Physiological Functions of Cyclic Electron Transport Around Photosystem I in Sustaining Photosynthesis and Plant Growth

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

Introduction

Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera.

Methods

Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.

Results and discussion

The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

STN7 is not essential for developmental acclimation of Arabidopsis to light intensity

Plants respond to changing light intensity in the short term through regulation of light harvesting, electron transfer, and metabolism to mitigate redox stress. A sustained shift in light intensity leads to a long-term acclimation response (LTR). This involves adjustment in the stoichiometry of photosynthetic complexes through de novo synthesis and degradation of specific proteins associated with the thylakoid membrane. The light-harvesting complex II (LHCII) serine/threonine kinase STN7 plays a key role in short-term light harvesting regulation and was also suggested to be crucial to the LTR. Arabidopsis plants lacking STN7 (stn7) shifted to low light experience higher photosystem II (PSII) redox pressure than the wild type or those lacking the cognate phosphatase TAP38 (tap38), while the reverse is true at high light, where tap38 suffers more. In principle, the LTR should allow optimisation of the stoichiometry of photosynthetic complexes to mitigate these effects. We used quantitative label-free proteomics to assess how the relative abundance of photosynthetic proteins varied with growth light intensity in wild-type, stn7, and tap38 plants. All plants were able to adjust photosystem I, LHCII, cytochrome b6 f, and ATP synthase abundance with changing white light intensity, demonstrating neither STN7 nor TAP38 is crucial to the LTR per se. However, stn7 plants grown for several weeks at low light (LL) or moderate light (ML) still showed high PSII redox pressure and correspondingly lower PSII efficiency, CO2 assimilation, and leaf area compared to wild-type and tap38 plants, hence the LTR is unable to fully ameliorate these symptoms. In contrast, under high light growth conditions the mutants and wild type behaved similarly. These data are consistent with the paramount role of STN7-dependent LHCII phosphorylation in tuning PSII redox state for optimal growth in LL and ML conditions.

Impact of engineering the ATP synthase rotor ring on photosynthesis in tobacco chloroplasts

The chloroplast ATP synthase produces the ATP needed for photosynthesis and plant growth. The trans-membrane flow of protons through the ATP synthase rotates an oligomeric assembly of c subunits, the c-ring. The ion-to-ATP ratio in rotary F1F0-ATP synthases is defined by the number of c-subunits in the rotor c-ring. Engineering the c-ring stoichiometry is, therefore, a possible route to manipulate ATP synthesis by the ATP synthase and hence photosynthetic efficiency in plants. Here, we describe the construction of a tobacco (Nicotiana tabacum) chloroplast atpH (chloroplastic ATP synthase subunit c gene) mutant in which the c-ring stoichiometry was increased from 14 to 15 c-subunits. Although the abundance of the ATP synthase was decreased to 25% of wild-type (WT) levels, the mutant lines grew as well as WT plants and photosynthetic electron transport remained unaffected. To synthesize the necessary ATP for growth, we found that the contribution of the membrane potential to the proton motive force was enhanced to ensure a higher proton flux via the c15-ring without unwanted low pH-induced feedback inhibition of electron transport. Our work opens avenues to manipulate plant ion-to-ATP ratios with potentially beneficial consequences for photosynthesis.

Research Progress in Improving Photosynthetic Efficiency

Photosynthesis is the largest mass- and energy-conversion process on Earth, and it is the material basis for almost all biological activities. The efficiency of converting absorbed light energy into energy substances during photosynthesis is very low compared to theoretical values. Based on the importance of photosynthesis, this article summarizes the latest progress in improving photosynthesis efficiency from various perspectives. The main way to improve photosynthetic efficiency is to optimize the light reactions, including increasing light absorption and conversion, accelerating the recovery of non-photochemical quenching, modifying enzymes in the Calvin cycle, introducing carbon concentration mechanisms into C₃ plants, rebuilding the photorespiration pathway, de novo synthesis, and changing stomatal conductance. These developments indicate that there is significant room for improvement in photosynthesis, providing support for improving crop yields and mitigating changes in climate conditions.

Rubisco deactivation and chloroplast electron transport rates co-limit photosynthesis above optimal leaf temperature in terrestrial plants

Net photosynthetic CO₂ assimilation rate (A_n) decreases at leaf temperatures above a relatively mild optimum (T_opt) in most higher plants. This decline is often attributed to reduced CO₂ conductance, increased CO₂ loss from photorespiration and respiration, reduced chloroplast electron transport rate (J), or deactivation of Ribulose-1,5-bisphosphate Carboxylase Oxygenase (Rubisco). However, it is unclear which of these factors can best predict species independent declines in A_n at high temperature. We show that independent of species, and on a global scale, the observed decline in A_n with rising temperatures can be effectively accounted for by Rubisco deactivation and declines in J. Our finding that A_n declines with Rubisco deactivation and J supports a coordinated down-regulation of Rubisco and chloroplast electron transport rates to heat stress. We provide a model that, in the absence of CO₂ supply limitations, can predict the response of photosynthesis to short-term increases in leaf temperature.

Seed priming with NaCl helps to improve tissue tolerance, potassium retention ability of plants, and protects the photosynthetic ability in two different legumes, chickpea and lentil, under salt stress

MAIN CONCLUSION

Seed priming with NaCl mimicked the conditions of natural priming to improve the tissue tolerance nature of sensitive legumes, which helps to maintain survivability and yield in mildly saline areas. Seed priming with NaCl is a seed invigoration technique that helps to improve plant growth by altering Na⁺ and K⁺ content under salt stress. Legumes are overall sensitive to salt and salinity hampers their growth and yield. Therefore, a priming (50 mM NaCl) experiment was performed with two different legume members [Cicer arietinum cv. Anuradha and Lens culinaris cv. Ranjan] and different morpho-physiological, biochemical responses at 50 mM, 100 mM, and 150 mM NaCl and molecular responses at 150 mM NaCl were studied in hydroponically grown nonprimed and primed members. Similarly, a pot experiment was performed at 80 mM Na⁺, to check the yield. Tissue Na⁺ and K⁺ content suggested NaCl-priming did not significantly alter the accumulation of Na⁺ among nonprimed and primed members but retained more K⁺ in cells, thus maintaining a lower cellular Na⁺/K⁺ ratio. Low osmolyte content (e.g., proline) in primed members suggested priming could minimize their overall osmolytic requirement. Altogether, these implied tissue tolerance (TT) nature might have improved in case of NaCl-priming as was also reflected by a better TT score (LC₅₀ value). An improved TT nature enabled the primed plants to maintain a significantly higher photosynthetic rate through better stomatal conductance. Along with this, a higher level of chlorophyll content and competent functioning of the photosynthetic subunits improved photosynthetic performance that ensured yield under stress. Overall, this study explores the potential of NaCl-priming and creates possibilities for considerably sensitive members; those in their nonprimed forms have no prospect in mildly saline agriculture.

Distinct contribution of two cyclic electron transport pathways to P700 oxidation

Cyclic electron transport (CET) around Photosystem I (PSI) acidifies the thylakoid lumen and downregulates electron transport at the cytochrome b6f complex. This photosynthetic control is essential for oxidizing special pair chlorophylls (P700) of PSI for PSI photoprotection. In addition, CET depending on the PROTON GRADIENT REGULATION 5 (PGR5) protein oxidizes P700 by moving a pool of electrons from the acceptor side of PSI to the plastoquinone pool. This model of the acceptor-side regulation was proposed on the basis of the phenotype of the Arabidopsis (Arabidopsis thaliana) pgr5-1 mutant expressing Chlamydomonas (Chlamydomonas reinhardtii) plastid terminal oxidase (CrPTOX2). In this study, we extended the research including the Arabidopsis chlororespiratory reduction 2-2 (crr2-2) mutant defective in another CET pathway depending on the chloroplast NADH dehydrogenase-like (NDH) complex. Although the introduction of CrPTOX2 did not complement the defect in the acceptor-side regulation by PGR5, the function of the NDH complex was complemented except for its reverse reaction during the induction of photosynthesis. We evaluated the impact of CrPTOX2 under fluctuating light intensity in the wild-type, pgr5-1 and crr2-2 backgrounds. In the high-light period, both PGR5- and NDH-dependent CET were involved in the induction of photosynthetic control, whereas PGR5-dependent CET preferentially contributed to the acceptor-side regulation. On the contrary, the NDH complex probably contributed to the acceptor-side regulation in the low-light period but not in the high-light period. We evaluated the sensitivity of PSI to fluctuating light and clarified that acceptor-side regulation was necessary for PSI photoprotection by oxidizing P700 under high light.

Cyclic electron flow around photosystem II in silico: How it works and functions in vivo

To date, cyclic electron flow around PSI (PSI-CEF) has been considered the primary (if not the only) mechanism accepted to adjust the ratio of linear vs cyclic electron flow that is essential to adjust the ratio of ATP/NADPH production needed for CO₂ carboxylation. Here we provide a kinetic model showing that cyclic electron flow within PSII (PSII-CEF) is essential to account for the accelerating rate of decay in flash-induced oscillations of O₂ yield as the PQ pool progressively reduces to PQH₂. Previously, PSII-CEF was modeled by backward transitions using empirical Markov models like Joliot-Kok (J-K) type. Here, we adapted an ordinary differential equation methodology denoted RODE1 to identify which microstates within PSII are responsible for branching between PSII-CEF and Linear Electron Flow (LEF). We applied it to simulate the oscillations of O₂ yield from both Chlorella ohadii, an alga that shows strong PSII-CEF attributed to high backward transitions, and Synechococcus elongatus sp. 7002, a widely studied model cyanobacterium. RODE2 simulations reveal that backward transitions occur in microstates that possess a Q_B^- semiquinone prior to the flash. Following a flash that forms microstates populating (Q_AQ_B)^2-, PSII-CEF redirects these two electrons to the donor side of PSII only when in the oxidized S₂ and S₃ states. We show that this backward transition pathway is the origin of the observed period-2 oscillations of flash O₂ yield and contributes to the accelerated decay of period-4 oscillations. This newly added pathway improved RODE1 fits for cells of both S. elongatus and C. ohadii. RODE2 simulations show that cellular adaptation to high light intensity growth is due to a decrease in Q_B availability (empty or blocked by Q^2-_B), or equivalently due to a decrease in the difference in reduction potential relative to Q_A/Q_A^-. PSII-CEF provides an alternative mechanism for rebalancing the NADPH:ATP ratio that occurs rapidly by adjusting the redox level of the PQ:PQH₂ pool and is a necessary process for energy metabolism in aquatic phototrophs.

Translational activation of ribosome-related genes at initial photoreception is dependent on signals derived from both the nucleus and the chloroplasts in Arabidopsis thaliana

Light is one of the indispensable elements that plants need in order to grow and develop. In particular, it is essential for inducing morphogenesis, such as suppression of hypocotyl elongation and cotyledon expansion, that plants undergo when they first emerge after germination. However, there is a lack of knowledge about the gene expression and, in particular, the translational levels that induce a response upon light exposure. We have investigated the translational expression of nuclear genes in Arabidopsis thaliana seedlings germinated in the dark and then exposed to blue monochromatic light. In this study, ribosome profiling analysis was performed in the blue-light-receptor mutant cry1cry2 and the light-signaling mutant hy5 to understand which signaling pathways are responsible for the changes in gene expression at the translational level after blue-light exposure. The analysis showed that the expression of certain chloroplast- and ribosome-related genes was up-regulated at the translational level in the wild type. However, in both mutants the translational up-regulation of ribosome-related genes was apparently compromised. This suggests that light signaling through photoreceptors and the HY5 transcription factor are responsible for translation of ribosome-related genes. To further understand the effect of photoreception by chloroplasts on nuclear gene expression, chloroplast function was inhibited by adding a photosynthesis inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), and a carotenoid synthesis inhibitor, norflurazon. The results show that inhibition of chloroplast function did not lead to an increase in the expression of ribosome-related genes at the translational level. These results suggest that signals from both the nucleus and chloroplasts are required to activate translation of ribosome-related genes during blue-light reception.

Improving plant heat tolerance through modification of Rubisco activase in C3 plants to secure crop yield and food security in a future warming world

The world's population may reach 10 billion by 2050, but 10% still suffer from food shortages. At the same time, global warming threatens food security by decreasing crop yields, so it is necessary to develop crops with enhanced resistance to high temperatures in order to secure the food supply. In this review, the role of Rubisco activase as an important factor in plant heat tolerance is summarized, based on the conclusions of recent findings. Rubisco activase is a molecular chaperone determining the activation of Rubisco, whose heat sensitivity causes reductions of photosynthesis at high temperatures. Thus, the thermostability of Rubisco activase is considered to be critical for improving plant heat tolerance. It has been shown that the introduction of thermostable Rubisco activase through gene editing into Arabidopsis thaliana and from heat-adapted wild Oryza species or C4Zea mays into Oryza sativa improves Rubisco activation, photosynthesis, and plant growth at high temperatures. We propose that developing a universal thermostable Rubisco activase could be a promising direction for further studies.

Structural insights into photosynthetic cyclic electron transport

During photosynthesis, light energy is utilized to drive sophisticated biochemical chains of electron transfers, converting solar energy into chemical energy that feeds most life on earth. Cyclic electron transfer/flow (CET/CEF) plays an essential role in efficient photosynthesis, as it balances the ATP/NADPH ratio required in various regulatory and metabolic pathways. Photosystem I, cytochrome b₆f, and NADH dehydrogenase (NDH) are large multisubunit protein complexes embedded in the thylakoid membrane of the chloroplast and key players in NDH-dependent CEF pathway. Furthermore, small mobile electron carriers serve as shuttles for electrons between these membrane protein complexes. Efficient electron transfer requires transient interactions between these electron donors and acceptors. Structural biology has been a powerful tool to advance our knowledge of this important biological process. A number of structures of the membrane-embedded complexes, soluble electron carrier proteins, and transient complexes composed of both have now been determined. These structural data reveal detailed interacting patterns of these electron donor-acceptor pairs, thus allowing us to visualize the different parts of the electron transfer process. This review summarizes the current state of structural knowledge of three membrane complexes and their interaction patterns with mobile electron carrier proteins.

Understanding source-sink interactions: Progress in model plants and translational research to crops

Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration. While we have learned much about how environmental conditions and diseases impact crop yield, until recently considerably less was known concerning endogenous factors, including within-plant nutrient allocation. In this review, we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field. In this respect we detail efforts aimed at improving and/or combining C₃, C₄, and CAM modes of photosynthesis, altering the chloroplastic electron transport chain, modulating photorespiration, adopting bacterial/algal carbon-concentrating mechanisms, and enhancing nitrogen- and water-use efficiencies. Moreover, we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford. Although source, transport, and sink functions are all covered in this review, we focus on discussing source functions because the majority of research has been conducted in this field. Nevertheless, considerable recent evidence, alongside the evidence from classical studies, demonstrates that both transport and sink functions are also incredibly important determinants of yield. We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.

Genetic manipulation of photosynthesis to enhance crop productivity under changing environmental conditions

Current global agricultural production needs to be increased to feed the unconstrained growing population. The changing climatic condition due to anthropogenic activities also makes the conditions more challenging to meet the required crop productivity in the future. The increase in crop productivity in the post green revolution era most likely became stagnant, or no major enhancement in crop productivity observed. In this review article, we discuss the emerging approaches for the enhancement of crop production along with dealing to the future climate changes like rise in temperature, increase in precipitation and decrease in snow and ice level, etc. At first, we discuss the efforts made for the genetic manipulation of chlorophyll metabolism, antenna engineering, electron transport chain, carbon fixation, and photorespiratory processes to enhance the photosynthesis of plants and to develop tolerance in plants to cope with changing environmental conditions. The application of CRISPR to enhance the crop productivity and develop abiotic stress-tolerant plants to face the current changing climatic conditions is also discussed.

The chloroplast GATA-motif of Mahonia bealei participates in alkaloid-mediated photosystem inhibition during dark to light transition

Mahonia bealei and Mahonia fortunei are important plant resources in Traditional Chinese Medicine that are valued for their high levels of benzylisoquinoline alkaloids (BIAs). Although the phytotoxic activity of BIAs has been recognized, information is limited on the mechanism of action by which these compounds regulate photosynthetic activity. Here, we performed comparative chloroplast genome analysis to examine insertions and deletions in the two species. We found a GATA-motif located in the promoter region of the ndhF gene of only M. bealei. K-mer frequency-based diversity analysis illustrated the close correlation between the GATA-motif and leaf phenotype. We found that the GATA-motif significantly inhibits GUS gene expression in tobacco during the dark-light transition (DLT). The expression of ndhF was downregulated in M. bealei and upregulated in M. fortunei during the DLT. NDH-F activity was remarkably decreased and exhibited a significant negative correlation with BIA levels in M. bealei during the DLT. Furthermore, the NADPH produced through photosynthetic metabolism was found to decrease in M. bealei during the DLT. Taken together, our results indicate that this GATA-motif might act as the functional site by which BIAs inhibit photosynthetic metabolism through downregulating ndhF expression during the DLT.

Plasticity of Arabidopsis rosette transcriptomes and photosynthetic responses in dynamic light conditions

With the high variability of natural growth environments, plants exhibit flexibility and resilience in regard to the strategies they employ to maintain overall fitness, including maximizing light use for photosynthesis, while simultaneously limiting light-associated damage. We measured distinct parameters of photosynthetic performance of Arabidopsis thaliana plants under dynamic light regimes. Plants were grown to maturity then subjected to the following 5-day (16 h light, 8 h dark) regime: Day 1 at constant light (CL) intensity during light period, representative of a common lab growth condition; Day 2 under sinusoidal variation in light intensity (SL) during the light period that is representative of changes occurring during a clear sunny day; Day 3 under fluctuating light (FL) intensity during the light period that simulates sudden changes that might occur with the movements of clouds in and out of the view of the sun; Day 4, repeat of CL; and Day 5, repeat of FL. We also examined the global transcriptome profile in these growth conditions based on obtaining RNA-sequencing (RNA-seq) data for whole plant rosettes. Our transcriptomic analyses indicated downregulation of photosystem I (PSI) and II (PSII) associated genes, which were correlated with elevated levels of photoinhibition as indicated by measurements of nonphotochemical quenching (NPQ), energy-dependent quenching (qE), and inhibitory quenching (qI) under both SL and FL conditions. Furthermore, our transcriptomic results indicated downregulation of tetrapyrrole biosynthesis associated genes, coupled with reduced levels of chlorophyll under both SL and FL compared with CL, as well as downregulation of photorespiration-associated genes under SL. We also noticed an enrichment of the stress response gene ontology (GO) terms for genes differentially regulated under FL when compared with SL. Collectively, our phenotypic and transcriptome analyses serve as useful resources for probing the underlying molecular mechanisms associated with plant acclimation to rapid light intensity changes in the natural environment.

Sufficient potassium improves inorganic phosphate-limited photosynthesis in Brassica napus by enhancing metabolic phosphorus fractions and Rubisco activity

Crop photosynthesis (A) and productivity are often limited by a combination of nutrient stresses, such that changes in the availability of one nutrient may affect the availability of another nutrient, in turn influencing A. In this study, we examined the synergistic effects of phosphorus (P) and potassium (K) on leaf A in a nutrient amendment experiment, in which P and K were added individually or in combination to Brassica napus grown under P and K co-limitation. The data revealed that the addition of P gradually removed the dominant limiting factor (i.e. the limited availability of P) and improved leaf A. Strikingly, the addition of K synergistically improved the overall uptake of P, mainly by boosting plant growth, and compensated for the physiological demand for P by prioritizing investment in metabolic pools of P (P-containing metabolites and inorganic phosphate, Pi). The enlarged pool of metabolically active P was partially associated with the upregulation of Pi regeneration through release from triose phosphates rather than replacement of P-containing lipids. This process mitigated P restrictions on A by maintaining the ATP/NADPH and NADPH/NADP⁺ ratios and increasing the content and activity of Rubisco. Our findings demonstrate that sufficient K increased Pi-limited A by enhancing metabolic P fractions and Rubisco activity. Thus, ionic synergism may be exploited to mitigate nutrient-limiting factors to improve crop productivity.

Effects of High Irradiance and Low Water Temperature on Photoinhibition and Repair of Photosystems in Marimo (Aegagropila linnaei) in Lake Akan, Japan

The green alga Aegagropila linnaei often forms spherical aggregates called "marimo" in Lake Akan in Japan. In winter, marimo are exposed to low water temperatures at 1-4 °C but protected from strong sunlight by ice coverage, which may disappear due to global warming. In this study, photoinhibition in marimo was examined at 2 °C using chlorophyll fluorescence and 830 nm absorption. Filamentous cells of A. linnaei dissected from marimo were exposed to strong light at 2 °C. Photosystem II (PSII) was markedly photoinhibited, while photosystem I was unaffected. When the cells with PSII damaged by the 4 h treatment were subsequently illuminated with moderate repair light at 2 °C, the maximal efficiency of PSII was recovered to the level before photoinhibition. However, after the longer photoinhibitory treatments, PSII efficiency did not recover by the repair light. When the cells were exposed to simulated diurnal light for 12 h per day, which was more ecological, the cells died within a few days. Our results showed new findings of the PSII repair at 2 °C and serious damage at the cellular level from prolonged high-light treatments. Further, we provided a clue to what may happen to marimo in Lake Akan in the near future.

Low Light Facilitates Cyclic Electron Flows around PSI to Assist PSII against High Temperature Stress

Photosystem II (PSII) of grapevine leaves is easily damaged under heat stress, but no such injury is observed when the leaves are heated in low light. To elucidate the mechanisms, we compared the photosynthetic characteristics of grapevine seedlings under heat treatments (42 °C) for 4 h in the dark or low light (200 μmol m^-2 s^-1). At 42 °C in the dark, the PSII maximum quantum yield (Fv/Fm) decreased significantly with the increase in time but did not change much in low light. The JIP (chlorophyll a fluorescence rise kinetics) test results showed that low light significantly alleviated the damage to the oxygen evolving complexes (OECs; the K-step was less visible) by heat stress. Further, in the presence of de novo D1 protein synthesis inhibitor chloramphenicol, Fv/Fm did not differ significantly between dark and light treatments under heat stress. The 50% re-reduction (RR50) of P700⁺ on cessation of far-red illumination was faster after light treatment than that in the dark. After exposure to 25 °C in a low light for 15 min, Y(NO) (the constitutive non-regulatory non-photochemical quenching) treated by heat stress and darkness was higher than that by heat stress and light. Overall, our results suggested that enhanced CEFs around PSI in low light could assist PSII against heat damage by maintaining the rate of PSII repair and inhibiting the non-radiative charge recombination in PSII reaction centers.

Enhanced abundance and activity of the chloroplast ATP synthase in rice through the overexpression of the AtpD subunit

ATP, produced by the light reactions of photosynthesis, acts as the universal cellular energy cofactor fuelling all life processes. Chloroplast ATP synthase produces ATP using the proton motive force created by solar energy-driven thylakoid electron transport reactions. Here we investigate how increasing abundance of ATP synthase affects leaf photosynthesis and growth of rice, Oryza sativa variety Kitaake. We show that overexpression of AtpD, the nuclear-encoded subunit of the chloroplast ATP synthase, stimulates both abundance of the complex, confirmed by immunodetection of thylakoid complexes separated by Blue Native-PAGE, and ATP synthase activity, detected as higher proton conductivity of the thylakoid membrane. Plants with increased AtpD content had higher CO2 assimilation rates when a stepwise increase in CO2 partial pressure was imposed on leaves at high irradiance. Fitting of the CO2 response curves of assimilation revealed that plants overexpressing AtpD had a higher electron transport rate (J) at high CO2, despite having wild-type-like abundance of the cytochrome b6f complex. A higher maximum carboxylation rate (Vcmax) and lower cyclic electron flow detected in transgenic plants both pointed to an increased ATP production compared with wild-type plants. Our results present evidence that the activity of ATP synthase modulates the rate of electron transport at high CO2 and high irradiance.

Phylogenomics, plastome degradation and mycoheterotrophy evolution of Neottieae (Orchidaceae), with emphasis on the systematic position and Loess Plateau-Changbai Mountains disjunction of Diplandrorchis

BACKGROUND

Mycoheterotrophy is a unique survival strategy adapted to dense forests and has attracted biologists' attention for centuries. However, its evolutionary origin and related plastome degradation are poorly understood. The tribe Neottieae contains various nutrition types, i.e., autotrophy, mixotrophy, and mycoheterotrophy. Here, we present a comprehensive phylogenetic analysis of the tribe based on plastome and nuclear ITS data. We inferred the evolutionary shift of nutrition types, constructed the patterns of plastome degradation, and estimated divergence times and ancestral ranges. We also used an integration of molecular dating and ecological niche modeling methods to investigate the disjunction between the Loess Plateau and Changbai Mountains in Diplandrorchis, a mycoheterotrophic genus endemic to China that was included in a molecular phylogenetic study for the first time.

RESULTS

Diplandrorchis was imbedded within Neottia and formed a clade with four mycoheterotrophic species. Autotrophy is the ancestral state in Neottieae, mixotrophy independently originated at least five times, and three shifts from mixotrophy to mycoheterotrophy independently occurred. The five mixotrophic lineages possess all plastid genes or lost partial/all ndh genes, whereas each of the three mycoheterotroph lineages has a highly reduced plastome: one lost part of its ndh genes and a few photosynthesis-related genes, and the other two lost almost all ndh, photosynthesis-related, rpo, and atp genes. These three mycoheterotrophic lineages originated at about 26.40 Ma, 25.84 Ma, and 9.22 Ma, respectively. Diplandrorchis had presumably a wide range in the Pliocene and migrated southward in the Pleistocene.

CONCLUSIONS

The Pleistocene climatic fluctuations and the resultant migration resulted in the Loess Plateau-Changbai Mountains disjunction of Diplandrorchis. In the evolution of mycoheterotrophic lineages, the loss of plastid-encoded genes and plastome degradation are staged and irreversible, constraining mycoheterotrophs to inhabit understories with low light levels. Accordingly, the rise of local forests might have promoted the origin of conditions in which mycoheterotrophy is advantageous.

A scheme for C4 evolution derived from a comparative analysis of the closely related C3, C3-C4 intermediate, C4-like, and C4 species in the genus Flaveria

A comparative analysis of the genus Flaveria showed a C₄ evolutionary process in which the anatomical and metabolic features of C₄ photosynthesis were gradually acquired through C₃-C₄ intermediate stages. C₄ photosynthesis has been acquired in multiple lineages of angiosperms during evolution to suppress photorespiration. Crops that perform C₄ photosynthesis exhibit high rates of CO₂ assimilation and high grain production even under high-temperature in semiarid environments; therefore, engineering C₄ photosynthesis in C₃ plants is of great importance in the application field. The genus Flaveria contains a large number of C₃, C₃-C₄ intermediate, C₄-like, and C₄ species, making it a good model genus to study the evolution of C₄ photosynthesis, and these studies indicate the direction for C₄ engineering. C₄ photosynthesis was acquired gradually through the C₃-C₄ intermediate stage. First, a two-celled C₂ cycle called C₂ photosynthesis was acquired by localizing glycine decarboxylase activity in the mitochondria of bundle sheath cells. With the development of two-cell metabolism, anatomical features also changed. Next, the replacement of the two-celled C₂ cycle by the two-celled C₄ cycle was induced by the acquisition of cell-selective expression in addition to the upregulation of enzymes in the C₄ cycle during the C₃-C₄ intermediate stage. This was supported by an increase in cyclic electron transport activity in response to an increase in the ATP/NADPH demand for metabolism. Suppression of the C₃ cycle in mesophyll cells was induced after the functional establishment of the C₄ cycle, and optimization of electron transport by suppressing the activity of photosystem II also occurred during the final phase of C₄ evolution.

Quantitative proteomics reveals redox-based functional regulation of photosynthesis under fluctuating light in plants

Photosynthesis involves a series of redox reactions and is the major source of reactive oxygen species in plant cells. Fluctuating light (FL) levels, which occur commonly in natural environments, affect photosynthesis; however, little is known about the specific effects of FL on the redox regulation of photosynthesis. Here, we performed global quantitative mapping of the Arabidopsis thaliana cysteine thiol redox proteome under constant light and FL conditions. We identified 8857 redox-switched thiols in 4350 proteins, and 1501 proteins that are differentially modified depending on light conditions. Notably, proteins related to photosynthesis, especially photosystem I (PSI), are operational thiol-switching hotspots. Exposure of wild-type A. thaliana to FL resulted in decreased PSI abundance, stability, and activity. Interestingly, in response to PSI photodamage, more of the PSI assembly factor PSA3 dynamically switches to the reduced state. Furthermore, the Cys199 and Cys200 sites in PSA3 are necessary for its full function. Moreover, thioredoxin m (Trx m) proteins play roles in redox switching of PSA3, and are required for PSI activity and photosynthesis. This study thus reveals a mechanism for redox-based regulation of PSI under FL, and provides insight into the dynamic acclimation of photosynthesis in a changing environment.

Commonalities and specialties in photosynthetic functions of PROTON GRADIENT REGULATION5 variants in Arabidopsis

The PROTON GRADIENT REGULATION5 (PGR5) protein is required for trans-thylakoid proton gradient formation and acclimation to fluctuating light (FL). PGR5 functionally interacts with two other thylakoid proteins, PGR5-like 1 (PGRL1) and 2 (PGRL2); however, the molecular details of these interactions are largely unknown. In the Arabidopsis (Arabidopsis thaliana) pgr5-1 mutant, the PGR5G130S protein accumulates in only small amounts. In this work, we generated a knockout allele of PGR5 (pgr5-Cas) using CRISPR-Cas9 technology. Like pgr5-1, pgr5-Cas is seedling-lethal under FL, but photosynthesis and particularly cyclic electron flow, as well as chlorophyll content, are less severely affected in both pgr5-Cas and pgrl1ab (which lacks PGRL1 and PGR5) than in pgr5-1. These differences are associated with changes in the levels of 260 proteins, including components of the Calvin-Benson cycle, photosystems II and I, and the NDH complex, in pgr5-1 relative to the wild type (WT), pgr5-Cas, and pgrl1ab. Some of the differences between pgr5-1 and the other mutant lines could be tentatively assigned to second-site mutations in the pgr5-1 line, identified by whole-genome sequencing. However, others, particularly the more pronounced photosynthetic defects and PGRL1 depletion (compared to pgr5-Cas), are clearly due to specific negative effects of the amino-acid substitution in PGR5G130S, as demonstrated by complementation analysis. Moreover, pgr5-1 and pgr5-Cas plants are less tolerant to long-term exposure to high light than pgrl1ab plants. These results imply that, in addition to the previously reported necessity of PGRL1 for optimal PGR5 function, PGR5 is required alongside PGRL1 to avoid harmful effects on plant performance.

Ascorbate peroxidase postcold regulation of chloroplast NADPH dehydrogenase activity controls cold memory

Exposure of Arabidopsis (Arabidopsis thaliana) to 4°C imprints a cold memory that modulates gene expression in response to a second (triggering) stress stimulus applied several days later. Comparison of plastid transcriptomes of cold-primed and control plants directly before they were exposed to the triggering stimulus showed downregulation of several subunits of chloroplast NADPH dehydrogenase (NDH) and regulatory subunits of ATP synthase. NDH is, like proton gradient 5 (PGR5)-PGR5-like1 (PGRL1), a thylakoid-embedded, ferredoxin-dependent plastoquinone reductase that protects photosystem I and stabilizes ATP synthesis by cyclic electron transport (CET). Like PGRL1A and PGRL1B transcript levels, ndhA and ndhD transcript levels decreased during the 24-h long priming cold treatment. PGRL1 transcript levels were quickly reset in the postcold phase, but expression of ndhA remained low. The transcript abundances of other ndh genes decreased within the next days. Comparison of thylakoid-bound ascorbate peroxidase (tAPX)-free and transiently tAPX-overexpressing or tAPX-downregulating Arabidopsis lines demonstrated that ndh expression is suppressed by postcold induction of tAPX. Four days after cold priming, when tAPX protein accumulation was maximal, NDH activity was almost fully lost. Lack of the NdhH-folding chaperonin Crr27 (Cpn60β4), but not lack of the NDH activity modulating subunits NdhM, NdhO, or photosynthetic NDH subcomplex B2 (PnsB2), strengthened priming regulation of zinc finger of A. thaliana 10, which is a nuclear-localized target gene of the tAPX-dependent cold-priming pathway. We conclude that cold-priming modifies chloroplast-to-nucleus stress signaling by tAPX-mediated suppression of NDH-dependent CET and that plastid-encoded NdhH, which controls subcomplex A assembly, is of special importance for memory stabilization.

Integrated Physiological, Transcriptomic, and Proteomic Analyses Reveal the Regulatory Role of Melatonin in Tomato Plants’ Response to Low Night Temperature

Melatonin is a direct free radical scavenger that has been demonstrated to increase plants’ resistance to a variety of stressors. Here, we sought to examine the effect of melatonin on tomato seedlings subjected to low night temperatures using an integrated physiological, transcriptomic, and proteomic approach. We found that a pretreatment with 100 μM melatonin increased photosynthetic and transpiration rates, stomatal apertures, and peroxidase activity, and reduced chloroplast damage of the tomato plant under a low night temperature. The melatonin pretreatment reduced the photoinhibition of photosystem I by regulating the balance of both donor- and acceptor-side restriction of PSI and by increasing electron transport. Furthermore, the melatonin pretreatment improved the photosynthetic performance of proton gradient regulation 5 (SlPGR5) and SlPGR5-like photosynthetic phenotype 1 (SlPGRL1)-suppressed transformants under a low night temperature stress. Transcriptomic and proteomic analyses found that the melatonin pretreatment resulted in the upregulation of genes and proteins related to transcription factors, signal transduction, environmental adaptation, and chloroplast integrity maintenance in low night temperature-stressed tomato plants. Collectively, our results suggest that melatonin can effectively improve the photosynthetic efficiency of tomato plants under a low night temperature and provide novel insights into the molecular mechanism of melatonin-mediated abiotic stress resistance.

Intensity and duration of salinity required to form adaptive response in C4 halophyte Kochia prostrata (L.) Shrad

Plant adaptation to salinity is a highly multifaceted process, harnessing various physiological mechanisms depending on the severity and duration of salt stress. This study focuses on the effects of 4- and 10-day treatments with low (100 mM NaCl) and moderate (200 mM NaCl) salinity on growth, CO₂/H₂O gas exchange, stomatal apparatus performance, the efficiency of photosystems I and II (PS I and II), content of key C₄ photosynthesis enzymes, and the accumulation of Na⁺, K⁺, and proline in shoots of the widespread forage C₄ halophyte Kochia prostrata. Our data show that 4 days of low salinity treatment resulted in a decrease in biomass, intensity of apparent photosynthesis, and cyclic electron transport around PS I. It was accompanied by an increase in transpiration and Rubisco and PEPC contents, while the Na⁺ and proline contents were low in K. prostrata shoots. By the 10th day of salinity, Na⁺ and proline have accumulated; PS I function has stabilized, while PS II efficiency has decreased due to the enhanced non-photochemical quenching of chlorophyll fluorescence (NPQ). Thus, under low salinity conditions, Na⁺ accumulated slowly and the imbalance between light and dark reactions of photosynthesis was observed. These processes might be induced by an early sodium signaling wave that affects cellular pH and ion homeostasis, ultimately disturbing photosynthetic electron transport. Another adaptive reaction more "typical" of salt-tolerant species was observed at 200 mM NaCl treatment. It proceeds in two stages. First, during the first 4 days, dry biomass and apparent photosynthesis decrease, whereas stomata sensitivity and dissipation energy during dark respiration increase. In parallel, an active Na⁺ accumulation and a decreased K⁺/Na⁺ ratio take place. Second, by the 10th day, a fully-fledged adaptive response was formed, when growth and apparent photosynthesis stabilized and stomata closed. Decreased dissipation energy, increased WUE, stabilization of Rubisco and PEPC contents, and decreased proline content testify to the completion of the adaptation and stabilization of the physiological state of plants. The obtained results allowed us to conclude that the formation of a full-fledged salt-tolerant response common for halophytes in K. prostrata occurs by the 10th day of moderate salinity.

An ancient function of PGR5 in iron delivery?

In all phototrophic organisms, the photosynthetic apparatus must be protected from light-induced damage. One important mechanism that mitigates photodamage in plants is antimycin A (AA)-sensitive cyclic electron flow (CEF), the evolution of which remains largely obscure. Here we show that proton gradient regulation 5 (PGR5), a key protein involved in AA-sensitive CEF, displays intriguing commonalities - including sequence and structural features - with a group of ferritin-like proteins. We therefore propose that PGR5 may originally have been involved in prokaryotic iron mobilization and delivery, which facilitated a primordial type of CEF as a side effect. The abandonment of the bacterioferritin system during the transformation of cyanobacterial endosymbionts into chloroplasts might have allowed PGR5 to functionally specialize in CEF.

Photosynthesis in sun and shade: the surprising importance of far-red photons

The current definition of photosynthetically active radiation includes only photons from 400 up to 700 nm, despite evidence of the synergistic interaction between far-red photons and shorter-wavelength photons. The synergy between far-red and shorter-wavelength photons has not been studied in sunlight under natural conditions. We used a filter to remove photons above 700 nm to quantify the effects on photosynthesis in diverse species under full sun, medium light intensity and vegetation shade. Far-red photons (701 to 750 nm) in sunlight are used efficiently for photosynthesis. This is especially important for leaves in vegetation shade, where far-red photons can be > 50% of the total incident photons between 400 and 750 nm. Far-red photons accounted for 24-25% of leaf gross photosynthesis (P_gross ) in a C₃ and a C₄ species when sunlight was filtered through a leaf, and 10-14% of leaf P_gross in a tree and an understory species in deep shade. Accounting for the photosynthetic activity of far-red photons is critical for accurate measurement and modeling of photosynthesis at single leaf, canopy and ecosystem scales. This, in turn, is crucial in understanding crop productivity, the global carbon cycle and climate change impacts on agriculture and ecosystems.

Granal thylakoid structure and function: explaining an enduring mystery of higher plants

In higher plants, photosystems II and I are found in grana stacks and unstacked stroma lamellae, respectively. To connect them, electron carriers negotiate tortuous multi-media paths and are subject to macromolecular blocking. Why does evolution select an apparently unnecessary, inefficient bipartition? Here we systematically explain this perplexing phenomenon. We propose that grana stacks, acting like bellows in accordions, increase the degree of ultrastructural control on photosynthesis through thylakoid swelling/shrinking induced by osmotic water fluxes. This control coordinates with variations in stomatal conductance and the turgor of guard cells, which act like an accordion's air button. Thylakoid ultrastructural dynamics regulate macromolecular blocking/collision probability, direct diffusional pathlengths, division of function of Cytochrome  b₆ f complex between linear and cyclic electron transport, luminal pH via osmotic water fluxes, and the separation of pH dynamics between granal and lamellar lumens in response to environmental variations. With the two functionally asymmetrical photosystems located distantly from each other, the ultrastructural control, nonphotochemical quenching, and carbon-reaction feedbacks maximally cooperate to balance electron transport with gas exchange, provide homeostasis in fluctuating light environments, and protect photosystems in drought. Grana stacks represent a dry/high irradiance adaptation of photosynthetic machinery to improve fitness in challenging land environments. Our theory unifies many well-known but seemingly unconnected phenomena of thylakoid structure and function in higher plants.

Exogenous Ca2+ priming can improve peanut photosynthetic carbon fixation and pod yield under early sowing scenarios in the field

Harnessing cold-resilient and calcium-enriched peanut production technology are crucial for high-yielding peanut cultivation in high-latitude areas. However, there is limited field data about how exogenous calcium (Ca²⁺) application would improve peanut growth resilience during exposure to chilling stress at early sowing (ES). To help address this problem, a two-year field study was conducted to assess the effects of exogenous foliar Ca²⁺ application on photosynthetic carbon fixation and pod yield in peanuts under different sowing scenarios. We measured plant growth indexes, leaf photosynthetic gas exchange, photosystems activities, and yield in peanuts. It was indicated that ES chilling stress at the peanut seedling stage led to the reduction of Pn, g_s, Tr, Ls, WUE, respectively, and the excessive accumulation of non-structural carbohydrates in leaves, which eventually induced a chilling-dependent feedback inhibition of photosynthesis due mainly to weaken growth/sink demand. While exogenous Ca²⁺ foliar application improved the export of nonstructural carbohydrates, and photosynthetic capacity, meanwhile activated cyclic electron flow, thereby enhancing growth and biomass accumulation in peanut seedlings undergoing ES chilling stress. Furthermore, ES combined with exogenous Ca²⁺ application can significantly enhance plant chilling resistance and peanut yield ultimately in the field. In summary, the above results demonstrated that exogenous foliar Ca²⁺ application restored the ES-linked feedback inhibition of photosynthesis, enhancing the growth/sink demand and the yield of peanuts.

Using synthetic biology to improve photosynthesis for sustainable food production

Photosynthesis is responsible for the primary productivity and maintenance of life on Earth, boosting biological activity and contributing to the maintenance of the environment. In the past, traditional crop improvement was considered sufficient to meet food demands, but the growing demand for food coupled with climate change has modified this scenario over the past decades. However, advances in this area have not focused on photosynthesis per se but rather on fixed carbon partitioning. In short, other approaches must be used to meet an increasing agricultural demand. Thus, several paths may be followed, from modifications in leaf shape and canopy architecture, improving metabolic pathways related to CO₂ fixation, the inclusion of metabolic mechanisms from other species, and improvements in energy uptake by plants. Given the recognized importance of photosynthesis, as the basis of the primary productivity on Earth, we here present an overview of the latest advances in attempts to improve plant photosynthetic performance. We focused on points considered key to the enhancement of photosynthesis, including leaf shape development, RuBisCO reengineering, Calvin-Benson cycle optimization, light use efficiency, the introduction of the C₄ cycle in C₃ plants and the inclusion of other CO₂ concentrating mechanisms (CCMs). We further provide compelling evidence that there is still room for further improvements. Finally, we conclude this review by presenting future perspectives and possible new directions on this subject.

Selenium content and nutritional quality of Brassica chinensis L enhanced by selenium engineered nanomaterials: The role of surface charge

Selenium engineered nanomaterials (Se ENMs)-enabled agriculture has developed rapidly, however, the roles of surface charge in the bioavailability and enrichment efficiency of Se ENMs are still unknown. Herein, various Se ENMs of homogenous size (40-60 nm) and different surface charges (3.2 ± 0.7, -29.0 ± 0.4, and 45.5 ± 1.3 mV) were prepared to explore the Se content and nutritional quality in Brassica chinensis L. The results demonstrated that soil application of various Se ENMs (0.05 mg kg^-1) displayed different bio-availabilities via modulating the secretion of root exudates (e.g., tartaric, malic, and citric acids), microbial community composition (e.g., Flavobacterium, Pseudomonas, Paracoccus, Bacillus and Rhizobium) and root cell wall. Negatively charged Se ENMs (Se (-)) showed the highest Se content in the shoot of B. chinensis (3.7-folds). Se (-) also significantly increased yield (156.9%) and improved nutritional quality (e.g., ascorbic acid, amino acids, flavonoids, fatty acids, and tricarboxylic acid) of B. chinensis. Moreover, after harvest, the Se (-) did not lead to significant change in Se residue in soil, but the amount of Se residue in soil was increased by 5.5% after applying the traditional Se fertilizer (selenite). Therefore, this study provides useful information for producing Se-fortified agricultural products, while minimizing environmental risk.

NADP+ supply adjusts the synthesis of photosystem I in Arabidopsis chloroplasts

In oxygenic photosynthesis, NADP+ acts as the final acceptor of the photosynthetic electron transport chain and receives electrons via the thylakoid membrane complex photosystem I (PSI) to synthesize NAPDH by the enzyme ferredoxin:NADP+ oxidoreductase. The NADP+/NADPH redox couple is essential for cellular metabolism and redox homeostasis. However, how the homeostasis of these two dinucleotides is integrated into chloroplast biogenesis remains largely unknown. Here, we demonstrate the important role of NADP+ supply for the biogenesis of PSI by examining the nad kinase 2 (nadk2) mutant in Arabidopsis (Arabidopsis thaliana), which demonstrates disrupted synthesis of NADP+ from NAD+ in chloroplasts. Although the nadk2 mutant is highly sensitive to light, the reaction center of photosystem II (PSII) is only mildly and likely only secondarily affected compared to the wild-type. Our studies revealed that the primary limitation of photosynthetic electron transport, even at low light intensities, occurs at PSI rather than at PSII in the nadk2 mutant. Remarkably, this primarily impairs the de novo synthesis of the two PSI core subunits PsaA and PsaB, leading to the deficiency of the PSI complex in the nadk2 mutant. This study reveals an unexpected molecular link between NADK activity and mRNA translation of psaA/B in chloroplasts that may mediate a feedback mechanism to adjust de novo biosynthesis of the PSI complex in response to a variable NADPH demand. This adjustment may be important to protect PSI from photoinhibition under conditions that favor acceptor side limitation.

Adenylates regulate Arabidopsis plastidial thioredoxin activities through the binding of a CBS domain protein

Cystathionine-β-synthase (CBS) domains are found in proteins of all living organisms and have been proposed to play a role as energy sensors regulating protein activities through their adenosyl ligand binding capacity. In plants, members of the CBSX protein family carry a stand-alone pair of CBS domains. In Arabidopsis (Arabidopsis thaliana), CBSX1 and CBSX2 are targeted to plastids where they have been proposed to regulate thioredoxins (TRXs). TRXs are ubiquitous cysteine thiol oxido-reductases involved in the redox-based regulation of numerous enzymatic activities as well as in the regeneration of thiol-dependent peroxidases. In Arabidopsis, 10 TRX isoforms have been identified in plastids and divided into five sub-types. Here, we show that CBSX2 specifically inhibits the activities of m-type TRXs toward two chloroplast TRX-related targets. By testing activation of NADP-malate dehydrogenase and reduction of 2-Cys peroxiredoxin, we found that TRXm1/2 inhibition by CBSX2 was alleviated in the presence of AMP or ATP. We also determined, by pull-down assays, a direct interaction of CBSX2 with reduced TRXm1 and m2 that was abolished in the presence of adenosyl ligands. In addition, we report that, compared with wild-type plants, the Arabidopsis T-DNA double mutant cbsx1 cbsx2 exhibits growth and chlorophyll accumulation defects in cold conditions, suggesting a function of plastidial CBSX proteins in plant stress adaptation. Together, our results show an energy-sensing regulation of plastid TRX m activities by CBSX, possibly allowing a feedback regulation of ATP homeostasis via activation of cyclic electron flow in the chloroplast, to maintain a high energy level for optimal growth.

Regulation of photosynthetic light reaction proteins via reversible phosphorylation

The regulation of photosynthesis occurs at different levels including the control of nuclear and plastid genes transcription, RNA processing and translation, protein translocation, assemblies and their post translational modifications. Out of all these, post translational modification enables rapid response of plants towards changing environmental conditions. Among all post-translational modifications, reversible phosphorylation is known to play a crucial role in the regulation of light reaction of photosynthesis. Although, phosphorylation of PS II subunits has been extensively studied but not much attention is given to other photosynthetic complexes such as PS I, Cytochrome b6f complex and ATP synthase. Phosphorylation reaction is known to protect photosynthetic apparatus in challenging environment conditions such as high light, elevated temperature, high salinity and drought. Recent studies have explored the role of photosynthetic protein phosphorylation in conferring plant immunity against the rice blast disease. The evolution of phosphorylation of different subunits of photosynthetic proteins occurred along with the evolution of plant lineage for their better adaptation to the changing environment conditions. In this review, we summarize the progress made in the research field of phosphorylation of photosynthetic proteins and highlights the missing links that need immediate attention.

The Central Circadian Clock Protein TaCCA1 Regulates Seedling Growth and Spike Development in Wheat (Triticum aestivum L.)

The biological functions of the circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits, are poorly understood. In this study, we characterized the core clock gene CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns, which are positively regulated by rhythmic histone modifications including histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 9 acetylation (H3K9Ac), and histone H3 lysine 36 trimethylation (H3K36me3). TaCCA1s are preferentially located in the nucleus and tend to form both homo- and heterodimers. TaCCA1 overexpression (TaCCA1-OE) transgenic wheat plants show disrupted circadian rhythmicity coupling with reduced chlorophyll and starch content, as well as biomass at seedling stage, also decreased spike length, grain number per spike, and grain size at the ripening stage. Further studies using DNA affinity purification followed by deep sequencing [DNA affinity purification and sequencing (DAP-seq)] indicated that TaCCA1 preferentially binds to sequences similarly to "evening elements" (EE) motif in the wheat genome, particularly genes associated with photosynthesis, carbon utilization, and auxin homeostasis, and decreased transcriptional levels of these target genes are observed in TaCCA1-OE transgenic wheat plants. Collectively, our study provides novel insights into a circadian-mediated mechanism of gene regulation to coordinate photosynthetic and metabolic activities in wheat, which is important for optimal plant growth and crop yield formation.

Systematics and Plastome Evolution in Schizaeaceae

While the family Schizaeaceae (Schizaeales) represents only about 0.4% of the extant fern species diversity, it differs from other ferns greatly in gross morphologies, niche preferences, and life histories. One of the most notable features in this family is its mycoheterotrophic life style in the gametophytic stage, which appears to be associated with extensive losses of plastid genes. However, the limited number of sequenced plastomes, and the lack of a well-resolved phylogenetic framework of Schizaeaceae, makes it difficult to gain any further insight. Here, with a comprehensive sampling of ~77% of the species diversity of this family, we first inferred a plastid phylogeny of Schizaeaceae using three DNA regions. To resolve the deep relationships within this family, we then reconstructed a plastome-based phylogeny focusing on a selection of representatives that covered all the major clades. From this phylogenomic backbone, we traced the evolutionary histories of plastid genes and examined whether gene losses were associated with the evolution of gametophytic mycoheterotrophy. Our results reveal that extant Schizaeaceae is comprised of four major clades-Microschizaea, Actinostachys, Schizaea, and Schizaea pusilla. The loss of all plastid NADH-like dehydrogenase (ndh) genes was confirmed to have occurred in the ancestor of extant Schizaeaceae, which coincides with the evolution of mycoheterotrophy in this family. For chlorophyll biosynthesis genes (chl), the losses were interpreted as convergent in Schizaeaceae, and found not only in Actinostachys, a clade producing achlorophyllous gametophytes, but also in S. pusilla with chlorophyllous gametophytes. In addition, we discovered a previously undescribed but phylogenetically distinct species hidden in the Schizaea dichotoma complex and provided a taxonomic treatment and morphological diagnostics for this new species-Schizaea medusa. Finally, our phylogenetic results suggest that the current PPG I circumscription of Schizaea is non-monophyletic, and we therefore proposed a three-genus classification moving a subset of Schizaea species sensu PPG I to a third genus-Microschizaea.

Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.

Role of melatonin in promoting plant growth by regulating carbon assimilation and ATP accumulation

Melatonin (MT) is a phytohormone important in mediating diverse plant growth processes. In this study, we performed transcriptomic, qRT-PCR, physiological and biochemical analyses of Brassica rapa seedlings in order to understand how MT promotes plant growth. The results showed that exogenous MT increased the rate of cyclic electron flow around photosystem (PS) I, fluorescence quantum yield, and electron transport efficiency between PSII and PSI to promote the vegetative growth of B. rapa seedlings without affecting oxidative stress level, as compared to control. However, MT treatment significantly reduced photosynthetic rate (Pn), transpiration rate (Tr), and stomatal conductance (Gs) by 2.25-, 1.23- and 3.50-fold at 0.05 level, respectively. This occurred in parallel with the down-regulation of the genes for carbon fixation in photosynthetic organisms in a KEGG pathway enrichment. More accelerated plant growth despite the reduced photosynthesis rate and the enhanced electron transport rate suggested that NADPH and adenosine triphosphate (ATP) were preferentially diverted into other anabolic reactions than the Calvin cycle upon MT application. MT treatment increased ATP level and facilitated carbon assimilation into primary metabolism that led to a significant enhancement of soluble protein, sucrose, and fructose, but a significant decrease in glucose content. MT-induced carbon assimilation into primary metabolism was driven by up-regulation of the genes for glutathione metabolism, Krebs cycle, ribosome, and DNA replication in a KEGG pathway enrichment, as well as down-regulation of the genes for secondary metabolites. Our results provide an insight into MT-mediated metabolic adjustments triggered by coordinate changes in a wide range of gene expression profiles to help improve the plant functionality.

High-throughput characterization, correlation, and mapping of leaf photosynthetic and functional traits in the soybean (Glycine max) nested association mapping population

Photosynthesis is a key target to improve crop production in many species including soybean [Glycine max (L.) Merr.]. A challenge is that phenotyping photosynthetic traits by traditional approaches is slow and destructive. There is proof-of-concept for leaf hyperspectral reflectance as a rapid method to model photosynthetic traits. However, the crucial step of demonstrating that hyperspectral approaches can be used to advance understanding of the genetic architecture of photosynthetic traits is untested. To address this challenge, we used full-range (500-2,400 nm) leaf reflectance spectroscopy to build partial least squares regression models to estimate leaf traits, including the rate-limiting processes of photosynthesis, maximum Rubisco carboxylation rate, and maximum electron transport. In total, 11 models were produced from a diverse population of soybean sampled over multiple field seasons to estimate photosynthetic parameters, chlorophyll content, leaf carbon and leaf nitrogen percentage, and specific leaf area (with R2 from 0.56 to 0.96 and root mean square error approximately <10% of the range of calibration data). We explore the utility of these models by applying them to the soybean nested association mapping population, which showed variability in photosynthetic and leaf traits. Genetic mapping provided insights into the underlying genetic architecture of photosynthetic traits and potential improvement in soybean. Notably, the maximum Rubisco carboxylation rate mapped to a region of chromosome 19 containing genes encoding multiple small subunits of Rubisco. We also mapped the maximum electron transport rate to a region of chromosome 10 containing a fructose 1,6-bisphosphatase gene, encoding an important enzyme in the regeneration of ribulose 1,5-bisphosphate and the sucrose biosynthetic pathway. The estimated rate-limiting steps of photosynthesis were low or negatively correlated with yield suggesting that these traits are not influenced by the same genetic mechanisms and are not limiting yield in the soybean NAM population. Leaf carbon percentage, leaf nitrogen percentage, and specific leaf area showed strong correlations with yield and may be of interest in breeding programs as a proxy for yield. This work is among the first to use hyperspectral reflectance to model and map the genetic architecture of the rate-limiting steps of photosynthesis.

Towards improved dynamic photosynthesis in C3 crops by utilizing natural genetic variation

Under field environments, fluctuating light conditions induce dynamic photosynthesis, which affects carbon gain by crop plants. Elucidating the natural genetic variations among untapped germplasm resources and their underlying mechanisms can provide an effective strategy to improve dynamic photosynthesis and, ultimately, improve crop yields through molecular breeding approaches. In this review, we first overview two processes affecting dynamic photosynthesis, namely (i) biochemical processes associated with CO2 fixation and photoprotection and (ii) gas diffusion processes from the atmosphere to the chloroplast stroma. Next, we review the intra- and interspecific variations in dynamic photosynthesis in relation to each of these two processes. It is suggested that plant adaptations to different hydrological environments underlie natural genetic variation explained by gas diffusion through stomata. This emphasizes the importance of the coordination of photosynthetic and stomatal dynamics to optimize the balance between carbon gain and water use efficiency under field environments. Finally, we discuss future challenges in improving dynamic photosynthesis by utilizing natural genetic variation. The forward genetic approach supported by high-throughput phenotyping should be introduced to evaluate the effects of genetic and environmental factors and their interactions on the natural variation in dynamic photosynthesis.

Into the Shadows and Back into Sunlight: Photosynthesis in Fluctuating Light

Photosynthesis is an important remaining opportunity for further improvement in the genetic yield potential of our major crops. Measurement, analysis, and improvement of leaf CO₂ assimilation (A) have focused largely on photosynthetic rates under light-saturated steady-state conditions. However, in modern crop canopies of several leaf layers, light is rarely constant, and the majority of leaves experience marked light fluctuations throughout the day. It takes several minutes for photosynthesis to regain efficiency in both sun-shade and shade-sun transitions, costing a calculated 10-40% of potential crop CO₂ assimilation. Transgenic manipulations to accelerate the adjustment in sun-shade transitions have already shown a substantial productivity increase in field trials. Here, we explore means to further accelerate these adjustments and minimize these losses through transgenic manipulation, gene editing, and exploitation of natural variation. Measurement andanalysis of photosynthesis in sun-shade and shade-sun transitions are explained. Factors limiting speeds of adjustment and how they could be modified to effect improved efficiency are reviewed, specifically nonphotochemical quenching (NPQ), Rubisco activation, and stomatal responses.

Regulation of Chloroplast ATP Synthase Modulates Photoprotection in the CAM Plant Vanilla planifolia

Generally, regulation of cyclic electron flow (CEF) and chloroplast ATP synthase play key roles in photoprotection for photosystems I and II (PSI and PSII) in C3 and C4 plants, especially when CO₂ assimilation is restricted. However, how CAM plants protect PSI and PSII when CO₂ assimilation is restricted is largely known. In the present study, we measured PSI, PSII, and electrochromic shift signals in the CAM plant Vanilla planifolia. The quantum yields of PSI and PSII photochemistry largely decreased in the afternoon compared to in the morning, indicating that CO₂ assimilation was strongly restricted in the afternoon. Meanwhile, non-photochemical quenching (NPQ) in PSII and the donor side limitation of PSI (Y(ND)) significantly increased to protect PSI and PSII. Under such conditions, proton gradient (∆pH) across the thylakoid membranes largely increased and CEF was slightly stimulated, indicating that the increased ∆pH was not caused by the regulation of CEF. In contrast, the activity of chloroplast ATP synthase (g_H⁺) largely decreased in the afternoon. At a given proton flux, the decreasing g_H⁺ increased ∆pH and thus contributed to the enhancement of NPQ and Y(ND). Therefore, in the CAM plant V. planifolia, the ∆pH-dependent photoprotective mechanism is mainly regulated by the regulation of g_H⁺ rather than CEF when CO₂ assimilation is restricted.

Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii

Different intensities of high temperatures affect the growth of photosynthetic cells in nature. To elucidate the underlying mechanisms, we cultivated the unicellular green alga Chlamydomonas reinhardtii under highly controlled photobioreactor conditions and revealed systems-wide shared and unique responses to 24-hour moderate (35°C) and acute (40°C) high temperatures and subsequent recovery at 25°C. We identified previously overlooked unique elements in response to moderate high temperature. Heat at 35°C transiently arrested the cell cycle followed by partial synchronization, up-regulated transcripts/proteins involved in gluconeogenesis/glyoxylate-cycle for carbon uptake and promoted growth. But 40°C disrupted cell division and growth. Both high temperatures induced photoprotection, while 40°C distorted thylakoid/pyrenoid ultrastructure, affected the carbon concentrating mechanism, and decreased photosynthetic efficiency. We demonstrated increased transcript/protein correlation during both heat treatments and hypothesize reduced post-transcriptional regulation during heat may help efficiently coordinate thermotolerance mechanisms. During recovery after both heat treatments, especially 40°C, transcripts/proteins related to DNA synthesis increased while those involved in photosynthetic light reactions decreased. We propose down-regulating photosynthetic light reactions during DNA replication benefits cell cycle resumption by reducing ROS production. Our results provide potential targets to increase thermotolerance in algae and crops.

A systems-wide analysis of the single-cell green alga Chlamydomonas reinhardti reveals shared and unique responses to moderate and acute high temperatures using multiple-level investigation of transcriptomics, proteomics, cell physiology, photosynthetic parameters, and cellular ultrastructure.

Structural elucidation of vascular plant photosystem I and its functional implications

In vascular plants, bryophytes and algae, the photosynthetic light reaction takes place in the thylakoid membrane where two transmembrane supercomplexes PSII and PSI work together with cytochrome b 6 f and ATP synthase to harvest the light energy and produce ATP and NADPH. Vascular plant PSI is a 600-kDa protein-pigment supercomplex, the core complex of which is partly surrounded by peripheral light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core to be used for charge separation. PSI is unique mainly in absorption of longer-wavelengths than PSII, fast excitation energy transfer including uphill energy transfer, and an extremely high quantum efficiency. From the early 1980s, a lot of effort has been dedicated to structural and functional studies of PSI-LHCI, leading to the current understanding of how more than 200 cofactors are kept at the correct distance and geometry to facilitate fast energy transfer in this supercomplex at an atomic level. In this review, we review the history of studies on vascular plant PSI-LHCI, summarise the present research progress on its structure, and present some new and further questions to be answered in future studies.

Yang cycle enzyme DEP1: its moonlighting functions in PSI and ROS production during leaf senescence

Ethylene-mediated leaf senescence and the compromise of photosynthesis are closely associated but the underlying molecular mechanism is a mystery. Here we reported that apple DEHYDRATASE-ENOLASE-PHOSPHATASE-COMPLEX1 (MdDEP1), initially characterized to its enzymatic function in the recycling of the ethylene precursor SAM, plays a role in the regulation of photosystem I (PSI) activity, activating reactive oxygen species (ROS) homeostasis, and negatively regulating the leaf senescence. A series of Y2H, Pull-down, CO-IP and Cell-free degradation biochemical assays showed that MdDEP1 directly interacts with and dephosphorylates the nucleus-encoded thylakoid protein MdY3IP1, leading to the destabilization of MdY3IP1, reduction of the PSI activity, and the overproduction of ROS in plant cells. These findings elucidate a novel mechanism that the two pathways intersect at MdDEP1 due to its moonlighting role in destabilizing MdY3IP1, and synchronize ethylene-mediated leaf senescence and the compromise of photosynthesis.