Editorial: special issue on photosynthesis—the basics, mechanisms, and applications

Photosynthesis is indispensable for sustaining almost all life forms on Earth, as it utilizes light energy from the sun to convert carbon dioxide into carbohydrates with electrons derived either from water or from other sources. This process is performed in the absence of oxygen by anoxygenic bacteria or with oxygen by cyanobacteria, various eukaryotic algae, and land plants. Both types involve initial “light reactions” driven by light energy that are performed by a number of membrane-protein complexes localized in the photosynthetic membranes, followed by carbon fixation reactions in the cytoplasm of cells or stroma of chloroplasts (Blankenship 2014). Biomass production by photosynthesis is essential for the global carbon cycle and is being increasingly explored as a renewable source of biofuels: researchers are seeking ways in which the reactions and enzymes used in photosynthesis can be exploited to serve as a template for artificial photosynthesis in order to produce clean, renewable energy from the sun (Wang et al. 2022, Mousazadeh et al. 2025, Shi et al. 2025). Thus, photosynthesis is very important not only for sustaining current life on Earth, but also for the sustainable future of mankind. A variety of techniques have been employed to study photosynthesis, such as those used in the fields of biochemistry, biophysics, genetics, plant physiology, ecology, structural biology, quantum chemistry, information technology, etc. The timescale of the experiments spans from picoseconds when studying the process of light energy absorption and transfer among pigments, to years when considering the fields of plant physiology and ecology. Such research has not only contributed to the elucidation of fundamental principles of photosynthesis, but it has also made many remarkable achievements in applying knowledge gained to agricultural sciences and to the development of artificial photosynthesis. Despite these advances, many questions remain to be answered both in basic and applied photosynthesis research, such as the exact mechanism of light-induced water-splitting and its artificial application, as well as the mechanism of cyclic electron transfer around photosystem I. In this special issue (SI), we collected a total of 19 papers (10 are review papers and 9 are primary research papers), mostly from the invited participants of the 2nd Asia-Oceania International Congress on Photosynthesis which was held in Kobe, Japan, during 18–21 September 2024. This congress was the second one in the series and had 303 participants, among which 177 were from Japan and 126 were from other countries in the Asia and Oceania regions. Various topics covering the basic principles of photosynthetic research to cutting-edge research covering the molecular mechanisms of photosynthesis, its regulation and application in the fields of agriculture and artificial photosynthesis, were presented and discussed at the congress, as reflected in this issue. We summarize the contents of these papers in the order of review papers and original articles below. Various topics ranging from bacterial light-harvesting systems to pod photosynthesis are covered in this SI. Light-harvesting complexes (LHCs) bind multiple pigment molecules, which significantly expand the light absorption cross-section of photosynthetic reaction centers (RCs) and also contribute critically to the folding and structural stability of LHCs. The in vitro reconstitution of LHC polypeptides with pigments provides a powerful approach to modify the protein sequence, pigment composition, and stoichiometry, enabling detailed investigation into the role of individual amino acid and pigment molecules within LHC proteins. Saga et al. (2025) summarize two strategies for the reconstitution of LHCII proteins from oxygenic photosynthetic organisms and LH antenna complexes from anoxygenic purple bacteria, respectively. They also provide an overview of previous studies on reconstituted LHCs, revealing functional insights into the molecular mechanisms underlying protein folding and efficient light-harvesting of LHCs, which could serve as a basis on which to improve light-harvesting efficiency through the modification and reconstitution of LHCs. The mechanism of water oxidation is a hot area in the study of photosynthesis. Ishikita and Saito (2025) review the proton and electron transfer pathways generated from the water-oxidizing site by the Mn4CaO5 cluster from a theoretical perspective based on the recently reported X-ray free electron laser structures of Photosystem II (PSII) at S1, S2, and S3 states. Notably, while an O6 insertion was observed experimentally during the transition from S2 to S3, this transition was modeled with and without O6 insertion based on theoretical studies. The advantages and disadvantages of both models (i.e. with or without O6 insertion) are discussed, highlighting the necessity for further experimental studies to verify this process. While the PSII core complex is highly conserved, its extrinsic proteins show considerable variability among cyanobacteria, algae, and land plants, reflecting evolutionary adaptations. Imaizumi and Ifuku (2025) present a textbook-style overview of the structural and functional diversity of PSII, with particular emphasis on the extrinsic subunits across oxygenic phototrophs. The article highlights their roles in stabilizing the oxygen-evolving complex, optimizing water-splitting activity, and protecting against photodamage. Comparative insights into these subunits provide a framework for understanding PSII evolution and its physiological specialization. State transition is an important feature of the light-harvesting system to balance the energy between Photosystem I (PSI) and PSII under different light conditions. Minagawa (2025) summarizes knowledge regarding the state transition gained using structural, biochemical, and phylogenetic approaches recently, emphasizing state transition as a photo-regulatory strategy to coordinate environmental light sensing with the optimization of energy capture, distribution and photoprotection. Recent structural studies have revealed a conserved RRpT motif in the phosphorylated LHCII which docks to a site formed by PsaH and PsaL proteins in the PSI complex. LHCII phosphorylation is primarily regulated by the redox state of the plastoquinone pool and its interaction with the cytochrome b6f complex, which acts through the conserved Ser/Thr kinases (Stt7/STN7) and PP2C-type phosphatases (TAP38/PPH1). The kinase is further modulated by thioredoxin receiving electrons from PSI, adding an additional layer of redox-dependent control. Compared to PSII photoinhibition, PSI photoinhibition has received less attention, yet it is now considered an intrinsic property of PSI. Sonoike (2025) has comprehensively reviewed the potential causes of PSI photoinhibition, its correlation with redox conditions, and the similarities and differences among various types of photoinhibition. This review emphasizes the over-reduction of the PSI acceptor side components as a key condition for PSI photoinhibition, and underscores the importance of regulating electron transport for PSI protection. Furthermore, the review provides an overview of diverse protective mechanisms that alleviate the over-reduction of PSI acceptor side, thereby protecting PSI. The chloroplast NADH dehydrogenase-like (NDH) complex functions as a ferredoxin-dependent plastoquinone reductase and mediates cyclic electron transport around PSI. Shikanai et al. (2025) summarize recent progress in research on the NDH complex, paying particular attention to its evolutionary trajectory. Drawing on mutant phenotypes in angiosperms, they discuss how the NDH complex may contribute to the generation of proton motive force under low-light conditions, especially during light intensity fluctuations. Interestingly, the NDH complex has been lost during evolution and is absent in some phototrophic lineages. However, phylogenetic analysis revealed that, aside from Orchidaceae, loss of the NDH complex is relatively uncommon among terrestrial plants, thus underscoring its physiological importance. The structure, function, and regulations of FoF1-ATP synthase have been studied extensively. Kohzuma et al. (2025) integrate structural, physiological, and evolutionary perspectives to highlight the unique regulatory features of the plastid F0F1-ATP synthase. Phylogenetic analysis of the γ subunit, often encoded by multiple genes in plants, reveals tissue-specific diversification into redox-sensitive and redox-insensitive forms. The authors suggest that redox regulation of the chloroplast ATP synthase is essential for maintaining bioenergetic and redox balance, enabling plants to adapt to fluctuating light environments. They propose this regulatory innovation as being a key evolutionary step in the success of terrestrial plants, providing a basis for further examining the regulatory properties of the chloroplast FoF1-ATP synthase. The thylakoid membrane is the scaffold for photosynthetic complexes involved in light energy conversion and the electron transport chain in blue-green algae and land plants, and thus can be regarded as the “solar panel” of oxygenic phototrophs. Thylakoid membrane organization requires coordinated synthesis and regulation of its building block molecules, including membrane lipids, protein complexes, pigments, and other cofactors, together with additional regulatory molecules that remodel the membrane. In this issue, two reviews address this topic. Fujii et al. (2025) provide an overview of the synthetic pathways of membrane lipids, proteins, and chlorophylls, emphasizing the need for coordinated regulation across different organellar sub-compartments. Notably, most of these biosynthetic pathways occur in close association with membranes. Recent advances are highlighted regarding the roles of plastid lipids in retrograde signaling, particularly their involvement in the expression of photosynthesis-associated nuclear-encoded genes and in chloroplast biogenesis from proplastids. Sakamoto (2025) summarizes current knowledge of the structural and functional features of the thylakoid membrane, with particular emphasis on insights gained from electron tomography and proteomic studies of sub-organellar compartments. This review highlights the importance of considering structural changes in the thylakoid membrane when examining the regulation of photosynthetic electron transport. The concept of “thylakostasis” to describe thylakoid homeostasis is introduced and remodeling processes mediated by recently identified proteins, including VIPP1, FZL, and CURT1, are discussed. This remodeling is now recognized as being far more dynamic than previously thought, enabling plants to adapt rapidly to environmental changes. Leaf photosynthesis has been intensively studied compared to reproductive tissues such as pods, which also supply significant assimilates, particularly under stress or during leaf senescence. In this issue, Zhang et al. (2025a) highlight the overlooked role of pod photosynthesis in Fabaceae and Brassicaceae crops, demonstrating its major contribution to seed yield and quality. The article underscores current methodological limitations in quantifying pod photosynthesis and introduces emerging high-throughput phenotyping approaches. Unlocking the genetic and physiological basis of pod photosynthesis offers a promising frontier for crop improvement and food security under climate change. Three papers provide insight into the structure and function of bacterial photosystems and biosynthesis of bacteriochlorophyll (BChl). Tao et al. (2025) report the excitation energy transfer (EET) dynamics and photoprotective mechanisms that take place in a purified RC and in the light-harvesting 1–RC complexes of a purple photosynthetic bacterium, Blastochloris viridis, which features Bchl b and two distinct carotenoids, 1,2-dihydroneurosporene and 1,2-dihydrolycopene. Further, they identified the triplet–triplet energy transfer processes from Bchl b to carotenoids, providing insights into the Bchl b-based light-harvesting systems. Uragami et al. (2025) report the reconstitution of spheroidene, a carotenoid known to achieve ~90% EET efficiency in the LH2 complex of Rhodobacter sphaeroides strain 2.4.1, into a carotenoid-less LH1 complex of Rhodospirillum (Rsp.) rubrum strain G9+, and confirmed an improvement in EET by this reconstitution. Sub-nanosecond time-resolved absorption spectroscopy revealed that the emergence of a long-lived BChl a cation coincides with shortened triplet lifetimes of both carotenoid and BChl a in the reconstituted system, implying altered photoprotective dynamics. These findings suggest that while spheroidene facilitates efficient energy transfer in LH1 from Rsp. rubrum, it may also perturb the native protein environment, hence compromising photoprotection. Harada et al. (2025) focused on BchU, a key enzyme in the biosynthesis of BChl c. In the green sulfur bacterium Chlorobaculum tepidum, BChl c plays a central role within the LHC chlorosomes. To address limitations in genetic approaches for this system, the authors studied the enzyme biochemistry and showed that BchU predominantly acts on substrates after hydration at the C-3 position, catalyzed by BchF or BchV. These findings provide crucial insights into the BChl c biosynthetic pathway. The oxidation states of Mn ions in the Mn4CaO5 cluster during S-state transition is still under extensive debate. Wang et al. (2025) systematically analyzed the oxidation states of all Mn ions in both native Mn₄CaO5 clusters (derived from previously reported PSII structures) and artificial Mn4CaO4 clusters, using the classical bond-valence sum method. Their analysis revealed that the oxidation states of all four Mn ions in the artificial clusters are consistent with those of the S₁ state in native PSII, whereas the values calculated from structural data are lower than expected for the three intermediate states (S₁, S₂, and S₃) of the native catalyst. They also proposed that the μ2–O (O4) bridge may participate in the O–O bond formation, based on their finding that this moiety exhibits high reactivity in their synthetic catalyst. This study provides mechanistic insights into the oxygen-evolving catalysis in both natural and artificial photosynthesis and underscores the potential of using simplified artificial systems to investigate complex biological processes. Light-driven electron transport is central to photosynthesis, and its initial steps involve electron transfer from the primary to the secondary plastoquinone (QA-to-QB), a process that occurs within PSII. The DE loop of the PSII subunit D2 plays a critical role in QA binding. Zhong et al. (2025) investigated two conserved residues in the DE loop of the D2 protein, delineating their roles in QA binding, non-heme iron and bicarbonate stabilization, and forward electron transfer. They show that introducing charged residues at either site severely impairs the assembly and photosynthetic efficiency of PSII. Their findings provide mechanistic insight into the role of these conserved residues in PSII photochemistry, and could benefit the rational design of highly efficient photosynthetic apparatuses. Kawakami et al. (2025) report a new method for isolating a phycobilisome (PBS)-PSII megacomplex from a thermophilic cyanobacterium Thermosynechococcus vulcanus NIES-2134, and characterize the megacomplex with biochemical approaches as well as with spectroscopy. The structure of the isolated PBS-PSII megacomplex were determined by 2D electron microscopy, and the energy transfer dynamics from PBS to PSII was studied by ultrafast spectroscopy. A combination of these approaches could lead to the full elucidation of the molecular mechanism of energy transfer from PBS to PSII in future. Thioredoxins (Trx) regulate numerous photosynthetic enzymes through redox-dependent dithiol–disulfide exchange of conserved cysteine residues. To gain insights into the diversity of Trx family proteins across photosynthetic organisms, Sugiyama and Yoshida (2025) have performed a comprehensive phylogenetic analysis. The results reveal their diverse evolutionary origins, including both cyanobacterial inheritance and recruitment from non-photosynthetic eukaryotes. Several lineage-specific gains and losses also illustrate how Trx diversification contributed to the development of redox regulation systems. These findings establish a reference dataset and a foundation for future studies on redox biology in plants and algae. Estimating plant productivity by remote sensing is essential for assessing global functions of natural and agricultural systems and how they respond to climate change. The photochemical reflectance index (PRI) is used as a proxy for photosynthesis, but its reliability under non-steady-state conditions has been unclear. Zhang et al. (2025b) have examined correlations between PRI, CO2 assimilation rate, the quantum yield of PSII, and non-photochemical quenching during photosynthesis induction in dark- and light-adapted leaves. They found that, when assimilation is limited by stomatal conductance under dynamic light, PRI-based estimates may overestimate productivity, highlighting the need for caution in interpreting remote-sensing data. Finally, Pandey and Subramanyam (2025) report the effects of drought stress on the pigment contents in various photosynthetic complexes isolated from Pisum sativum with sucrose density gradient centrifugation. It was found that while the pigment type and content of LHCII trimers were marginally changed, significant alterations were observed in the PSII core, PSII-LHLCII, and PSI-LHCI complexes under drought stress. These results are discussed in relation to the zeaxanthin cycle in the context of photoinhibition and photoprotection mechanisms. As mentioned above, the articles collected in this SI are at the cutting edge of research in photosynthesis conducted primarily by researchers from the Asia and Oceania regions, and also from researchers elsewhere in the world. We hope that these articles promote further research to ultimately achieve a complete understanding of photosynthesis as well as the realization of artificial photosynthesis to create a sustainable future. We thank Tetsuya Higashiyama, Editor-in-Chief of Plant and Cell Physiology, for giving us the opportunity to organize this special issue, and Liliana Costa, Managing Editor, for her continuous support. The authors have no conflicts of interest to disclosure. This special issue was partly supported by KAKENHI grant for Transformative Research Area (A) (Photosynthesis Ubiquity, 23A305) from Ministry of Education, Culture, Sports, Science and Technology (MEXT). No data is associated with this paper.