Biology subjects

Kumazawa, M.

Publications and source records attributed to Kumazawa, M..

10 recordsLinked to original sources

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

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↗

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↗

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↗

bioRxiv2021

Coral symbionts exhibit a polycistronic flavodiiron gene leading to functional proteins in photosynthesis

Photosynthesis in cyanobacteria, green algae, and basal land plants is protected against excess reducing pressure on the photosynthetic chain by flavodiiron proteins (FLV) that dissipate photosynthetic electrons by reducing O2. In these organisms, the genes encoding FLV are always conserved in the form of a pair of two-type isozymes (FLVA and FLVB) that are believed to function in O2 photo-reduction as a heterodimer. While coral symbionts (dinoflagellates of the family Symbiodiniaceae) are the only algae to harbor FLV in photosynthetic red plastid lineage, only one gene is found in transcriptomes and its role and activity remain unknown. Here, we characterized the FLV genes in Symbiodiniaceae and found that its coding region is composed of tandemly repeated FLV sequences. By measuring the O2-dependent electron flow and P700 oxidation, we suggest that this atypical FLV is active in vivo. Based on the amino-acid sequence alignment and the phylogenetic analysis, we conclude that in coral symbionts, the gene pair for FLVA and FLVB have been fused to construct one coding region for a hybrid enzyme, which presumably occurred when or after both genes were inherited from basal green algae to the dinoflagellate. Immunodetection suggested the FLV polypeptide to be cleaved by a post-translational mechanism, adding it to the rare cases of polycistronic genes in eukaryotes. Our results demonstrate that FLV are active in coral symbionts with genomic arrangement that is unique to these species. The implication of these unique features on their symbiotic living environment is discussed.

plant biology↗