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Open research questions in Photosynthetic Processes and Mechanisms

38 unresolved questions extracted from the limitations and future-work sections of 229 Photosynthetic Processes and Mechanisms papers in our library. Each links back to the study that raised it.

What the literature leaves open

  • Prochlorococcus and Synechococcus, along with their cyanophages, dominate oligotrophic oceans and experience persistent HL exposure, yet the molecular basis of PSII adaptation in these systems remains poorly understood.

    Molecular Basis of High-light Adaptation in Cyanobacteria and Cyanophages through the D1/D2 subunits of Photosystem II · 2026 · DOI

  • Evidence from Arabidopsis and other systems indicates that CK signaling delays chlorophyll catabolism, slows disassembly of photosynthetic complexes, supports chloroplast-related gene expression, and limits ROS-driven acceleration of senescence. The recent observation in detached Arabidopsis leaves that CKs can transiently and reversibly downregulate PSII photochemistry during prolonged darkness adds an important nuance. In such contexts, CK action may protect leaves by lowering electron pressure and improving redox control before later photosynthetic competence is maintained, indicating that transient photosynthetic down-modulation can be part of the protective response (Krieger‐Liszkay et al., 2019; Domı́nguez and Cejudo, 2021; Kábrtová et al., 2026). Several lines of evidence indicate that CKs actively reprogram the transcriptome of mature leaves and buffer redox-dependent feedbacks associated with photosynthetic decline.

    Cytokinin availability and chloroplast functional lifetime in senescing leaves · 2026 · DOI

  • Photosystem I (PSI) converts light into chemical energy with near-unity quantum efficiency, yet its energy-transfer and charge-separation mechanisms remain debated.

    Excitonic energy transfer in red algal Photosystem I reveals an evolutionary bridge between cyanobacteria and plants · 2026 · DOI

  • Summary 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.

    Evolutionary origin and photoprotective role of Lhcx in the centric diatom <i>Chaetoceros gracilis</i> · 2026 · DOI

  • To investigate the functional significance of this cell-specific expression, we generated gene-edited lines of the NADP-ME C4 grass Setaria viridis lacking either PGRL1 paralog.

    Cell-preferential PGRL1 paralogs provide distinct modes of photoprotection in C4 photosynthesis · 2026 · DOI

  • While ambient CO2 acclimation is well-studied, responses to hyperoxia remain poorly understood, despite its frequent occurrence in nature under high light.

    Natural genetic variation reveals divergent transcriptomic responses to hyperoxia in two Chlamydomonas reinhardtii ecotypes · 2026 · DOI

  • These advances pave the way for the determination of ancient CO 2 levels from the stable isotope composition of fossilized plant remains, particularly for understudied, yet fossil‐rich, periods of geologic time.

    A century of research on carbon isotope discrimination during photosynthesis: from early breakthroughs to future goals · 2026 · DOI

  • The present study investigated how phyA engages with autophagy to mediate FRL signaling under nutrient starvation in Arabidopsis, a process whose mechanisms remain unclear.

    The signaling mechanism of <scp>phyA</scp> involves direct interaction with <scp>ATG8</scp> to regulate <scp>HY5</scp> autophagic degradation under nutrient starvation · 2026 · DOI

  • Significance StatementPhotosynthetic and electron-uptake capabilities make Rhodopseudomonas palustris a promising candidate for a biotechnology chassis, but the regulation of these processes is insufficiently understood in this organism, as R.

    The AadR-FixK hierarchy coordinates iron-responsive metabolism via Fur-family regulators in Rhodopseudomonas palustris TIE-1 · 2026 · DOI

  • Summary: Connectivity between mesophyll (M) and bundle sheath (BS) cells must improve during the evolution of C4 photosynthesis to facilitate large metabolite fluxes between these cell types, but the trait combinations that enhance M–BS connectivity and the points at which these enhancements occur along the C3 to C4 evolutionary trajectory remain unknown.

    Improved mesophyll–bundle sheath connectivity is achieved via different mechanisms in C 2 vs C 4 Alternanthera · 2026

  • It is well known that the stacking of thylakoids and the lateral macro-organization of the pigment–protein complexes in the membrane are interrelated (reviewed by Musta´rdy and Garab 2003; Dekker and Boekema 2005) but dgd1 is poorly characterized in this respect.

    Creutzfeldt-Jakob disease in the Philippines: diagnostic and management challenges from the first multicenter registry · 2026 · DOI

  • It is well known that the stacking of thylakoids and the lateral macro-organization of the pigment–protein complexes in the membrane are interrelated (reviewed by Musta´rdy and Garab 2003; Dekker and Boekema 2005) but dgd1 is poorly characterized in this respect.

    Multi-UAV Collaborative Path Planning Based on CycA-MASAC Reinforcement Learning in GPS-Denied Environment · 2026 · DOI

  • It is well known that the stacking of thylakoids and the lateral macro-organization of the pigment–protein complexes in the membrane are interrelated (reviewed by Musta´rdy and Garab 2003; Dekker and Boekema 2005) but dgd1 is poorly characterized in this respect.

    Mapping ICT-Based Interventions for Autism Spectrum Disorder: A Global Bibliometric and Scientometric Analysis · 2026 · DOI

  • While the CCM and nitrogen assimilation have been shown to share some regulatory pathways, how the CCM impacts the response to nitrogen deprivation remains underexplored.

    CO2 fixation mediated by the carbon concentrating mechanism enables a rapid response to nitrogen deprivation in cyanobacteria · 2026 · DOI

  • In the algal pyrenoid, an organelle responsible for one-third of global carbon fixation, CO2-delivering thylakoid membranes must penetrate a phase-separated condensate of the CO2-fixing enzyme Rubisco, but the mechanism governing membrane recruitment into the condensate remains unknown.

    A bifunctional coiled-coil protein generates the membrane-within-condensate architecture of the CO2-fixing pyrenoid · 2026 · DOI

  • Biosynthesis of the linear tetrapyrrole phycocyanobilin (PCB) by the ferredoxin-dependent bilin reductase (FDBRs) PcyA is essential for light-harvesting and regulatory processes in diverse photosynthetic organisms, yet its evolutionary origins are not fully understood.

    Evolutionary insights into bilin biosynthesis: Functional characterization of pre-PcyA enzymes · 2026 · DOI

  • These findings provide valuable insights for applied breed- ing programs. Identification of SNP differences and varia- tions within promoter regions of PSI and PSII genes may be particularly relevant for studies on climate resilience. Although gene expression analysis was not performed in the present study, future investigations incorporating in-depth molecular analyses will be essential to elucidate the regula- tory effects of SNPs and indels within promoter fragments and their contribution to stress-responsive gene regulation. In conclusion, the promoter regions of chloroplast- encoded photosystem genes in Beta exhibit a highly conserved regulatory architecture characterized by the coordinated presence of PEP and NEP elements. This dual- promoter framework likely ensures robust and flexible tran- scriptional control under varying environmental conditions. While overall sequence conservation reflects strong evo- lutionary constraint, the presence of minor SNPs, particu- larly in B. corolliflora, highlights subtle genetic variation that may contribute to adaptive regulation rather than major functional divergence. Together, these findings suggest that Beta chloroplast promoters are finely tuned to balance transcriptional stabil- ity with limited regulatory plasticity, providing a molecular basis for maintaining photosynthetic efficiency and resil- ience under abiotic stress. These insights offer a foundation for exploiting promoter variation in future breeding strate- gies aimed at improving stress tolerance in sugar beet. Future research should prioritize three key directions to translate these genomic insights into practical applications. Page 15 of 18 98 First, functional validation of identified cis-elements through expression profiling under controlled stress conditions, pro- moter–reporter assays, and transgenic analyses will con- firm their regulatory roles and stress-response mechanisms. Second, the integration of chloroplast genomic insights with advanced gene-editing technologies, such as CRISPR- based promoter modification, offers a promising approach to fine-tune photosystem gene regulation and improve plant performance under climate-induced stress without introduc- ing foreign DNA. Third, expanding chloroplast comparative studies across a wider range of Beta accessions, including underutilized wild populations and landraces, will further elucidate the molecular mechanisms underlying stress resil- ience and uncover additional genetic diversity for breeding. Together, these efforts will guide the development of high- yielding, climate-resilient sugar beet cultivars for sustain- able agriculture in the face of global environmental change. Supplementary Information The online version contains supplementary material available at h t t p s : / / d o i . o r g / 1 0 . 1 0 0 7 / s 1 0 1 4 2 - 0 2 6 - 0 1 8 8 3 - 3 . Acknowledgements Noreen Aslam is thankful to TUBITAK for sup- porting her studies. Mehmet Örgeç was supported by the TÜBİTAK Scientist Support Programs Directorate (BİDEB), 2211-A National PhD Scholarship Program, and The Higher Education Council (YÖK) through 100/2000 Doctoral Scholarship Program. Author contributions Conceptualization: MS, MTW and SG. Method- ology: MS, MTW and MCB. Formal analysis and investigation: MS, Abdullah, NB, IA, MCB, NA, MO, MTW, EG and SG. Writing - origi- nal draft preparation: Abdullah, MS, NA, MTW and SG. Writing - re- view and editing: MS, Abdullah, MTW, MCB, NA, MO, EG and SG. Funding acquisition: SG. Resources: IA, MTW, and SG. Supervision: MTW and SG. Funding This work was supported by Scientific and Technological Re- search Council of Türkiye (TÜBİTAK) (Grant No. KBAG-120O596) to Songul Gurel. Data availability The sequencing data of the sugar beet genotypes were deposited to NCBI under the accession numbers PV151546 PV069735, PV069737, PV069736, PV135462, PV135457, PV135461, PV135459, PV135458, PV135460.

    Comparative Chloroplast Genomics of Sugar Beet and Wild Relatives: Insights into Photosystem Gene Regulation and Stress Tolerance · 2026 · DOI

  • 1c00576 Raszewski G, Renger T (2008) Light harvesting in photosystem II core complexes is limited by the transfer to the trap: can the core complex turn into a photoprotective mode? J Am Chem Soc 130(13):4431–4446.

    Tuning the F695 fluorescent state in photosystem II using site-directed mutagenesis in Synechocystis sp. PCC 6803 · 2026 · DOI

  • Taken together, recent work supports a view of the Chlamydomonas CCM as a coupled system in which Ci transport, energy supply, pyrenoid architecture, and regulation are inseparable. Flexible Ci uptake routes, lumen acidification, chloroplast–mitochondrial cooperation, CO2 retention, and multilayered control circuits together determine whether Rubisco remains supplied with high local CO2 under fluctuating environments. At the same time, conservation of individual regulatory modules is uneven across green algae. CCM1/CIA5-dependent transcriptional regulation, and possibly LCR1-type branch-specific control, appear relatively restricted, whereas CAS-linked chloroplast Ca2+ signaling has functional counterparts in both Chlamydomonas and land plants. The next challenge is to identify how the system switches between carbon- − replete HC conditions and CO2-limiting LC/VLC states. The upstream CO2/HCO3 sensor for CCM1/CIA5 remains unknown, and one plausible possibility is that sensing − sensing can be is mediated by a multi-component signaling module rather than by a single receptor. As a conceptual analogy, Arabidopsis guard cells show that CO2/HCO3 distributed across interacting proteins. The HT1–MPK4/12 module functions as a − sensor, and CA4 can regulate the SLAC1 anion channel through a primary CO2/HCO3 binding function that is separable from CA catalytic activity (Takahashi et al., 2022; Xia et al., 2026). These findings raise the possibility that Chlamydomonas CO2 sensing may also involve modular interactions among CAs, kinases, and membrane transport proteins, although no equivalent upstream sensor has yet been identified in Chlamydomonas. KEY1 now provides a mechanistic entry point into condensate-level CCM regulation. Because KEY1 is induced by CO2-limiting stress in a CCM1/CIA5- dependent manner (Shimamura et al., 2026), transcriptional induction provides a route into pyrenoid phase control. Mechanistically, KEY1 phosphorylates EPYC1 at Rubisco- binding sites, weakens Rubisco–EPYC1 interactions, and regulates pyrenoid size, number, and dissolution (He et al., 2026). This raises the reciprocal question of whether 11 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 CO2-limiting acclimation also induces phosphatase activities that reset EPYC1 phosphorylation and restore pyrenoid condensability. No phosphatase has yet been shown to dephosphorylate EPYC1 or to promote pyrenoid condensation. Nevertheless, identifying phosphatase activities induced under CO2-limiting conditions is now a testable way to examine whether pyrenoid assembly is regulated by reversible phosphorylation. Time-resolved phosphoproteomics, acute kinase and phosphatase perturbations, and in vitro reconstitution of Rubisco–EPYC1–KEY1 reactions with candidate phosphatases could reveal whether pyrenoid assembly is actively tuned by reversible phosphorylation cycles. The distinction between transferring CCM components and recreating their regulatory logic is important for engineering. Current efforts to build pyrenoid-based CCMs in plants have focused mainly on transferring or reconstituting structural and catalytic components, such as Rubisco condensation, pyrenoid matrix formation, CO2- retention structures, transport steps, and CAs (Atkinson et al., 2020; Fei et al., 2022; Catherall et al., 2025). These approaches establish the feasibility of component transfer, but they do not yet recreate the regulatory logic by which the Chlamydomonas CCM is switched on, restrained, spatially reorganized, and energetically coordinated according to CO2 availability. Thus, a “switchable CCM” should be viewed at present as a design principle emerging from Chlamydomonas regulation rather than as an already demonstrated crop-engineering module. Future designs may need to combine pyrenoid components with plant-compatible regulatory systems, such as inducible promoters, carbon- or energy-responsive sensors, and reversible phosphorylation switches, so that CCM activity can track carbon status, light-dependent energy supply, and developmental context. For heterologous photosynthetic systems, the ability to switch CCM activity in response to carbon and energy status may be as critical as the choice of individual transporters, CAs, or pyrenoid structural components.

    Regulatory Logic of the Chlamydomonas CO2-Concentrating Mechanism: Coupling Carbon Flux, Energy Supply, and Pyrenoid Architecture · 2026 · DOI

  • Protein expression was optimized for E. coli at 16 °C for 16 h and for insect cells (Sf9) at 72 h post-infection, but temporal kinetics of KEY1 and EPYC1 expression during these induction periods and the relationship between expression timing and phosphorylation patterns have not been characterized.

    Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions · 2026 · DOI

  • The KEY1∆RBM deletion mutant was expressed and purified but functional comparisons between full-length KEY1 and KEY1∆RBM regarding their capacity to disrupt EPYC1-mediated phase separation and regulate pyrenoid condensate size across different cell cycle phases are not detailed in the methods or results.

    Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions · 2026 · DOI

  • The Phos-tag gel electrophoresis method was applied to detect EPYC1 phosphorylation states, but the paper does not specify which phosphorylation sites on EPYC1 are directly targeted by KEY1 or whether multiple phosphorylation events at different residues contribute differentially to phase separation disruption throughout the cell cycle.

    Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions · 2026 · DOI

  • Cell fractionation and immunoblotting experiments (Fig. 4g) were performed using standard lysis buffers (50 mM HEPES, pH 7.0) at a single pH condition; the pH-dependent effects on KEY1 kinase activity and pyrenoid condensate disruption across the physiological pH range of chloroplast stroma (pH 7.2–7.8) remain unexplored.

    Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions · 2026 · DOI

  • The KEY1 kinase purification protocol utilized two distinct expression systems (E. coli and baculovirus/insect cells) that yielded different final protein preparations; the comparative biochemical activity and phosphorylation efficiency of 6His–KEY1-EC versus 6His–KEY1-IC on EPYC1 phase separation interactions has not been systematically evaluated.

    Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions · 2026 · DOI

  • SHMT1 capacity may become limiting in genetic backgrounds with strongly enhanced photorespiratory flux, such as lines with elevated GDC activity, but this remains to be experimentally tested.

    Arabidopsis photorespiration is not limited by mitochondrial serine hydroxymethyltransferase 1 · 2026 · DOI

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