Dynamic response of photorespiration in fluctuating light environments

Bioconversion of CO2 into valuable bioproducts via synthetic modular co-culture of engineered Chlamydomonas reinhardtii and Escherichia coli

With increasing concern over environmental problems and energy crises, interest in the biological conversion of CO2 into bioproducts is growing. Although microalgae efficiently utilize CO2, their metabolic engineering remains challenging. In contrast, while synthetic biology tools are advanced for many heterotrophic bacteria, these organisms cannot directly utilize CO2. As such, a modular co-culture system with a glycolate dehydrogenase 1 (GYD1) deficient Chlamydomonas reinhardtii mutant and Escherichia coli was developed. The GYD1 mutant secretes glycolic acid via photorespiration, which E. coli metabolizes via the glyoxylate cycle. E. coli growth was improved by implementing two-stage continuous systems to 2.0 mg L-1 h-1 on CO2. The production of green fluorescent protein (0.52 ng L-1 h-1) and lycopene (6.3 μg L-1 h-1) was also demonstrated. This study represents a successful case of a synthetic modular co-culture with a microalga and a heterotrophic bacterium, potentially contributing to sustainable industrial processes and reducing environmental impact.

Comprehensive analysis of the effects on photosynthesis and energy balance in tomato leaves under magnesium deficiency

Magnesium (Mg), as an essential and central mineral element for chlorophyll biosynthesis, plays a crucial role in plant photosynthesis. Magnesium deficiency inevitably affects the photosynthetic ability of leaves, thereby impairing the yield and quality of crops. However, few studies have revealed the intrinsic mechanisms by which Mg deficiency hinders growth and photosynthesis, particularly by analyzing the processes of light capture, dissipation, absorption, and utilization in tomato. The experiment studied the effects of Mg deficiency on internal structure of leaves, light absorption, electron transfer, photophosphorylation, and carbon assimilation, combined with transcriptome data analyses and key gene screening in tomato leaves. The results showed that Mg deficiency induced obvious leaf chlorosis and damaged stomatal structure, irregular chloroplast structure and degraded thylakoid lamellae, thereby resulting in lower chlorophyll content, net photosynthetic rate, water use efficiency, and biomass. Decreased expression of 11 genes related to light-harvesting antenna proteins suggested that Mg deficiency weakened the light absorption capacity of tomato leaves, Additionally, Mg deficiency inactivated the photochemical reaction centers of photosystem I (PSI) and photosystem II (PSII), and decreased the expression of related genes (PSAA, PSAB, PSBA, and PSBB), leading to a reduction in electron transfer capacity from the donor side of PSII to PSI. Furthermore, Mg deficiency inhibited ATP synthesis and weakened carbohydrate assimilation by reducing carboxylation capacity of the Rubisco enzyme, Rubisco carboxylation rate (Vmax), and triose phosphate transport rate (TPU). The accumulation of carbohydrates in the leaves reduced the efficiency of the Calvin-Benson cycle and ATP/NADPH in Mg-deficient leaves. The down-expressed genes related to cyclic electron transfer (CRR7, NDHB, PNSB, PNSB4, PNSB5) further demonstrated that Mg deficiency may weaken cyclic electron transfer during photosynthesis. Therefore, the reduction in the photosynthetic capacity of Mg-deficient tomato plants was the result of a combination of decreased carbon assimilation capacity, damaged photosynthetic components, changed photosynthetic electron transport and distribution. The findings of this study provide a comprehensive understanding of the underlying mechanisms by which Mg deficiency reduces the photosynthetic performance of tomato leaves and offer a theoretical basis for breeding Mg-tolerant tomato varieties.

A cytosolic glyoxylate shunt complements the canonical photorespiratory pathway in Arabidopsis

Photorespiration functions in part to support photosynthetic performance, especially under stress such as high light, yet the underlying mechanisms are poorly understood. To identify modulators of photorespiration under high light, we have isolated genetic suppressors of the photorespiratory mutant hpr1 (hydroxypyruvate reductase 1) from Arabidopsis. A suppressor that partially rescues hpr1 is mapped to GLYR1, which encodes the cytosolic glyoxylate reductase 1 that converts glyoxylate to glycolate. Independent glyr1 mutants also partially rescue hpr1 and another photorespiratory mutant, catalase 2. Our genetic, transcriptomic and metabolic profiling analyses together reveal a connection between cytosolic glyoxylate and a non-canonical photorespiratory route mediated by HPR2, which we name the photorespiratory glyoxylate shunt. This shunt complements the canonical photorespiratory pathway and is especially critical when high photorespiratory fluxes are required and when the major photorespiratory pathway is deficient. Our findings support the metabolic flexibility of photorespiration and may help to improve crop performance under stress.

Chassis engineering for high light tolerance in microalgae and cyanobacteria

Oxygenic photosynthesis in microalgae and cyanobacteria is considered an important chassis to accelerate energy transition and mitigate global warming. Currently, cultivation systems for photosynthetic microbes for large-scale applications encountered excessive light exposure stress. High light stress can: affect photosynthetic efficiency, reduce productivity, limit cell growth, and even cause cell death. Deciphering photoprotection mechanisms and constructing high-light tolerant chassis have been recent research focuses. In this review, we first briefly introduce the self-protection mechanisms of common microalgae and cyanobacteria in response to high light stress. These mechanisms mainly include: avoiding excess light absorption, dissipating excess excitation energy, quenching excessive high-energy electrons, ROS detoxification, and PSII repair. We focus on the species-specific differences in these mechanisms as well as recent advancements. Then, we review engineering strategies for creating high-light tolerant chassis, such as: reducing the size of the light-harvesting antenna, optimizing non-photochemical quenching, optimizing photosynthetic electron transport, and enhancing PSII repair. Finally, we propose a comprehensive exploration of mechanisms: underlying identified high light tolerant chassis, identification of new genes pertinent to high light tolerance using innovative methodologies, harnessing CRISPR systems and artificial intelligence for chassis engineering modification, and introducing plant photoprotection mechanisms as future research directions.

Increasing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination

As global temperatures rise, improving crop yields will require enhancing the thermotolerance of crops. One approach for improving thermotolerance is using bioengineering to increase the thermostability of enzymes catalysing essential biological processes. Photorespiration is an essential recycling process in plants that is integral to photosynthesis and crop growth. The enzymes of photorespiration are targets for enhancing plant thermotolerance as this pathway limits carbon fixation at elevated temperatures. We explored the effects of temperature on the activity of the photorespiratory enzyme glycerate kinase (GLYK) from various organisms and the homologue from the thermophilic alga Cyanidioschyzon merolae was more thermotolerant than those from mesophilic plants, including Arabidopsis thaliana. To understand enzyme features underlying the thermotolerance of C. merolae GLYK (CmGLYK), we performed molecular dynamics simulations using AlphaFold-predicted structures, which revealed greater movement of loop regions of mesophilic plant GLYKs at higher temperatures compared to CmGLYK. Based on these simulations, hybrid proteins were produced and analysed. These hybrid enzymes contained loop regions from CmGLYK replacing the most mobile corresponding loops of AtGLYK. Two of these hybrid enzymes had enhanced thermostability, with melting temperatures increased by 6 °C. One hybrid with three grafted loops maintained higher activity at elevated temperatures. Whilst this hybrid enzyme exhibited enhanced thermostability and a similar Km for ATP compared to AtGLYK, its Km for glycerate increased threefold. This study demonstrates that molecular dynamics simulation-guided structure-based recombination offers a promising strategy for enhancing the thermostability of other plant enzymes with possible application to increasing the thermotolerance of plants under warming climates.

Enhancing crop yields to ensure food security by optimizing photosynthesis

The crop yields achieved through traditional plant breeding techniques appear to be nearing a plateau. Therefore, it is essential to accelerate advancements in photosynthesis, the fundamental process by which plants convert light energy into chemical energy, to further enhance crop yields. Research focused on improving photosynthesis holds significant promise for increasing sustainable agricultural productivity and addressing challenges related to global food security. This review examines the latest advancements and strategies aimed at boosting crop yields by enhancing photosynthetic efficiency. There has been a linear increase in yield over the years in historically released germplasm selected through traditional breeding methods, and this increase is accompanied by improved photosynthesis. We explore various aspects of the light reactions designed to enhance crop yield, including light harvest efficiency through smart canopy systems, expanding the absorbed light spectrum to include far-red light, optimizing non-photochemical quenching, and accelerating electron transport flux. At the same time, we investigate carbon reactions that can enhance crop yield, such as manipulating Rubisco activity, improving the Calvin-Benson-Bassham (CBB) cycle, introducing CO2 concentrating mechanisms (CCMs) in C3 plants, and optimizing carbon allocation. These strategies could significantly impact crop yield enhancement and help bridge the yield gap.

Bicarbonate use reduces the photorespiration in Ottelia alismoides adapting to the CO2-fluctuated aquatic systems

Underwater CO2 concentration fluctuates extremely in natural water bodies. Under low CO2, the unique CO2 concentrating mechanism in aquatic plants, bicarbonate use, can suppress photorespiration. However, it remains unknown (1) to what extent bicarbonate use reduces photorespiration, (2) how exactly photorespiration varies between bicarbonate-users and CO2-obligate users under CO2-fluctuated environments, and (3) what are differences in Rubisco characteristics between these two types of aquatic plants. In the present study, the bicarbonate user Ottelia alismoides and its phylogenetically close CO2-obligate user Blyxa japonica were chosen to answer these questions. The results showed that bicarbonate use saved ~13% carbon loss under low CO2 via decreasing photorespiration in O. alismoides. Through bicarbonate use, the photorespiration of O. alismoides was kept stable both under high and low underwater CO2 concentrations, while the photorespiration significantly increased in the CO2-obligate user B. japonica under low CO2. However, B. japonica showed a significantly higher photosynthesis rate than O. alsimoides when CO2 was sufficient. These differences could be related to the kinetic characteristics of Rubisco showing a higher carboxylation turnover rate (Kcat) in B. japonica, and the similar affinity to CO2 (Kc) and specificity factor (Sc/o) in these two species that might be determined by the variation of six amino acid residuals in Rubisco large subunit sequences, especially the site 281 (A vs. S) and 282 (H vs. F). All these differences in photorespiration and kinetic characteristics of Rubisco could explain the distribution patterns of bicarbonate users and CO2-obligate users in the field.

Elevated CO2 Shifts Photosynthetic Constraint from Stomatal to Biochemical Limitations During Induction in Populus tomentosa and Eucalyptus robusta

The relative impacts of biochemical and stomatal limitations on photosynthesis during photosynthetic induction have been well studied for diverse plants under ambient CO2 concentration (Ca). However, a knowledge gap remains regarding how the various photosynthetic components limit duction efficiency under elevated CO2. In this study, we experimentally investigated the influence of elevated CO2 (from 400 to 800 μmol mol-1) on photosynthetic induction dynamics and its associated limitation components in two broadleaved tree species, Populus tomentosa and Eucalyptus robusta. The results show that elevated CO2 increased the steady-state photosynthesis rate (A) and decreased stomatal conductance (gs) and the maximum carboxylation rate (Vcmax) in both species. While E. robusta exhibited a decrease in the linear electron transport rate (J) and the fraction of open reaction centers in photosynthesis II (qL), P. tomentosa showed a significant increase in non-photochemical quenching (NPQ). With respect to non-steady-state photosynthesis, elevated CO2 significantly reduced the induction time of A following a shift from low to high light intensity in both species. Time-integrated limitation analysis during induction revealed that elevated CO2 reduces the relative impacts of stomatal limitations in both species, consequently shifting the predominant limitation on induction efficiency from stomatal to biochemical components. Additionally, species-specific changes in qL and NPQ suggest that elevated CO2 may increase biochemical limitation by affecting energy allocation between carbon fixation and photoprotection. These findings suggest that, in a future CO2-rich atmosphere, plants productivity under fluctuating light may be primarily constrained by photochemical and non-photochemical quenching.

Evaluation of the phytotoxicity and accumulation potential of nitro-polycyclic aromatic hydrocarbon, 3-nitrofluoranthene, on water status, photosystem II efficiency, antioxidant activity and ROS accumulation in Salvinia natans

Organic pollutants, which have become one of the most striking problems of today, raise concerns about the spread of polyaromatic hydrocarbon (PAH) compounds into ecosystems and their toxic effects on living organisms. The purpose of this study was to determine how harmful 3-nitrofluoranthene (3-NF) exposure was to Salvinia natans, a freshwater macrophyte. Furthermore, it clarifies how this aquatic plant, which is frequently used in phytoremediation of water contaminants and wastewater treatments, interacts with PAHs and contributes to the development of bioremediation methods. In S. natans exposed to stress (10 μM (3-NF10), 25 μM (3-NF25), 50 μM (3-NF50), 100 μM (3-NF100), 250 μM (3-NF250), 500 μM (3-NF500), 1000 μM (3-NF1000) 3-nitrofluoranthene), 3-NF accumulation, oxidative stress indicators, photosynthetic efficiency, and antioxidant system activity alterations were investigated for this objective. The findings demonstrated that S. natans could effectively accumulate 3-NF, and at a concentration of 1000 μM, the 3-NF content in the leaves reached approximately 1112 mg/kg. While its adverse effects on growth (RGR) and photosynthesis (Fv/Fm) remained mild up to a concentration of 250 μM, the severity of the inhibitions increased at higher concentrations. On the other hand, exposure to 3-NF triggered the antioxidant system in S. natans plants and resulted in an increase of 60 %, 80 %, 47 % and 27 % in superoxide dismutase (SOD) activity in 3-NF10-25-50-100 groups, respectively. Conversely, in comparison to control plants, higher concentrations of 3-NF treatments resulted in insufficient antioxidant activity, increased lipid peroxidation (TBARS concentration), and hydrogen peroxide (H2O2). In conclusion, S. natans plants tolerated 3-NF accumulation up to 250 μM concentration despite limitations in growth suppression and photosynthetic capacity, proving that S. natans has the potential to be used in phytoextraction studies of 3-NF-polluted waters.

Re-evaluating the energy balance of the many routes of carbon flow through and from photorespiration

Photorespiration is an essential process related to photosynthesis that is initiated following the oxygenation reaction catalyzed by rubisco, the initial enzyme of the Calvin-Benson-Bassham cycle. This reaction produces an inhibitory intermediate that is recycled back into the Calvin-Benson-Bassham cycle by photorespiration which requires the use of energy and the release of a portion of the carbon as CO2. The energy use and CO2 release of canonical photorespiration form a foundation for biochemical models used to describe and predict leaf carbon exchange and energy use (ATP and NAPDH). The ATP and NADPH demand of canonical photorespiration is thought to be different than that of the Calvin-Benson-Bassham cycle, requiring increased flexibility in the ratio of ATP and NADPH from the light reactions. Photorespiration requires many reactions across the chloroplasts, mitochondria and peroxisomes and involves many intermediates. Growing evidence indicates that these intermediates do not all stay in photorespiration as typically assumed and instead feed into other aspects of metabolism and leave as glycine, serine, and methylene-THF. Here we discuss how alternative flux through and from canonical photorespiration alters the ATP and NADPH requirements of metabolism following rubisco oxygenation using additional derivations of biochemical models of leaf photosynthesis and energetics. Using these new derivations, we determine that the ATP and NADPH demands of photorespiration are highly sensitive to alternative flux in ways that fundamentally changes how photorespiration contributes to the ratio of total ATP and NADPH demand. Specifically, alternative flows of carbon through photorespiration could reduce ATP and NADPH demand ratio to values below what is produced from linear electron transport.

Exploring natural genetic variation in photosynthesis-related traits of barley in the field

Optimizing photosynthesis is considered an important strategy for improving crop yields to ensure food security. To evaluate the potential of using photosynthesis-related parameters in crop breeding programs, we measured chlorophyll fluorescence along with growth-related and morphological traits of 23 barley inbred lines across different developmental stages in field conditions. The photosynthesis-related parameters were highly variable, changing with light intensity and developmental progression of plants. Yet, the variation in photosystem II quantum yield observed among the inbred lines in the field largely reflected the variation in CO2 assimilation properties in controlled climate chamber conditions, confirming that the chlorophyll fluorescence-based technique can provide proxy parameters of photosynthesis to explore genetic variation under field conditions. Heritability (H2) of the photosynthesis-related parameters in the field ranged from 0.16 for the quantum yield of non-photochemical quenching to 0.78 for the fraction of open photosystem II center. Two parameters, the maximum photosystem II efficiency in the light-adapted state (H2=0.58) and the total non-photochemical quenching (H2=0.53), showed significant positive and negative correlations, respectively, with yield-related traits (dry weight per plant and net straw weight) in the barley inbred lines. These results indicate the possibility of improving crop yield through optimizing photosynthetic light use efficiency by conventional breeding programs.

Photorespiratory glycine contributes to photosynthetic induction during low to high light transition

Leaves experience near-constant light fluctuations daily. Past studies have identified many limiting factors of slow photosynthetic induction when leaves transition from low light to high light. However, the contribution of photorespiration in influencing photosynthesis during transient light conditions is largely unknown. This study employs dynamic measurements of gas exchange and metabolic responses to examine the contribution of photorespiration in constraining net rates of carbon assimilation during light induction. This work indicates that photorespiratory glycine accumulation during the early light induction contributes 5-7% to the additional carbon fixed relative to the low light conditions. Mutants with large glycine pools under photorespiratory conditions (5-formyl THF cycloligase and hydroxypyruvate reductase 1) showed a transient spike in net CO2 assimilation during light induction, with glycine buildup accounting for 22-36% of the extra carbon assimilated. Interestingly, levels of many C3 cycle intermediates remained relatively constant in both mutants and wild-type throughout the light induction period where glycine accumulated, indicating that recycling of carbon into the C3 cycle via photorespiration is not needed to maintain C3 cycle activity under transient conditions. Furthermore, our data show that oxygen transient experiments can be used as a proxy to identify the photorespiratory component of light-induced photosynthetic changes.

Overexpression of MPV17/PMP22-like protein 2 gene decreases production of radical oxygen species in Pyropia yezoensis (Bangiales, Rhodophyta)

The northward shift of Pyropia yezoensis aquaculture required the breeding of germplasms with tolerance to the oxidative stress due to the high light conditions of the North Yellow Sea area. The MPV17/PMP22 family proteins were identified as a molecule related to reactive oxygen species (ROS) metabolism. Here, one of the MPV17 homolog genes designated as PyM-LP2 was selected for functional identification by introducing the encoding sequence region/reverse complementary fragment into the Py. yezoensis genome. Although the photosynthetic activity, the respiratory rate, and the ROS level in wild type (WT) and different gene-transformed algal strains showed similar levels under normal conditions, the overexpression (OE) strain exhibited higher values of photosynthesis, respiration, and reducing equivalents pool size but lower intracellular ROS production under stress conditions compared with the WT. Conversely, all the above parameters showed opposite variation trends in RNAi strain as those in the OE strain. This implied that the PyM-LP2 protein was involved in the mitigation of the oxidative stress. Sequence analysis revealed that this PyM-LP2 protein was assorted to peroxisomes and might serve as a poring channel for transferring malate (Mal) to peroxisomes. By overexpressing PyM-LP2, the transfer of Mal from chloroplasts to peroxisomes was enhanced under stress conditions, which promoted photorespiration and ultimately alleviated excessive reduction of the photosynthetic electron chain. This research lays the groundwork for the breeding of algae with enhanced resistance to oxidative stresses.

Differential photosynthetic plasticity of Amazonian tree species in response to light environments

To investigate how and to what extent there are differences in the photosynthetic plasticity of trees in response to different light environments, six species from three successional groups (late successional, mid-successional, and pioneers) were exposed to three different light environments [deep shade - DS (5% full sunlight - FS), moderate shade - MS (35% FS) and full sunlight - FS]. Maximum net photosynthesis (Amax), leaf N partitioning, stomatal, mesophile, and biochemical limitations (SL, ML, and BL, respectively), carboxylation velocity (Vcmax), and electron transport (Jmax) rates, and the state of photosynthetic induction (IS) were evaluated. Higher values of Amax, Vcmax, and Jmax in FS were observed for pioneer species, which invested the largest amount of leaf N in Rubisco. The lower IS for pioneer species reveals its reduced ability to take advantage of sunflecks. In general, the main photosynthetic limitations are diffusive, with SL and ML having equal importance under FS, and ML decreasing along with irradiance. The leaf traits, which are more determinant of the photosynthetic process, respond independently in relation to the successional group, especially with low light availability. An effective partitioning of leaf N between photosynthetic and structural components played a crucial role in the acclimation process and determined the increase or decrease of photosynthesis in response to the light conditions.

Nanoplastics inhibit carbon fixation in algae: The effect of aging

Despite the considerable efforts devoted to the toxicological assessment of nanoplastics, the effect of UV-irradiation induced aging, a realistic environmental process, on the toxicity of nanoplastics toward microalgae and its underlying mechanisms remain largely unknown. Herein, this study comparatively investigated the toxicities of polystyrene nanoplastics (nano-PS) and the UV-aged nano-PS on the eukaryotic alga Chlorella vulgaris, focusing on evaluating their inhibitory effects on carbon fixation. Exposure to environmentally relevant concentrations (0.1-10 mg/L) of nano-PS caused severe damage to chloroplast, inhibited the photosynthetic efficiency and electron transport, and suppressed the activities of carbon fixation related enzymes. Multi-omics results revealed that nano-PS interfered with energy supply by disrupting light reactions and TCA cycle and hindered the Calvin cycle, thereby inhibiting the photosynthetic carbon fixation of algae. The above alterations partially recovered after a recovery period. The aged nano-PS were less toxic than the pristine ones as evidenced by the mitigated inhibitory effect on algal growth and carbon fixation. The aging process introduced oxygen-containing functional groups on the surface of nano-PS, increased the hydrophilicity of nano-PS, limited their attachment on algal cells, and thus reduced the toxicity. The findings of this work highlight the potential threat of nanoplastics to the global carbon cycle.

Mesophyll conductance limits photosynthesis in fluctuating light under combined drought and heat stresses

Drought and heat stresses usually occur concomitantly in nature, with increasing frequency and intensity of both stresses expected due to climate change. The synergistic agricultural impacts of these compound climate extremes are much greater than those of the individual stresses. However, the mechanisms by which drought and heat stresses separately and concomitantly affect dynamic photosynthesis have not been thoroughly assessed. To elucidate this, we used tomato (Solanum lycopersicum) seedlings to measure dynamic photosynthesis under individual and compound stresses of drought and heat. Individual drought and heat stresses limited dynamic photosynthesis at the stages of diffusional conductance to CO2 and biochemistry, respectively. However, the primary limiting factor for photosynthesis shifted to mesophyll conductance under the compound stresses. Compared with the control, photosynthetic carbon gain in fluctuating light decreased by 38%, 73%, and 114% under the individual drought, heat, and compound stresses, respectively. Therefore, compound stresses caused a greater reduction in photosynthetic carbon gain in fluctuating light conditions than individual stress. These findings highlight the importance of mitigating the effects of compound climate extremes on crop productivity by targeting mesophyll conductance and improving dynamic photosynthesis.

The role of photorespiration in preventing feedback regulation via ATP synthase in Nicotiana tabacum

Photorespiration consumes substantial amounts of energy in the forms of adenosine triphosphate (ATP) and reductant making the pathway an important component in leaf energetics. Because of this high reductant demand, photorespiration is proposed to act as a photoprotective electron sink. However, photorespiration consumes more ATP relative to reductant than the C3 cycle meaning increased flux disproportionally increases ATP demand relative to reductant. Here we explore how energetic consumption from photorespiration impacts the flexibility of the light reactions in nicotiana tabacum. Specifically, we demonstrate that decreased photosynthetic efficiency (ϕII ) at low photorespiratory flux was related to feedback regulation at the chloroplast ATP synthase. Additionally, decreased ϕII at high photorespiratory flux resulted in the accumulation of photoinhibition at photosystem II centers. These results are contrary to the proposed role of photorespiration as a photoprotective electron sink. Instead, our results suggest a novel role of ATP consumption from photorespiration in maintaining ATP synthase activity, with implications for maintaining energy balance and preventing photodamage that will be critical for plant engineering strategies.

Identification and Functional Characterization of cis-Regulatory Elements of Key Photorespiratory Genes in Response to Short-Term Abiotic Stress Conditions

The cis-regulatory elements (CREs) are the short stretches of noncoding DNA upstream of a gene, which play a critical role in fine-tuning gene expression. Photorespiration is a multi-organellar, energy-expensive biochemical process that remains intricately linked to photosynthesis and is conserved in plants. Recently, much focus has been devoted in generating plants with engineered alternative photorespiratory bypasses to enhance photosynthetic efficiency without compromising the beneficial aspect of photorespiration. Varied constitutive or inducible promoters for generating transgenic plants harboring multiple transgenes have been introduced over years; however, most of them suffer from unintended effects. Consequently, a demand for synthetic tunable promoters based on canonical CRE signatures derived from native genes is on the rise. Here, in this chapter, we have provided a detailed method for in silico identification and characterization of CREs associated with photorespiration. In addition to the detailed protocol, we have presented an example of a typical result and explained the significance of the result. Specifically, the method covers how to identify and generate tunable synthetic promoters based on native CREs using three key photorespiratory genes from Arabidopsis and two web-based tools, namely, PlantPAN3.0 and AthaMap. Finally, we have also furnished a protocol on how to test the efficacies of the synthetic promoters harboring predicted CREs using transient tobacco expression coupled with luciferase-based promoter assay in response to ambient conditions and under short-term abiotic stress conditions.

Using Dynamic Gas Exchange Measurements During Oxygen Transients to Study Nonsteady-State Photorespiration

Leaf-level gas exchange is widely used to investigate the largest carbon fluxes in illuminated leaves, offering a nondestructive way to investigate the impact of photorespiration on plant carbon balance. Modern commercial gas exchange systems allow high temporal resolution measurements under changing environments, aiding the development of nonsteady-state approaches for measuring dynamic photosynthetic responses. Here, we describe a nonsteady-state technique for acquiring the dynamic response of net CO2 assimilation to changes in photorespiratory fluxes manipulated by O2 mole fractions. This technique allows for the screening of plant genotypes with variations in their efficiencies of photorespiration under nonsteady-state conditions.

Visualizing the dynamics of plant energy organelles

Plant organelles predominantly rely on the actin cytoskeleton and the myosin motors for long-distance trafficking, while using microtubules and the kinesin motors mostly for short-range movement. The distribution and motility of organelles in the plant cell are fundamentally important to robust plant growth and defense. Chloroplasts, mitochondria, and peroxisomes are essential organelles in plants that function independently and coordinately during energy metabolism and other key metabolic processes. In response to developmental and environmental stimuli, these energy organelles modulate their metabolism, morphology, abundance, distribution and motility in the cell to meet the need of the plant. Consistent with their metabolic links in processes like photorespiration and fatty acid mobilization is the frequently observed inter-organellar physical interaction, sometimes through organelle membranous protrusions. The development of various organelle-specific fluorescent protein tags has allowed the simultaneous visualization of organelle movement in living plant cells by confocal microscopy. These energy organelles display an array of morphology and movement patterns and redistribute within the cell in response to changes such as varying light conditions, temperature fluctuations, ROS-inducible treatments, and during pollen tube development and immune response, independently or in association with one another. Although there are more reports on the mechanism of chloroplast movement than that of peroxisomes and mitochondria, our knowledge of how and why these three energy organelles move and distribute in the plant cell is still scarce at the functional and mechanistic level. It is critical to identify factors that control organelle motility coupled with plant growth, development, and stress response.

Growth in fluctuating light buffers plants against photorespiratory perturbations

Photorespiration (PR) is the pathway that detoxifies the product of the oxygenation reaction of Rubisco. It has been hypothesized that in dynamic light environments, PR provides a photoprotective function. To test this hypothesis, we characterized plants with varying PR enzyme activities under fluctuating and non-fluctuating light conditions. Contrasting our expectations, growth of mutants with decreased PR enzyme levels was least affected in fluctuating light compared with wild type. Results for growth, photosynthesis and metabolites combined with thermodynamics-based flux analysis revealed two main causal factors for this unanticipated finding: reduced rates of photosynthesis in fluctuating light and complex re-routing of metabolic fluxes. Only in non-fluctuating light, mutants lacking the glutamate:glyoxylate aminotransferase 1 re-routed glycolate processing to the chloroplast, resulting in photooxidative damage through H2O2 production. Our results reveal that dynamic light environments buffer plant growth and metabolism against photorespiratory perturbations.

Beyond photorespiration: the significance of glycine and serine in leaf metabolism

The elucidation and removal of photorespiratory metabolic constraints will be necessary to improve crop yield in the next agricultural revolution. Fu et al. studied metabolic fluxes in the photorespiratory pathway and report that serine is the major export, whereas dynamic alterations in glycine pools orchestrate CO2 assimilation during the induction and relaxation of photorespiration.

Recent developments in the engineering of Rubisco activase for enhanced crop yield

Rubisco activase (RCA) catalyzes the release of inhibitory sugar phosphates from ribulose-1,6-biphosphate carboxylase/oxygenase (Rubisco) and can play an important role in biochemical limitations of photosynthesis under dynamic light and elevated temperatures. There is interest in increasing RCA activity to improve crop productivity, but a lack of understanding about the regulation of photosynthesis complicates engineering strategies. In this review, we discuss work relevant to improving RCA with a focus on advances in understanding the structural cause of RCA instability under heat stress and the regulatory interactions between RCA and components of photosynthesis. This reveals substantial variation in RCA thermostability that can be influenced by single amino acid substitutions, and that engineered variants can perform better in vitro and in vivo under heat stress. In addition, there are indications RCA activity is controlled by transcriptional, post-transcriptional, post-translational, and spatial regulation, which may be important for balancing between carbon fixation and light capture. Finally, we provide an overview of findings from recent field experiments and consider the requirements for commercial validation as part of efforts to increase crop yields in the face of global climate change.

The role of photorespiration in plant immunity

To defend themselves in the face of biotic stresses, plants employ a sophisticated immune system that requires the coordination of other biological and metabolic pathways. Photorespiration, a byproduct pathway of oxygenic photosynthesis that spans multiple cellular compartments and links primary metabolisms, plays important roles in defense responses. Hydrogen peroxide, whose homeostasis is strongly impacted by photorespiration, is a crucial signaling molecule in plant immunity. Photorespiratory metabolites, interaction between photorespiration and defense hormone biosynthesis, and other mechanisms, are also implicated. An improved understanding of the relationship between plant immunity and photorespiration may provide a much-needed knowledge basis for crop engineering to maximize photosynthesis without negative tradeoffs in plant immunity, especially because the photorespiratory pathway has become a major target for genetic engineering with the goal to increase photosynthetic efficiency.

Activation of CO2 assimilation during photosynthetic induction is slower in C4 than in C3 photosynthesis in three phylogenetically controlled experiments

INTRODUCTION

Despite their importance for the global carbon cycle and crop production, species with C₄ photosynthesis are still somewhat understudied relative to C₃ species. Although the benefits of the C₄ carbon concentrating mechanism are readily observable under optimal steady state conditions, it is less clear how the presence of C₄ affects activation of CO₂ assimilation during photosynthetic induction.

METHODS

In this study we aimed to characterise differences between C₄ and C₃ photosynthetic induction responses by analysing steady state photosynthesis and photosynthetic induction in three phylogenetically linked pairs of C₃ and C₄ species from Alloteropsis, Flaveria, and Cleome genera. Experiments were conducted both at 21% and 2% O₂ to evaluate the role of photorespiration during photosynthetic induction.

RESULTS

Our results confirm C₄ species have slower activation of CO₂ assimilation during photosynthetic induction than C₃ species, but the apparent mechanism behind these differences varied between genera. Incomplete suppression of photorespiration was found to impact photosynthetic induction significantly in C₄ Flaveria bidentis, whereas in the Cleome and Alloteropsis C₄ species, delayed activation of the C₃ cycle appeared to limit induction and a potentially supporting role for photorespiration was also identified.

DISCUSSION

The sheer variation in photosynthetic induction responses observed in our limited sample of species highlights the importance of controlling for evolutionary distance when comparing C₃ and C₄ photosynthetic pathways.

Integrated flux and pool size analysis in plant central metabolism reveals unique roles of glycine and serine during photorespiration

Photorespiration is an essential process juxtaposed between plant carbon and nitrogen metabolism that responds to dynamic environments. Photorespiration recycles inhibitory intermediates arising from oxygenation reactions catalysed by Rubisco back into the C₃ cycle, but it is unclear what proportions of its nitrogen-containing intermediates (glycine and serine) are exported into other metabolisms in vivo and how these pool sizes affect net CO₂ gas exchange during photorespiratory transients. Here, to address this uncertainty, we measured rates of amino acid export from photorespiration using isotopically non-stationary metabolic flux analysis. This analysis revealed that ~23-41% of the photorespiratory carbon was exported from the pathway as serine under various photorespiratory conditions. Furthermore, we determined that the build-up and relaxation of glycine pools constrained a large portion of photosynthetic acclimation during photorespiratory transients. These results reveal the unique and important roles of glycine and serine in successfully maintaining various photorespiratory fluxes that occur under environmental fluctuations in nature and providing carbon and nitrogen for metabolism.