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

Structures of PSI-FCPI from Thalassiosira pseudonana grown under high light provide evidence for convergent evolution and light-adaptive strategies in diatom FCPIs

Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for light harvesting and energy quenching under marine environments. Here we report two cryo-electron microscopic structures of photosystem I (PSI) with either 13 or five fucoxanthin chlorophyll a/c-binding protein Is (FCPIs) at 2.78 and 3.20 Å resolutions from Thalassiosira pseudonana grown under high light (HL) conditions. Among them, five FCPIs are stably associated with the PSI core, these include Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3. The eight additional Lhcr-type FCPIs are loosely associated with the PSI core and detached under the present purification conditions. The pigments of this centric diatom showed a higher proportion of chlorophylls a, diadinoxanthins, and diatoxanthins; some of the chlorophyll as and diadinoxanthins occupy the locations of fucoxanthins found in the huge PSI-FCPI from another centric diatom Chaetoceros gracilis grown under low-light conditions. These additional chlorophyll as may form more energy transfer pathways and additional diadinoxanthins may form more energy dissipation sites relying on the diadinoxanthin-diatoxanthin cycle. These results reveal the assembly mechanism of FCPIs and corresponding light-adaptive strategies of T. pseudonana PSI-FCPI, as well as the convergent evolution of the diatom PSI-FCPI structures.

Chloroplast Functionality at the Interface of Growth, Defense, and Genetic Innovation: A Multi-Omics and Technological Perspective

Chloroplasts are important in plant growth, development, and defense mechanisms, making them central to addressing global agricultural challenges. This review explores the multi-faceted contributions of chloroplasts, including photosynthesis, hormone biosynthesis, and stress signaling, which orchestrate the trade-off between growth and defense. Advancements in chloroplast genomics, transcription, translation, and proteomics have deepened our understanding of their regulatory functions and interactions with nuclear-encoded proteins. Case studies have demonstrated the potential of chloroplast-targeted strategies, such as the expression of elongation factor EF-2 for heat tolerance and flavodiiron proteins for drought resilience, to enhance crop productivity and stress adaptation. Future research directions should focus on the need for integrating omics data with nanotechnology and synthetic biology to develop sustainable and resilient agricultural systems. This review uniquely integrates recent advancements in chloroplast genomics, transcriptional regulation, and synthetic biology to present a holistic perspective on optimizing plant growth and stress tolerance. We emphasize the role of chloroplast-driven trade-off in balancing growth and immunity, leveraging omics technologies and emerging biotechnological innovations. This comprehensive approach offers new insights into sustainable agricultural practices, making it a significant contribution to the field.

Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I

BACKGROUND

All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). There is an increasing number of PS I 3D structures deposited in the Protein Data Bank (PDB). The Triangular Spatial Relationship (TSR)-based algorithm converts 3D structures into integers (TSR keys). A comprehensive study was conducted, by taking advantage of the PS I 3D structures and the TSR-based algorithm, to answer three questions: (i) Are electron cofactors including P700, A-1 and A0, which are chemically identical chlorophylls, structurally different? (ii) There are two electron transfer chains (A and B branches) in PS I. Are the cofactors on both branches structurally different? (iii) Are the amino acids in cofactor binding sites structurally different from those not in cofactor binding sites?

RESULTS

The key contributions and important findings include: (i) a novel TSR-based method for representing 3D structures of pigments as well as for quantifying pigment structures was developed; (ii) the results revealed that the redox cofactor, P700, are structurally conserved and different from other redox factors. Similar situations were also observed for both A-1 and A0; (iii) the results demonstrated structural differences between A and B branches for the redox cofactors P700, A-1, A0 and A1 as well as their cofactor binding sites; (iv) the tryptophan residues close to A0 and A1 are structurally conserved; (v) The TSR-based method outperforms the Root Mean Square Deviation (RMSD) and the Ultrafast Shape Recognition (USR) methods.

CONCLUSIONS

The structural analyses of redox cofactors and their binding sites provide a foundation for understanding the unique chemical and physical properties of each redox cofactor in PS I, which are essential for modulating the rate and direction of energy and electron transfers.

Ultrafast kinetics of PSI-LHCI super-complex from the moss Physcomitrella patens

Photosystem I (PSI) is a large membrane photosynthetic complex that harvests sunlight and drives photosynthetic electron transport. In both green algae and higher plants, PSI's ultrafast energy transfer and charge separation kinetics have been characterized. In contrast, it is not yet clear in Physcomitrella patens, even though moss is one of the earliest land plants and represents a critical stage in plant evolution. Here, we measured the time-resolved fluorescence of purified Pp PSI-LHCI at both room temperature (RT) and 77 K. Compared to the PSI kinetics of Arabidopsis thaliana at RT, we found that although the overall trapping time of Pp PSI-LHCI is nearly identical, ∼46 ps, their lifetimes at different wavelength regions differ. Specifically, Pp PSI-LHCI is slower in energy trapping below 720 nm but faster beyond. The slow-down of energy transfer between bulk chlorophylls (Chls, <720 nm) in Pp PSI-LHCI is probably because of the larger spatial gap between the PSI core and LHCI belt, and the acceleration of trapping at longer wavelength is most likely due to the lack of low-energy red-shifted Chls (red Chls). Indeed, time-resolved fluorescence results at 77 K revealed only three types of red Chls of 702 nm, 712 nm, and 720 nm in Pp PSI-LHCI but failed to detect the red Chls of 735 nm that present in LHCI in higher plants. Finally, we briefly discussed the evolutionary adaptations of PSI-LHCI in the context of red Chls from green algae to mosses and to land plants.

Structural insights into the assembly and energy transfer of haptophyte photosystem I-light-harvesting supercomplex

Haptophyta represents a major taxonomic group, with plastids derived from the primary plastids of red algae. Here, we elucidated the cryoelectron microscopy structure of the photosystem I-light-harvesting complex I (PSI-LHCI) supercomplex from the haptophyte Isochrysis galbana. The PSI core comprises 12 subunits, which have evolved differently from red algae and cryptophytes by losing the PsaO subunit while incorporating the PsaK subunit, which is absent in diatoms and dinoflagellates. The PSI core is encircled by 22 fucoxanthin-chlorophyll a/c-binding light-harvesting antenna proteins (iFCPIs) that form a trilayered antenna arrangement. Moreover, a pigment-binding subunit, LiFP, which has not been identified in any other previously characterized PSI-LHCI supercomplexes, was determined in I. galbana PSI-iFCPI, presumably facilitating the interactions and energy transfer between peripheral iFCPIs and the PSI core. Calculation of excitation energy transfer rates by computational simulations revealed that the intricate pigment network formed within PSI-iFCPI ensures efficient transfer of excitation energy. Overall, our study provides a solid structural foundation for understanding the light-harvesting and energy transfer mechanisms in haptophyte PSI-iFCPI and provides insights into the evolution and structural variations of red-lineage PSI-LHCIs.

Structural Diversity in Eukaryotic Photosynthetic Light Harvesting

Photosynthesis has been using energy from sunlight to assimilate atmospheric CO2 for at least 3.5 billion years. Through evolution and natural selection, photosynthetic organisms have flourished in almost all aquatic and terrestrial environments. This is partly due to the diversity of light-harvesting complex (LHC) proteins, which facilitate photosystem assembly, efficient excitation energy transfer, and photoprotection. Structural advances have provided angstrom-level structures of many of these proteins and have expanded our understanding of the pigments, lipids, and residues that drive LHC function. In this review, we compare and contrast recently observed cryo-electron microscopy structures across photosynthetic eukaryotes to identify structural motifs that underlie various light-harvesting strategies. We discuss subtle monomer changes that result in macroscale reorganization of LHC oligomers. Additionally, we find recurring patterns across diverse LHCs that may serve as evolutionary stepping stones for functional diversification. Advancing our understanding of LHC protein-environment interactions will improve our capacity to engineer more productive crops.

Uncovering the photosystem I assembly pathway in land plants

Photosystem I (PSI) is one of two large pigment-protein complexes responsible for converting solar energy into chemical energy in all oxygenic photosynthetic organisms. The PSI supercomplex consists of the PSI core complex and peripheral light-harvesting complex I (LHCI) in eukaryotic photosynthetic organisms. However, how the PSI complex assembles in land plants is unknown. Here we describe PHOTOSYSTEM I BIOGENESIS FACTOR 8 (PBF8), a thylakoid-anchored protein in Arabidopsis thaliana that is required for PSI assembly. PBF8 regulates two key consecutive steps in this process, the building of two assembly intermediates comprising eight or nine subunits, by interacting with PSI core subunits. We identified putative PBF8 orthologues in charophytic algae and land plants but not in Cyanobacteria or Chlorophyta. Our data reveal the major PSI assembly pathway in land plants. Our findings suggest that novel assembly mechanisms evolved during plant terrestrialization to regulate PSI assembly, perhaps as a means to cope with terrestrial environments.

Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium

Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral reef ecosystems. Here, we determine the cryo-electron microscopy structure of Symbiodinium photosystem I (PSI) supercomplex with a PSI core composed of 13 subunits including 2 previously unidentified subunits, PsaT and PsaU, as well as 13 peridinin-Chl a/c-binding light-harvesting antenna proteins (AcpPCIs). The PSI-AcpPCI supercomplex exhibits distinctive structural features compared to their red lineage counterparts, including extended termini of PsaD/E/I/J/L/M/R and AcpPCI-1/3/5/7/8/11 subunits, conformational changes in the surface loops of PsaA and PsaB subunits, facilitating the association between the PSI core and peripheral antennae. Structural analysis and computational calculation of excitation energy transfer rates unravel specific pigment networks in Symbiodinium PSI-AcpPCI for efficient excitation energy transfer. Overall, this study provides a structural basis for deciphering the mechanisms governing light harvesting and energy transfer in Symbiodinium PSI-AcpPCI supercomplexes adapted to their symbiotic ecosystem, as well as insights into the evolutionary diversity of PSI-LHCI among various photosynthetic organisms.

Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens

In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss Physcomitrium patens (P. patens) represents a well-studied primary land-dwelling photosynthetic autotroph branching from the common ancestor of green algae and land plants at the early stage of evolution. P. patens possesses at least three types of PSI with different antenna sizes. The largest PSI form (PpPSI-L) exhibits a unique organization found neither in flowering plants nor in algae. Its formation is mediated by the P. patens-specific LHC protein, Lhcb9. While previous studies have revealed the overall architecture of PpPSI-L, its assembly details and the relationship between different PpPSI types remain unclear. Here we report the high-resolution structure of PpPSI-L. We identified 14 PSI core subunits, one Lhcb9, one phosphorylated LHCII trimer and eight LHCI monomers arranged as two belts. Our structural analysis established the essential role of Lhcb9 and the phosphorylated LHCII in stabilizing the complex. In addition, our results suggest that PpPSI switches between different types, which share identical modules. This feature may contribute to the dynamic adjustment of the light-harvesting capability of PSI under different light conditions.

Growth and Photosynthetic Efficiency of Microalgae and Plants with Different Levels of Complexity Exposed to a Simulated M-Dwarf Starlight

Oxygenic photosynthetic organisms (OPOs) are primary producers on Earth and generate surface and atmospheric biosignatures, making them ideal targets to search for life from remote on Earth-like exoplanets orbiting stars different from the Sun, such as M-dwarfs. These stars emit very low light in the visible and most light in the far-red, an issue for OPOs, which mostly utilize visible light to photosynthesize and grow. After successfully testing procaryotic OPOs (cyanobacteria) under a simulated M-dwarf star spectrum (M7, 365-850 nm) generated through a custom-made lamp, we tested several eukaryotic OPOs: microalgae (Dixoniella giordanoi, Microchloropsis gaditana, Chromera velia, Chlorella vulgaris), a non-vascular plant (Physcomitrium patens), and a vascular plant (Arabidopsis thaliana). We assessed their growth and photosynthetic efficiency under three light conditions: M7, solar (SOL) simulated spectra, and far-red light (FR). Microalgae grew similarly in SOL and M7, while the moss P. patens showed slower growth in M7 with respect to SOL. A. thaliana grew similarly in SOL and M7, showing traits typical of shade-avoidance syndrome. Overall, the synergistic effect of visible and far-red light, also known as the Emerson enhancing effect, could explain the growth in M7 for all organisms. These results lead to reconsidering the possibility and capability of the growth of OPOs and are promising for finding biosignatures on exoplanets orbiting the habitable zone of distant stars.

Structural insights into a unique PSI-LHCI-LHCII-Lhcb9 supercomplex from moss Physcomitrium patens

Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that diverged from aquatic green algae and evolved into land plants. The moss Physcomitrium patens (P. patens) has a light-harvesting complex (LHC) superfamily more diverse than those of green algae and higher plants. Here, we solved the structure of a PSI-LHCI-LHCII-Lhcb9 supercomplex from P. patens at 2.68 Å resolution using cryo-electron microscopy. This supercomplex contains one PSI-LHCI, one phosphorylated LHCII trimer, one moss-specific LHC protein, Lhcb9, and one additional LHCI belt with four Lhca subunits. The complete structure of PsaO was observed in the PSI core. One Lhcbm2 in the LHCII trimer interacts with PSI core through its phosphorylated N terminus, and Lhcb9 mediates assembly of the whole supercomplex. The complicated pigment arrangement provided important information for possible energy-transfer pathways from the peripheral antennae to the PSI core.

Dynamic Regulation of the Light-Harvesting System through State Transitions in Land Plants and Green Algae

Photosynthesis constitutes the only known natural process that captures the solar energy to convert carbon dioxide and water into biomass. The primary reactions of photosynthesis are catalyzed by the photosystem II (PSII) and photosystem I (PSI) complexes. Both photosystems associate with antennae complexes whose main function is to increase the light-harvesting capability of the core. In order to maintain optimal photosynthetic activity under a constantly changing natural light environment, plants and green algae regulate the absorbed photo-excitation energy between PSI and PSII through processes known as state transitions. State transitions represent a short-term light adaptation mechanism for balancing the energy distribution between the two photosystems by relocating light-harvesting complex II (LHCII) proteins. The preferential excitation of PSII (state 2) results in the activation of a chloroplast kinase which in turn phosphorylates LHCII, a process followed by the release of phosphorylated LHCII from PSII and its migration to PSI, thus forming the PSI-LHCI-LHCII supercomplex. The process is reversible, as LHCII is dephosphorylated and returns to PSII under the preferential excitation of PSI. In recent years, high-resolution structures of the PSI-LHCI-LHCII supercomplex from plants and green algae were reported. These structural data provide detailed information on the interacting patterns of phosphorylated LHCII with PSI and on the pigment arrangement in the supercomplex, which is critical for constructing the excitation energy transfer pathways and for a deeper understanding of the molecular mechanism of state transitions progress. In this review, we focus on the structural data of the state 2 supercomplex from plants and green algae and discuss the current state of knowledge concerning the interactions between antenna and the PSI core and the potential energy transfer pathways in these supercomplexes.