Physiological, cytological, and transcriptomic analyses reveal temperature response mechanisms in a temperature-sensitive yellow-leaf mutant of wax gourd.

The supramolecular architecture of light-harvesting complex 2 (LH2) and light-harvesting complex 1-reaction center (LH1-RC) complexes underpins the near-unity quantum efficiency of photosynthesis in purple bacteria. Constructing artificial photosynthetic systems that structurally and functionally mimic these natural assemblies remains a critical challenge. Here, we report a spherical chromatophore nanomicelle system that mimics both LH2 and LH1-RC in water. This system is constructed through hierarchical coassembly of an amphiphilic porphyrin-based bacteriochlorophyll analogue and a cationic molecular nickel catalyst. Cryogenic electron microscopy directly resolves high-resolution ring-like structures on the nanomicelle surface, providing the first visual confirmation of the biomimetic architecture. The system achieves photocatalytic hydrogen evolution with a turnover number exceeding 667,000 over 72 h and a turnover frequency of above 9000 h-1 with an absolute hydrogen yield of 1.34 μmol─40 times greater than the nonassembled free molecular system─along with an initial external quantum efficiency of 6.8% at 435 nm. This outstanding performance originates from the well-defined spatial organization of the photosensitizers and catalysts, which facilitates efficient light harvesting and directional energy/electron transfer. Our work establishes a promising strategy for constructing high-performance artificial photosynthetic systems through rational biomimetic design.

Cyanobacteria are a highly taxonomically and ecologically diverse group of oxygenic phototrophs that have colonized many different environments on our planet. Despite their differences, almost all cyanobacteria rely on highly efficient light-harvesting protein complexes, termed phycobilisomes, for effective photosynthesis. Phycobilisomes, along with the phycobiliproteins that make them up, have maintained their function throughout evolutionary history while also diversifying to optimize energy capture and transfer in different conditions. Here, we use a combination of evolutionary proteomics, phylogenomics, and structural bioinformatics to probe how phycobiliproteins have maintained their function while adapting to different habitats. Using high-resolution native mass spectrometry, we show that the two most abundant phycobiliprotein complexes, phycocyanin and allophycocyanin, are highly dynamic. Moreover, upon mixing phycobiliproteins from cyanobacterial strains representing diverse environments and evolutionary lineages, heterologous phycobiliprotein complexes rapidly form, comprising building blocks from different cyanobacterial strains. Bioinformatics and structural prediction methods allow us to identify critical residues involved in these interactions. We thus demonstrate that key structural features within the phycobiliprotein components have remained conserved over three billion years of cyanobacterial evolution, ensuring effective photosynthesis across a wide variety of natural environments.

Spectroscopic studies of energy transport through the photosynthetic apparatus have been crucial to expanding our understanding of biological energy conversion. Correlating spectroscopic information to the electronic structure and function in these complex systems remains highly challenging, however. While cryogenic experimental conditions help in improving the effective spectral resolution and sample stability, the observed fine-grained dynamics do not necessarily reflect in vivo functionality. To address this issue, we target the temperature dependence of energy migration in light-harvesting complex 2 of purple bacteria. Temperature- and polarization-controlled two-dimensional electronic spectroscopy reveal rapid exciton immobilization at low temperatures, while intensity-dependent experiments allow identification of transport barriers. We find that exciton trapping, dominating the dynamics at 80 K, becomes negligible above 150 K, implying that observations at cryogenic temperatures do not always directly reflect biological function. We additionally find that considerable care and explicit modeling may be necessary for correct interpretation of multiexciton experiments.

Leaf color mutants are key resources for uncovering the molecular mechanisms of chloroplast development and photosynthesis. Here, we identified a novel yellow-green melon mutant, ‘ygp2’, which displays yellow-green leaves and dwarfism throughout development. Genetic analysis indicated that the trait is controlled by a single recessive nuclear gene. Map-based cloning delimited the candidate region to an 805 kb interval on chromosome 11, within which only one missense mutation was identified in MELO13C_11G242690, encoding a triosephosphate isomerase (CmpdTPI). Phylogenetic analysis suggested its plastid localization, which was confirmed by transient expression of CmpdTPI-GFP in tobacco. The ‘ygp2’ mutant exhibited significantly reduced TPI enzyme activity and net photosynthetic rate. Transcriptome analysis revealed downregulation of genes related to light-harvesting complexes, cell division, and the cell cycle. These results demonstrate that the point mutation in CmpdTPI impairs chloroplast function and photosynthesis, leading to the yellow-green phenotype in melon. This study provides insight into the role of plastidial TPI in chlorophyll metabolism and chloroplast development.

In plants, the process of state transition regulates the allocation of sunlight energy between Photosystem II (PSII) and PSI. However, the implications of state transitions for harmonizing electron transport rates between photosystems, and a full quantitative picture of this process, remain underexplored. We integrated quantitative biology (biochemical and biophysical approaches) with in vivo spectroscopy on wild-type Arabidopsis and protein phosphorylation mutants. This combination facilitated monitoring of Chl redistribution and its functional implications for light harvesting and electron transport. Our findings demonstrate the reallocation of 12% of highly phosphorylated 'extra' light-harvesting complex II under state 2 from stacked to unstacked thylakoids. This reduces the number of Chls per PSII from 216 to 182, while increasing the number in PSI from 187 to 223. Such Chl redistribution compensates for differences in photosystem stoichiometry and photochemical quantum efficiencies, thereby precisely synchronizing electron transport rates in both photosystems. Mutant analyses corroborate that this regulatory mechanism involves reversible phosphorylation. We inferred that state transitions optimize linear electron transport, leaving no additional capacity for cyclic electron transport. Furthermore, the results suggest that the controversies about long-range migration of LHCII from stacked to unstacked thylakoid domains arise from differences in phosphorylation levels.

There are non-negligible exciton couplings and coherent oscillations in the excitation energy transfer within the light-harvesting complex and the exciton dynamics. In addition, the exciton dynamics depends on a variety of system parameters, such as electron coupling, electron-phonon coupling, and the site energy of each chromophore. In order to investigate the detailed interaction process, we propose an extended perturbation theory approach and derive the coherent dynamics of reduced density matrices under arbitrary orthogonal transformations. Our method quantitatively presents the dependence of system parameters on exciton state dynamics and the mathematical analysis of coherent dynamics, expands the application boundary of standard Förster and modified Redfield theories, and provides a mathematical description in the general case with an arbitrary basis. In the two-level dimer system, our model provides an excellent correspondence with the calculation of numerically exact hierarchical equations of motion. As an application, we quantitatively describe the long-lived vibronic coherence within recombinant allophycocyanin and the electron coherence process between chromophores within cryptophyte phycocyanin 645.

Photosystem I (PSI) is one of the two photosystems conserved from cyanobacteria to vascular plants, and associates with multiple light-harvesting complexes (LHCs) that capture and transfer solar energy. Liverworts such as Marchantia polymorpha occupy an early evolutionary position among land plants and faced major challenges during terrestrial adaptation, including desiccation, strong light, and UV radiation. We reveal the cryo-electron microscopic structures of PSI-LHCI monomer and homodimer from the liverwort M. polymorpha at resolutions of 1.94 and 2.52 Å, respectively. The high-resolution map allows identification of the cofactors of the monomer and reveal differences between the liverwort and moss, another clade of bryophytes. The PSI-LHCI monomer-monomer is stabilized by PsaG and PsaH interactions on the stromal side, which causes the bending and twisting of the homodimer. PsaM interacts with PsaB tightly, indicating a key role of PsaM in mediating the dimerization.

Photosynthesis, the biological process of converting light energy into chemical energy, involves light harvesting, charge separation and electron transport, proton translocation, ATP synthesis, and carbon fixation, among other processes. Adjacent photosynthetic complexes may assemble into supramolecular complexes to couple and regulate their functions. Here, we review the progress of structural biology studies of photosynthetic supramolecular complexes, such as those that have light-harvesting complexes assembled with photosystem II (PSII) or photosystem I (PSI), both PSII and PSI, or bacterial reaction center complexes. The intricate architectures of the NADH dehydrogenase-like (NDH) complex and PSI-NDH supercomplex, revealed through cryo-electron microscopy studies, provide crucial frameworks for understanding the molecular mechanisms of cyclic electron flow in cyanobacteria and plants. Furthermore, structural studies have also yielded detailed insights into the assembly and repair of PSII, regulation of ATP synthase, and carbon fixation. The review concludes with a summary of the emerging directions of structural biology studies of photosynthetic supramolecular complexes.

Photoacclimation strategies of different phytoplankton species revealed by physiological, biochemical, and comparative proteomic analyses.

Golden coloration of Ginkgo biloba can be driven by fine-tuning of pigment, flavonoid, and terpene metabolism.

Planar arrangement of bacteriochlorophyll c aggregates in chlorosomes of Chloroflexus aurantiacus.

Excited states of embedded chromophores are highly influenced by their interaction with the environment. Herein, we present a machine-learning (ML) framework capable of predicting the different environmental contributions to excitation energies of chromophores in a polarizable embedding. Our ML models are built in a hierarchical structure to capture both the effect of ground-state polarization and the response of the polarizable environment to the electronic transition. With the use of the right descriptors, the models trained on the quantum mechanics/molecular mechanics (QM/MM) calculations in a nonpolarizable environment are able to successfully predict the effects of a polarizable environment on excitation energies. The ML models are applied to three chromophores present in light-harvesting complexes (chlorophyll a, chlorophyll b, and lutein) and are used to reproduce the excitonic structure of a multichromophoric system unseen in the training set to a level of accuracy offered by a polarizable QM/MM calculation, while taking a fraction of its time.

Stratified marine systems are often characterized by a deep chlorophyll maximum (DCM); however, the taxonomic and functional dynamics of protist assemblages within this layer remain poorly understood. We integrated microscopy, pigment-based CHEMTAX analysis, 18S rRNA metabarcoding, and metatranscriptomics to compare protist communities in the surface and DCM layers of the northeastern East China Sea. Microscopy and pigment data revealed higher cell abundances, increased chlorophyll- a levels, and distinct pigment signatures at the DCM, particularly for haptophytes, chlorophytes, and pelagophytes. Amplicon sequencing revealed increased representation of chlorophyte and Syndiniales at depth, whereas metatranscriptomic profiles showed elevated transcriptional activity in diatoms, dinoflagellates, and chlorophytes. Functional gene analyses revealed DCM-specific upregulation of photosystem I subunits, light-harvesting complex proteins, and nitrogen assimilation pathways, indicating photoacclimation and nutrient exploitation under low-light, nutrient-rich conditions. Syndiniales were abundant in DNA-based data but mostly transcriptionally inactive, suggesting dormancy or parasitic stages, while diatoms exhibited high transcriptional activity despite low DNA abundance. These findings indicate a clear decoupling between taxonomic presence and metabolic activity, emphasizing that ecological roles cannot be inferred from abundance alone. Our findings identify the DCM as a biogeochemical hotspot shaped by taxon-specific metabolic strategies and vertical niche partitioning, underscoring the key role of protists in sustaining productivity and carbon cycling in stratified ocean ecosystems.

The photosystem II (PSII)-light-harvesting complex II (LHCII) supercomplex within plant thylakoid membranes plays a central role in photosynthesis. Multiple PSII-LHCII supercomplexes within the thylakoid membranes assemble into higher-order supramolecular structures in response to environmental light conditions. In this study, we used high-speed atomic force microscopy (AFM) to visualize isolated thylakoid membranes. This enabled the observation of PSII-LHCII supercomplexes in a physiologically relevant environment. AFM imaging and biochemical analyses revealed disrupted semicrystalline-array-like PSII-LHCII assemblies under high-light acclimation. Detailed image analysis, combined with three-dimensional PSII model fitting, revealed two distinct configurations of the semicrystalline arrays: parallel and offset. Although the parallel array remained stable, the offset array was destabilized in a PsbS-dependent manner under high-light acclimation. These findings demonstrate that high-light acclimation and PsbS correlate with PSII-LHCII supercomplex organization in isolated membranes.

Peanuts (Arachis hypogaea L.) exhibit a high demand for calcium, second only to nitrogen and potassium, with calcium playing a critical role in their growth, development, and nitrogen fixation. However, the mechanisms underlying calcium-mediated regulation of peanut growth and nitrogen fixation remain poorly understood. In this study, we employed nitrogen-efficient (Puhua 66, Huayu 20) and nitrogen-inefficient (Puhua 28, Shanhua 14) peanut varieties in a two-year field experiment using a split-plot design. The main plots comprised two treatments: standard fertilization (CK) and calcium supplementation (Ca), while the sub-plots consisted of different peanut varieties. We analyzed growth parameters, physiological responses, and transcriptomic profiles. Our results demonstrated that calcium application significantly increased malondialdehyde (MDA) content in leaves while reducing peroxidase (POD) activity, enhancing pod dry matter accumulation, and promoting earlier plant maturation. Additionally, calcium application elevated the activities of nitrate reductase (NR) and glutamine synthetase (GS) (P < 0.01), thereby improving nitrogen and calcium accumulation in pods, their allocation efficiency, and the overall utilization rates of nitrogen and calcium fertilizers. Transcriptomic analysis revealed 166 differentially expressed genes (DEGs) in nitrogen-efficient varieties and 343 DEGs in nitrogen-inefficient varieties under calcium supplementation, with 67 DEGs shared between the two groups. Functional annotation and qRT-PCR validation were performed on these DEGs.Furthermore, weighted gene co-expression network analysis (WGCNA) indicated that calcium supplementation significantly up-regulated genes associated with sucrose synthase, β-amylase, GTPase-activating proteins, light-harvesting chlorophyll-protein complexes (Lhca2, Lhca3), photosynthetic electron transport (PetF, PetJ), phosphatidylinositol phospholipase C2, inositol-3-phosphate synthase, TMV resistance protein, ABC transporters, ethylene-responsive transcription factors (EIN1, EIN2, EIN3), alkylamine oxidase, glutamate dehydrogenase, and aspartate synthase. These findings suggest that calcium application modulates carbohydrate metabolism, nitrogen assimilation, plant-pathogen interactions, and photosynthetic processes through differential gene expression, ultimately enhancing leaf physiological activity, dry matter partitioning, pod yield, and early maturation in peanuts.

Modeling optical spectra of pigment-protein complexes requires accurate treatment of both excitonic and vibronic interactions. While nonperturbative approaches, such as the hierarchical equations of motion, are, in principle, numerically exact, they are computationally demanding, making the use of approximate lineshape theories appealing. However, the biases introduced by these perturbative treatments still need assessment. Here, we systematically compare methods based on cumulant expansion and successive approximations against exact calculations. Using chlorophyll dimers in the water-soluble chlorophyll-binding protein and the CP29 light-harvesting complex as test systems, we analyze absorption spectra under varying coupling strengths. Our results show that vibronic renormalization of excitonic coupling can be captured by the partially Markovian complex Redfield (cR) theory, whereas fully non-Markovian approaches are essential for reproducing the intensities of vibronic sidebands. A model that treats electronic transitions involving high-frequency vibrational modes as localized recovers many of the non-Markov and non-secular effects. We extend our analysis to fluorescence spectra, which pose more difficulties because excitonic and vibrational states are entangled before emission. While non-Markovian methods still perform better for fluorescence, their performance in reproducing vibronic sidebands is less than satisfactory. Our results allow quantifying the errors made by approximate theories and define a reliability range for spectroscopic simulations.

Proteins are generally characterized by three-dimensional structures that are well suited for their specific function. It is much less accepted that a particular flexibility or plasticity of a protein is essential for performing its function. The latter plasticity encompasses the stochastic motions of small protein sidechains on the picosecond timescale that serve as "lubricating grease", allowing slower functionally relevant conformational changes. Some remarkable examples of potential correlations between protein dynamics and function were observed for pigment-protein complexes in photosynthesis. For example, electron transfer and protein plasticity are concurrently suppressed in Photosystem II upon decreases in temperature or hydration, thus suggesting a prominent functional role of protein dynamics. An unusual dynamics-function correlation was observed for the major light-harvesting complex II, where the dynamics of charged protein residues affect the pigment absorption frequencies in photosynthetic light-harvesting. Generally, proteins exhibit a wide variety of motions on multiple time and length scales. However, there is an approach to characterize the plasticity of a protein as a single effective force constant that permits a straightforward comparison between different protein systems. Within this review, we determine the latter effective force constant for three photosynthetic proteins in different functional and organizational states. The force constant values determined appear to be rather different for each protein and are consistent with the requirements imposed by the various functions. These findings highlight the individual character of a protein's flexibility and the role(s) it is playing for the specific function.

Utilization of minor red-shifted chlorophyll a for oxygenic photosynthesis under far-red light in green algae.

Time-resolved electron paramagnetic resonance (TR-EPR), combined with magnetophotoselection (MPS), provides a powerful approach to probe exciton states in multichromophoric systems where photoexcitation populates a triplet state localized on a specific chromophore. This scenario occurs in the peridinin-chlorophyll protein (PCP) from dinoflagellates, which contains clusters of peridinins surrounding chlorophyll a. Here, we present MPS-TR-EPR data for PCP from Heterocapsa pygmaea and a high-salt PCP variant from Amphidinium carterae. Spectral analysis reveals the orientation of the optical transition dipole moments (TDMs), reflecting the chromophore contributions to the exciton states. The results indicate a predominant role of Per614/624 in the lowest singlet exciton state, consistent with theoretical models, while, at the same time, also suggesting refinements to better align the models with the experimentally determined TDM orientations. These findings provide constraints relevant to understanding molecular strategies for optimizing light absorption and energy transfer in light-harvesting complexes.