs evolved from a common ancestor, with green plants subsequently acquiring them via horizontal gene transfer. To investigate the functional role of Lhcx1, we generated knockout mutants of Chaetoceros gracilis, a diatom with low Lhcx redundancy. The lhcx1 mutants nearly abolished NPQ, and time-resolved fluorescence measurements revealed that Lhcx1-mediated quenching occurs in energetically detached antenna complexes. Clear-native PAGE with Amphipol further indicated that CgLhcx1 interacts with the FCP L-dimer, functioning as a peripheral antenna for the C2S2M2 PSII-FCPII supercomplex. Notably, under high-light acclimation, lhcx1 mutants exhibited higher PSII effective quantum yields than wild type, attributable to reduced antenna size and enhanced carbon fixation capacity. The absence of NPQ accelerated high-light acclimation and was accompanied by increased xanthophyll accumulation, indicating that compensatory mechanisms can enhance overall photosynthetic efficiency. Together, these findings reveal the evolutionary origin of Lhcx/Lhcsr proteins and define the molecular basis of Lhcx1-mediated photoprotection in diatoms, providing fundamental insights into LHC-based photoprotection across photosynthetic lineages.

plant biology↗

bioRxiv2025

The protective role of chloroplast NADH dehydrogenase-like complex (NDH) against PSI photoinhibition under chilling stress

Chilling stress induces photosystem I (PSI) photoinhibition in various plants, severely impairing their growth. However, the mechanisms suppressing chilling-induced PSI photoinhibition remain unclear. This study aimed to identify factors preventing PSI photoinhibition by comparing two cucumber cultivars with different susceptibilities to PSI photoinhibition and chilling stress tolerance. In the chilling-sensitive cultivar, partial degradation of the CF1-{gamma} subunit of chloroplast ATPase led to uncoupling of the thylakoid membrane. In addition, electron efflux from Fe-S clusters downstream of PSI was restricted under chilling stress, resulting in highly reduced Fe-S clusters. Notably, this PSI over-reduction in the chilling-sensitive cultivar was observed not only under chilling stress but also under fluctuating light conditions, limited CO2 conditions, and during the transition from darkness to light, suggesting that cyclic electron flow contributes to cultivar differences in PSI photoinhibition. Indeed, the chilling-tolerant cultivar exhibited higher activity of the chloroplast NADH dehydrogenase-like complex (NDH) and suppressed reactive oxygen species (ROS) accumulation during the early stages of chilling stress. In contrast, in the chilling-sensitive cultivar, destabilization of PSI-NDH supercomplex under chilling stress led to the loss of NDH activity, resulting in severe PSI over-reduction. This study provides evidence that NDH acts as a crucial electron sink to prevent PSI photoinhibition and provides new insights into the mechanisms underlying low-temperature stress tolerance.

plant biology↗

bioRxiv2025

PSII photoinhibition as a protective strategy against PSI photoinhibition: Maintaining PSI in an oxidized state by suppressing PSII activity under environmental stress

Photosystem I (PSI) can be photoinhibited by excessive electron flow from Photosystem II (PSII), causing serious growth inhibition due to PSIs limited repair capacity. In contrast, PSII is more susceptible to photoinhibition under stress but has an efficient repair system. Consequently, PSII photoinhibition is considered a protective mechanism that mitigates PSI over-reduction. However, this photoprotective role under environmental stress remains unexplored in intact plants without using mutants or chemical treatments. To address this, we examined the relationship between PSII photoinhibition and susceptibility to PSI photoinhibition under two representative stresses that selectively induce PSI photoinhibition: chilling stress and fluctuating light, using A. thaliana and cucumber. Under chilling stress, A. thaliana exhibited marked PSII photoinhibition and maintained active PSI, whereas cucumber showed insufficient PSII downregulation and suffered PSI photoinhibition. In addition, when fluctuating light treatment was applied to plants with various Fv/Fm (the maximum quantum yield of PSII), plants with reduced Fv/Fm maintained oxidized PSI, and PSI photoinhibition progressed slowly. The susceptibility to PSI photoinhibition under fluctuating light strongly correlated with Fv/Fm, providing clear evidence that PSII photoinhibition protects PSI in vivo. Interestingly, even in plants where P700 remained oxidized during saturation pulses due to PSII photoinhibition, the iron-sulfur clusters (Fe-S clusters) remained reduced. However, the re-oxidation rate of reduced Fe-S clusters was enhanced in PSII-photoinhibited plants, suggesting that charge recombination to P700+ with reduced components on the acceptor side would suppress ROS generation downstream of PSI. This study clarifies how PSII photoinhibition suppresses PSI photoinhibition and prevents ROS-induced damage in wild-type plants under environmental stress.

plant biology↗

bioRxiv2024

Antimycin A induces light hypersensitivity of photosystem II in the presence of QB-site binding herbicides

Photosynthetic electron transport consists of linear electron flow and two cyclic electron flow (CEF) pathways around photosystem I (PSI). PGR5-dependent CEF-PSI is thought to be the major CEF-PSI pathway and an important regulator of photosynthetic electron transfer. Antimycin A (AA) is commonly recognized as an inhibitor of PGR5-dependent CEF-PSI in photosynthesis. Although previous findings imply that AA may also affect photosystem II (PSII), which does not participate in CEF-PSI, these "secondary effects" tend to be neglected, and AA is often used for inhibition of PGR5-dependent CEF-PSI as if it were a specific inhibitor. Here, we investigated the direct effects of AA on PSII using isolated spinach PSII membranes, and spinach and Chlamydomonas thylakoid membranes. Measurements of QA- reoxidation kinetics showed that AA affects the acceptor side of PSII and inhibits electron transport within PSII. Furthermore, repetitive Fv/Fm measurements revealed that, in the presence of QB-site binding inhibitors, AA treatment results in severe photoinhibition even from a single-turnover flash. The direct effects of AA on PSII are non-negligible and caution is required when using AA as an inhibitor of PGR5-dependent CEF-PSI. Meanwhile, we found that the commercially available compound AA3, which is a component of the AA complex, inhibits PGR5-dependent CEF-PSI without having notable effects on PSII. Thus, we propose that AA3 should be used for the physiological study of the PGR5-dependent CEF-PSI.

plant biology↗

bioRxiv2024

Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplex

Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll a/c-binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom Thalassiosira pseudonana CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein-protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from T. pseudonana and the diatom Chaetoceros gracilis, underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.

plant biology↗

bioRxiv2024

Unraveling the Evolutionary Trajectory of LHCI in Red-Lineage Algae: Conservation, Diversification, and Neolocalization

Red algae and the secondary symbiotic algae that engulfed a red alga as an endosymbiont are called red-lineage algae. They comprise key marine taxa including diatoms, Haptophyta, and Cryptophyta. Several photosystem (PS) I-light-harvesting complex I (LHCI) structures have been reported from red-lineage algae --two red algae Cyanidioschyzon merolae (Cyanidiophyceae), Porphyridium purpureum (Rhodophytina), a diatom Chaetoceros gracilis and a Cryptophyte Chroomonas placoidea. Here, we clarified the orthologous relation of LHCIs in red-lineage algae by combining a detailed phylogenetic analysis of LHCIs and the structural information of PSI-LHCI. We found that the seven Lhcr groups in LHCI are conserved in Rhodophytina; Furthermore, during both genome reduction in Cyanidioschyzonales of red algae and endosymbiosis leading to Cryptophyta, some LHCIs were lost and replaced by existing or differentiated LHCIs. Especially in Cryptophyta, uniquely diversified Lhcrs form three sets of heterotrimers contributed to the expansion of the antenna size of PSI, supporting the modern ecological success of this taxon. We denominated "neolocalization" to these examples of flexible reorganization of LHCIs. This study provides new insights into the evolutionary process of LHCIs associated with PSI in the red-lineage algae and clarifies the need for both molecular phylogeny and structural information to elucidate the plausible evolutionary history of LHCI.

evolutionary biology↗

bioRxiv2023

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 their structural variety in photosystem I-LHC (PSI-LHCI) supercomplexes has been shown. However, structural and evolutionary correlations of red-lineage LHCs are unknown. Here we determined a 1.92-[A] resolution cryo-electron 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, and subsequently investigated these correlations through structural comparisons and phylogenetic analysis. The PSI-LHCI structure shows five LHCI subunits together with 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 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.

plant biology↗

bioRxiv2022

Proton-pumping rhodopsins in marine diatoms

Diatoms are a major phytoplankton group responsible for about 20% of Earths primary production. They carry out photosynthesis inside the plastid, an organelle obtained through eukaryote-eukaryote endosymbiosis. Recently, microbial rhodopsin, a photoreceptor distinct from chlorophyll-based photosystems, has been identified in certain diatoms. However, the physiological function of diatom rhodopsin is not well understood. Here we show that the diatom rhodopsin acts as a light-driven proton pump and localizes to the outermost membrane of the four membrane-bound complex plastids. Heterologous expression techniques were used to investigate the protein function and subcellular localization of diatom rhodopsin. Using model simulations, we further evaluated the physiological role of the acidic pool in the plastid produced by proton-transporting rhodopsin. Our results propose that the rhodopsin-derived acidic pool may be involved in a photosynthetic CO2-concentrating mechanism and assist CO2 fixation in diatom cells.

microbiology↗

bioRxiv2021

Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e., fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identified 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggested that these FCPs could be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, had orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seemed to be diversified in each diatom species, and the number of Lhcqs differed among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs was common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provided insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage. One sentence summaryPhylogenetic analysis of fucoxanthin-chlorophyll a/c proteins in C. gracilis revealed five major subfamilies and one minor subfamily, providing insights into the diversification of light-harvesting systems in red algae.

plant biology↗