A Limited Role for Carbonic Anhydrase in C4 Photosynthesis as Revealed by a ca1ca2 Double Mutant in Maize

The poetry of nitrogen and carbon metabolic shifts: The role of C/N in pitaya phase change

Pitaya, a desert plant, has an underexplored flowering mechanism due to a lack of functional validation assays. This study reveals that the transition from vegetative to generative growth in pitaya is regulated by significant metabolic shift, underscoring the importance of understanding and address the challenging issue pitaya's phase change. Lateral buds from 6-years-old 'Guanhuahong' pitaya (Hylocereus monacanthus) plants were collected on April 8th, 18th, and 28th 2023, representing early, middle, and late stages of phase transition, respectively. Results showed diminished nitrogen levels concurrent with increased carbon levels and carbon-to-nitrogen (C/N) ratios during pitaya phase transition. Transcriptomic analysis identified batches of differentially expressed genes (DEGs) involved in downregulating nitrogen metabolism and upregulating carbon metabolism. These batches of genes play a central role in the metabolic shifts that predominantly regulate the transition to the generative phase in pitaya. This study unveils the intricate regulatory network involving 6 sugar synthesis and transport, 11 photoperiod (e.g., PHY, CRY, PIF) and 6 vernalization (e.g., VIN3) pathways, alongside 11 structural flowering genes (FCA, FLK, LFY, AGL) out of a vast array of potential candidates in pitaya phase change. These findings provide insights into the metabolic pathways involved in pitaya's phase transition, offering a theoretical framework for managing flowering, guiding breeding strategies to optimize flowering timing and improve crop yields under varied nitrogen conditions.

Enhancing Photosynthesis and Plant Productivity through Genetic Modification

Enhancing crop photosynthesis through genetic engineering technologies offers numerous opportunities to increase plant productivity. Key approaches include optimizing light utilization, increasing cytochrome b6f complex levels, and improving carbon fixation. Modifications to Rubisco and the photosynthetic electron transport chain are central to these strategies. Introducing alternative photorespiratory pathways and enhancing carbonic anhydrase activity can further increase the internal CO2 concentration, thereby improving photosynthetic efficiency. The efficient translocation of photosynthetically produced sugars, which are managed by sucrose transporters, is also critical for plant growth. Additionally, incorporating genes from C4 plants, such as phosphoenolpyruvate carboxylase and NADP-malic enzymes, enhances the CO2 concentration around Rubisco, reducing photorespiration. Targeting microRNAs and transcription factors is vital for increasing photosynthesis and plant productivity, especially under stress conditions. This review highlights potential biological targets, the genetic modifications of which are aimed at improving photosynthesis and increasing plant productivity, thereby determining key areas for future research and development.

A Carbonic Anhydrase, ZmCA4, Contributes to Photosynthetic Efficiency and Modulates CO2 Signaling Gene Expression by Interacting with Aquaporin ZmPIP2;6 in Maize

Carbonic anhydrase (CA) catalyzes the reversible CO2 hydration reaction that produces bicarbonate for phosphoenolpyruvate carboxylase (PEPC). This is the initial step for transmitting the CO2 signal in C4 photosynthesis. However, it remains unknown whether the maize (Zea mays L.) CA gene, ZmCA4, plays a role in the maize photosynthesis process. In our study, we found that ZmCA4 was relatively highly expressed in leaves and localized in the chloroplast and the plasma membrane of mesophyll protoplasts. Knock-out of ZmCA4 reduced CA activity, while overexpression of ZmCA4 increased rubisco activity, as well as the quantum yield and relative electron transport rate in photosystem II. Overexpression of ZmCA4 enhanced maize yield-related traits. Moreover, ZmCA4 interacted with aquaporin ZmPIP2;6 in bimolecular fluorescence complementation and co-immunoprecipitation experiments. The double-knock-out mutant for ZmPIP2;6 and ZmCA4 genes showed reductions in its growth, CA and PEPC activities, assimilation rate and photosystem activity. RNA-Seq analysis revealed that the expression of other ZmCAs, ZmPIPs, as well as CO2 signaling pathway homologous genes, and photosynthetic-related genes was all altered in the double-knock-out mutant compared with the wild type. Altogether, our study's findings point to a critical role of ZmCA4 in determining photosynthetic capacity and modulating CO2 signaling regulation via its interaction with ZmPIP2;6, thus providing insight into the potential genetic value of ZmCA4 for maize yield improvement.

Photosynthesis and food security: the evolving story of C4 rice

Traditional "Green Revolution" cereal breeding strategies to improve yield are now reaching a plateau in our principal global food crop rice. Photosynthesis has now become a major target of international consortia to increase yield potential. Synthetic biology is being used across multiple large projects to improve photosynthetic efficiency. This review follows the genesis and progress of one of the first of these consortia projects, now in its 13th year; the Bill and Melinda Gates funded C4 Rice Project. This project seeks to install the biochemical and anatomical attributes necessary to support C4 photosynthesis in the C3 crop rice. Here we address the advances made thus far in installing the biochemical pathway and some of the key targets yet to be reached.

Exploring the potential of Δ17O in CO2 for determining mesophyll conductance

Mesophyll conductance to CO2 from the intercellular air space to the CO2-H2O exchange site has been estimated using δ18O measurements (gm18). However, the gm18 estimates are affected by the uncertainties in the δ18O of leaf water where the CO2-H2O exchange takes place and the degree of equilibration between CO2 and H2O. We show that measurements of Δ17O (i.e.Δ17O=δ17O-0.528×δ18O) can provide independent constraints on gm (gmΔ17) and that these gm estimates are less affected by fractionation processes during gas exchange. The gm calculations are applied to combined measurements of δ18O and Δ17O, and gas exchange in two C3 species, sunflower (Helianthus annuus L. cv. 'sunny') and ivy (Hedera hibernica L.), and the C4 species maize (Zea mays). The gm18 and gmΔ17 estimates agree within the combined errors (P-value, 0.876). Both approaches are associated with large errors when the isotopic composition in the intercellular air space becomes close to the CO2-H2O exchange site. Although variations in Δ17O are low, it can be measured with much higher precision compared with δ18O. Measuring gmΔ17 has a few advantages compared with gm18: (i) it is less sensitive to uncertainty in the isotopic composition of leaf water at the isotope exchange site and (ii) the relative change in the gm due to an assumed error in the equilibration fraction θeq is lower for gmΔ17 compared with gm18. Thus, using Δ17O can complement and improve the gm estimates in settings where the δ18O of leaf water varies strongly, affecting the δ18O (CO2) difference between the intercellular air space and the CO2-H2O exchange site.

Nanomaterials in agriculture for plant health and food safety: a comprehensive review on the current state of agro-nanoscience

In the modern epoch, nanotechnology took forward the agriculture and food industry with new tools that promise to increase food production sustainably. It also anticipated that it would become a driving economic force shortly. Nanotechnology has the potential to reduce agricultural inputs, enrich the soil by absorbing nutrients, manage plant diseases, and detect diseases. The aim of the present review is to cover the potential aspects of nanoscience and its trend-setting appliances in modern agriculture and food production. This review focuses on the impact of various nanomaterials on plant health to improve agricultural production and its cooperative approach to food production. Nanotechnology has great potential compared to conventional approaches. The appealing path of nanotrends in the farming sector raises hopes and illuminates the route of innovative technologies to overcome various diseases in plants with an enhanced yield to meet the growing global population's need for food security.

Genome-wide identification, evolution, and expression analysis of carbonic anhydrases genes in soybean (Glycine max)

Carbonic anhydrases (CAs), as zinc metalloenzymes, are ubiquitous in nature and play essential roles in diverse biological processes. Although CAs have been broadly explored and studied, comprehensive characteristics of CA gene family members in the soybean (Glycine max) are still lacking. A total of 35 CA genes (GmCAs) were identified; they distributed on sixteen chromosomes of the soybean genome and can be divided into three subfamilies (α-type, β-type, and γ-type). Bioinformatics analysis showed that the specific GmCA gene subfamily or clade exhibited similar characteristics and that segmental duplications took the major role in generating new GmCAs. Furthermore, the synteny and evolutionary constraints analyses of CAs among soybean and distinct species provided more detailed evidence for GmCA gene family evolution. Cis-element analysis of promoter indicated that GmCAs may be responsive to abiotic stress and regulate photosynthesis. Moreover, the expression patterns of GmCAs varied in different tissues at diverse developmental stages in soybean. Additionally, we found that eight representative GmCAs may be involved in the response of soybean to low phosphorus stress. The systematic investigation of the GmCA gene family in this study will provide a valuable basis for further functional research on soybean CA genes.

Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops

As compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions. Non-photosynthetic isoforms of carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), the decarboxylating enzymes NAD/NADP-malic enzyme (NAD/NADP-ME), and phosphoenolpyruvate carboxykinase (PEPCK), and finally pyruvate orthophosphate dikinase (PPDK) catalyze reactions that are essential for major plant metabolism pathways, such as the tricarboxylic acid (TCA) cycle, maintenance of cellular pH, uptake of nutrients and their assimilation. Consistent with this view differential expression pattern of these non-photosynthetic C3 isoforms has been observed in different tissues across the plant developmental stages, such as germination, grain filling, and leaf senescence. Also abundance of these C3 isoforms is increased considerably in response to environmental fluctuations particularly during abiotic stress. Here we review the vital roles played by C3 isoforms of C4 enzymes and the probable mechanisms by which they help plants in acclimation to adverse growth conditions. Further, their potential applications to increase the agronomic trait value of C3 crops is discussed.

A Changing Light Environment Induces Significant Lateral CO2 Diffusion within Maize Leaves

A leaf structure with high porosity is beneficial for lateral CO₂ diffusion inside the leaves. However, the leaf structure of maize is compact, and it has long been considered that lateral CO₂ diffusion is restricted. Moreover, lateral CO₂ diffusion is closely related to CO₂ pressure differences (ΔCO₂). Therefore, we speculated that enlarging the ΔCO₂ between the adjacent regions inside maize leaves may result in lateral diffusion when the diffusion resistance is kept constant. Thus, the leaf structure and gas exchange of maize (C₄), cotton (C₃), and other species were explored. The results showed that maize and sorghum leaves had a lower mesophyll porosity than cotton and cucumber leaves. Similar to cotton, the local photosynthetic induction resulted in an increase in the ΔCO₂ between the local illuminated and the adjacent unilluminated regions, which significantly reduced the respiration rate of the adjacent unilluminated region. Further analysis showed that when the adjacent region in the maize leaves was maintained under a steady high light, the photosynthesis induction in the local regions not only gradually reduced the ΔCO₂ between them but also progressively increased the steady photosynthetic rate in the adjacent region. Under field conditions, the ΔCO₂, respiration, and photosynthetic rate of the adjacent region were also markedly changed by fluctuating light in local regions in the maize leaves. Consequently, we proposed that enlarging the ΔCO₂ between the adjacent regions inside the maize leaves results in the lateral CO₂ diffusion and supports photosynthesis in adjacent regions to a certain extent under fluctuating light.

Mesophyll conductance response to short-term changes in pCO2 is related to leaf anatomy and biochemistry in diverse C4 grasses

Mesophyll CO₂ conductance (g_m ) in C₃ species responds to short-term (minutes) changes in environment potentially due to changes in leaf anatomical and biochemical properties and measurement artefacts. Compared with C₃ species, there is less information on g_m responses to short-term changes in environmental conditions such as partial pressure of CO₂ (pCO₂ ) across diverse C₄ species and the potential determinants of these responses. Using 16 C₄ grasses we investigated the response of g_m to short-term changes in pCO₂ and its relationship with leaf anatomy and biochemistry. In general, g_m increased as pCO₂ decreased (statistically significant increase in 12 species), with percentage increases in g_m ranging from +13% to +250%. Greater increase in g_m at low pCO₂ was observed in species exhibiting relatively thinner mesophyll cell walls along with greater mesophyll surface area exposed to intercellular air spaces, leaf N, photosynthetic capacity and activities of phosphoenolpyruvate carboxylase and Rubisco. Species with greater CO₂ responses of g_m were also able to maintain their leaf water-use efficiencies (TE_i ) under low CO₂ . Our study advances understanding of CO₂ response of g_m in diverse C₄ species, identifies the key leaf traits related to this response and has implications for improving C₄ photosynthetic models and TE_i through modification of g_m .

Multigene manipulation of photosynthetic carbon metabolism enhances the photosynthetic capacity and biomass yield of cucumber under low-CO2 environment

Solar greenhouses are important in the vegetable production and widely used for the counter-season production in the world. However, the CO₂ consumed by crops for photosynthesis after sunrise is not supplemented and becomes chronically deficient due to the airtight structure of solar greenhouses. Vegetable crops cannot effectively utilize light resources under low-CO₂ environment, and this incapability results in reduced photosynthetic efficiency and crop yield. We used cucumber as a model plant and generated several sets of transgenic cucumber plants overexpressing individual genes, including β-carbonic anhydrase 1 (CsβCA1), β-carbonic anhydrase 4 (CsβCA4), and sedoheptulose-1,7-bisphosphatase (CsSBP); fructose-1,6-bisphosphate aldolase (CsFBA), and CsβCA1 co-expressing plants; CsβCA4, CsSBP, and CsFBA co-expressing plants (14SF). The results showed that the overexpression of CsβCA1, CsβCA4, and 14SF exhibited higher photosynthetic and biomass yield in transgenic cucumber plants under low-CO₂ environment. Further enhancements in photosynthesis and biomass yield were observed in 14SF transgenic plants under low-CO₂ environment. The net photosynthesis biomass yield and photosynthetic rate increased by 49% and 79% compared with those of the WT. However, the transgenic cucumbers of overexpressing CsFBA and CsSBP showed insignificant differences in photosynthesis and biomass yield compared with the WT under low-CO₂.environment. Photosynthesis, fluorescence parameters, and enzymatic measurements indicated that CsβCA1, CsβCA4, CsSBP, and CsFBA had cumulative effects in photosynthetic carbon assimilation under low-CO₂ environment. Co-expression of this four genes (CsβCA1, CsβCA4, CsSBP, and CsFBA) can increase the carboxylation activity of RuBisCO and promote the regeneration of RuBP. As a result, the 14SF transgenic plants showed a higher net photosynthetic rate and biomass yield even under low-CO₂environment.These findings demonstrate the possibility of cultivating crops with high photosynthetic efficiency by manipulating genes involved in the photosynthetic carbon assimilation metabolic pathway.

Evolution of Crassulacean acid metabolism in response to the environment: past, present, and future

Crassulacean acid metabolism (CAM) is a mode of photosynthesis that evolved in response to decreasing CO2 levels in the atmosphere some 20 million years ago. An elevated ratio of O2 relative to CO2 caused many plants to face increasing stress from photorespiration, a process exacerbated for plants living under high temperatures or in water-limited environments. Today, our climate is again rapidly changing and plants' ability to cope with and adapt to these novel environments is critical for their success. This review focuses on CAM plant responses to abiotic stressors likely to dominate in our changing climate: increasing CO2 levels, increasing temperatures, and greater variability in drought. Empirical studies that have assessed CAM responses are reviewed, though notably these are concentrated in relatively few CAM lineages. Other aspects of CAM biology, including the effects of abiotic stress on the light reactions and the role of leaf succulence, are also considered in the context of climate change. Finally, more recent studies using genomic techniques are discussed to link physiological changes in CAM plants with the underlying molecular mechanism. Together, the body of work reviewed suggests that CAM plants will continue to thrive in certain environments under elevated CO2. However, how CO2 interacts with other environmental factors, how those interactions affect CAM plants, and whether all CAM plants will be equally affected remain outstanding questions regarding the evolution of CAM on a changing planet.

Transcriptomic and Metabolomic Analysis Reveal Possible Molecular Mechanisms Regulating Tea Plant Growth Elicited by Chitosan Oligosaccharide

Chitosan oligosaccharide (COS) plays an important role in the growth and development of tea plants. However, responses in tea plants trigged by COS have not been thoroughly investigated. In this study, we integrated transcriptomics and metabolomics analysis to understand the mechanisms of chitosan-induced tea quality improvement and growth promotion. The combined analysis revealed an obvious link between the flourishing development of the tea plant and the presence of COS. It obviously regulated the growth and development of the tea and the metabolomic process. The chlorophyll, soluble sugar, and amino acid content in the tea leaves was increased. The phytohormones, carbohydrates, and amino acid levels were zoomed-in in both transcript and metabolomics analyses compared to the control. The expression of the genes related to phytohormones transduction, carbon fixation, and amino acid metabolism during the growth and development of tea plants were significantly upregulated. Our findings indicated that alerted transcriptomic and metabolic responses occurring with the application of COS could cause efficiency in substrates in pivotal pathways and hence, elicited plant growth.

Two major metabolic factors for an efficient NADP-malic enzyme type C4 photosynthesis

Compared to the large number of studies focused on the factors controlling C3 photosynthesis efficiency, there are relatively fewer studies of the factors controlling photosynthetic efficiency in C4 leaves. Here, we used a dynamic systems model of C4 photosynthesis based on maize (Zea mays) to identify features associated with high photosynthetic efficiency in NADP-malic enzyme (NADP-ME) type C4 photosynthesis. We found that two additional factors related to coordination between C4 shuttle metabolism and C3 metabolism are required for efficient C4 photosynthesis: (1) accumulating a high concentration of phosphoenolpyruvate through maintaining a large PGA concentration in the mesophyll cell chloroplast and (2) maintaining a suitable oxidized status in bundle sheath cell chloroplasts. These identified mechanisms are in line with the current cellular location of enzymes/proteins involved in the starch synthesis, the Calvin-Benson cycle and photosystem II of NADP-ME type C4 photosynthesis. These findings suggested potential strategies for improving C4 photosynthesis and engineering C4 rice.

Lack of leaf carbonic anhydrase activity eliminates the C4 carbon-concentrating mechanism requiring direct diffusion of CO2 into bundle sheath cells

Carbonic anhydrase (CA) performs the first enzymatic step of C₄ photosynthesis by catalysing the reversible hydration of dissolved CO₂ that diffuses into mesophyll cells from intercellular airspaces. This CA-catalysed reaction provides the bicarbonate used by phosphoenolpyruvate carboxylase to generate products that flow into the C₄ carbon-concentrating mechanism (CCM). It was previously demonstrated that the Zea mays ca1ca2 double mutant lost 97% of leaf CA activity, but there was little difference in the growth phenotype under ambient CO₂ partial pressures (pCO₂ ). We hypothesise that since CAs are among the fastest enzymes, minimal activity from a third CA, CA8, can provide the inorganic carbon needed to drive C₄ photosynthesis. We observed that removing CA8 from the maize ca1ca2 background resulted in plants that had 0.2% of wild-type leaf CA activity. These ca1ca2ca8 plants had reduced photosynthetic parameters and could only survive at elevated pCO₂ . Photosynthetic and carbon isotope analysis combined with modelling of photosynthesis and carbon isotope discrimination was used to determine if ca1ca2ca8 plants had a functional C₄ cycle or were relying on direct CO₂ diffusion to ribulose 1,5-bisphosphate carboxylase/oxygenase within bundle sheath cells. The results suggest that leaf CA activity in ca1ca2ca8 plants was not sufficient to sustain the C₄ CCM.

Limitation of C4 photosynthesis by low carbonic anhydrase activity increases with temperature but does not influence mesophyll CO2 conductance

The CO2-concentrating mechanism (CCM) in C4 plants is initiated by the uptake of bicarbonate (HCO3-) via phosphoenolpyruvate carboxylase (PEPC). Generation of HCO3- for PEPC is determined by the interaction between mesophyll CO2 conductance and the hydration of CO2 to HCO3- by carbonic anhydrase (CA). Genetic reduction of CA was previously shown not to limit C4 photosynthesis under ambient atmospheric partial pressures of CO2 (pCO2). However, CA activity varies widely across C4 species and it is unknown if there are specific environmental conditions (e.g. high temperature) where CA may limit HCO3- production for C4 photosynthesis. Additionally, CA activity has been suggested to influence mesophyll conductance, but this has not been experimentally tested. We hypothesize that CA activity can limit PEPC at high temperatures, particularly at low pCO2, but does not directly influence gm. Here we tested the influence of genetically reduced CA activity on photosynthesis and gm in the C4 plant Zea mays under a range of pCO2 and temperatures. Reduced CA activity limited HCO3- production for C4 photosynthesis at low pCO2 as temperatures increased, but did not influence mesophyll conductance. Therefore, high leaf CA activity may enhance C4 photosynthesis under high temperature when stomatal conductance restricts the availability of atmospheric CO2.

Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions

Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source-sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.

Updating the steady-state model of C4 photosynthesis

C4 plants play a key role in world agriculture. For example, C4 crops such as maize and sorghum are major contributors to food production in both developed and developing countries, and the C4 grasses sugarcane, miscanthus, and switchgrass are major plant sources of bioenergy. In the challenge to manipulate and enhance C4 photosynthesis, steady-state models of leaf photosynthesis provide an important tool for gas exchange analysis and thought experiments that can explore photosynthetic pathway changes. Here a previous C4 photosynthetic model developed by von Caemmerer and Furbank has been updated with new kinetic parameterization and temperature dependencies added. The parameterization was derived from experiments on the C4 monocot, Setaria viridis, which for the first time provides a cohesive parameterization. Mesophyll conductance and its temperature dependence have also been included, as this is an important step in the quantitative correlation between the initial slope of the CO2 response curve of CO2 assimilation and in vitro phosphoenolpyruvate carboxylase activity. Furthermore, the equations for chloroplast electron transport have been updated to include cyclic electron transport flow, and equations have been added to calculate the electron transport rate from measured CO2 assimilation rates.

Updating the steady-state model of C4 photosynthesis

C4 plants play a key role in world agriculture. For example, C4 crops such as maize and sorghum are major contributors to food production in both developed and developing countries, and the C4 grasses sugarcane, miscanthus, and switchgrass are major plant sources of bioenergy. In the challenge to manipulate and enhance C4 photosynthesis, steady-state models of leaf photosynthesis provide an important tool for gas exchange analysis and thought experiments that can explore photosynthetic pathway changes. Here a previous C4 photosynthetic model developed by von Caemmerer and Furbank has been updated with new kinetic parameterization and temperature dependencies added. The parameterization was derived from experiments on the C4 monocot, Setaria viridis, which for the first time provides a cohesive parameterization. Mesophyll conductance and its temperature dependence have also been included, as this is an important step in the quantitative correlation between the initial slope of the CO2 response curve of CO2 assimilation and in vitro phosphoenolpyruvate carboxylase activity. Furthermore, the equations for chloroplast electron transport have been updated to include cyclic electron transport flow, and equations have been added to calculate the electron transport rate from measured CO2 assimilation rates.

Modeling photosynthetic resource allocation connects physiology with evolutionary environments

The regulation of resource allocation in biological systems observed today is the cumulative result of natural selection in ancestral and recent environments. To what extent are observed resource allocation patterns in different photosynthetic types optimally adapted to current conditions, and to what extent do they reflect ancestral environments? Here, we explore these questions for C₃, C₄, and C₃–C₄ intermediate plants of the model genus Flaveria. We developed a detailed mathematical model of carbon fixation, which accounts for various environmental parameters and for energy and nitrogen partitioning across photosynthetic components. This allows us to assess environment-dependent plant physiology and performance as a function of resource allocation patterns. Models of C₄ plants optimized for conditions experienced by evolutionary ancestors perform better than models accounting for experimental growth conditions, indicating low phenotypic plasticity. Supporting this interpretation, the model predicts that C₄ species need to re-allocate more nitrogen between photosynthetic components than C₃ species to adapt to new environments. We thus hypothesize that observed resource distribution patterns in C₄ plants still reflect optimality in ancestral environments, allowing the quantitative inference of these environments from today’s plants. Our work allows us to quantify environmental effects on photosynthetic resource allocation and performance in the light of evolutionary history.

Molecular Characterization of Carbonic Anhydrase Genes in Lotus japonicus and Their Potential Roles in Symbiotic Nitrogen Fixation

Carbonic anhydrase (CA) plays a vital role in photosynthetic tissues of higher plants, whereas its non-photosynthetic role in the symbiotic root nodule was rarely characterized. In this study, 13 CA genes were identified in the model legume Lotus japonicus by comparison with Arabidopsis CA genes. Using qPCR and promoter-reporter fusion methods, three previously identified nodule-enhanced CA genes (LjαCA2, LjαCA6, and LjβCA1) have been further characterized, which exhibit different spatiotemporal expression patterns during nodule development. LjαCA2 was expressed in the central infection zone of the mature nodule, including both infected and uninfected cells. LjαCA6 was restricted to the vascular bundle of the root and nodule. As for LjβCA1, it was expressed in most cell types of nodule primordia but only in peripheral cortical cells and uninfected cells of the mature nodule. Using CRISPR/Cas9 technology, the knockout of LjβCA1 or both LjαCA2 and its homolog, LjαCA1, did not result in abnormal symbiotic phenotype compared with the wild-type plants, suggesting that LjβCA1 or LjαCA1/2 are not essential for the nitrogen fixation under normal symbiotic conditions. Nevertheless, the nodule-enhanced expression patterns and the diverse distributions in different types of cells imply their potential functions during root nodule symbiosis, such as CO₂ fixation, N assimilation, and pH regulation, which await further investigations.

Transcriptional analysis of sweet corn hybrids in response to crowding stress

Crop tolerance to crowding stress, specifically plant population density, is an important target to improve productivity in processing sweet corn. Due to limited knowledge of biological mechanisms involved in crowding stress in sweet corn, a study was conducted to 1) investigate phenotypic and transcriptional response of sweet corn hybrids under different plant densties, 2) compare the crowding stress response mechanisms between hybrids and 3) identify candidate biological mechanisms involved in crowding stress response. Yield per hectare of a tolerant hybrid (DMC21-84) increased with plant density. Yield per hectare of a sensitive hybrid (GSS2259P) declined with plant density. Transcriptional analysis found 694, 537, 359 and 483 crowding stress differentially expressed genes (DEGs) for GSS2259P at the Fruit Farm and Vegetable Farm and for DMC21-84 at the Fruit Farm and Vegetable Farm, respectively. Strong transcriptional change due to hybrid was observed. Functional analyses of DEGs involved in crowding stress also revealed that protein folding and photosynthetic processes were common response mechanisms for both hybrids. However, DEGs related to starch biosynthetic, carbohydrate metabolism, and ABA related processes were significant only for DMC21-84, suggesting the genes have closer relationship to plant productivity under stress than other processes. These results collectively provide initial insight into potential crowding stress response mechanisms in sweet corn.

Transition From Proto-Kranz-Type Photosynthesis to HCO3 - Use Photosynthesis in the Amphibious Plant Hygrophila polysperma

Hygrophila polysperma is a heterophyllous amphibious plant. The growth of H. polysperma in submerged conditions is challenging due to the low CO2 environment, increased resistance to gas diffusion, and bicarbonate ion (HCO3 -) being the dominant dissolved inorganic carbon source. The submerged leaves of H. polysperma have significantly higher rates of underwater photosynthesis compared with the terrestrial leaves. 4,4'-Diisothiocyanatostilbene-2,2'-disulfonate (DIDS), an anion exchanger protein inhibitor, and ethoxyzolamide (EZ), an inhibitor of internal carbonic anhydrase, repressed underwater photosynthesis by the submerged leaves. These results suggested that H. polysperma acclimates to the submerged condition by using HCO3 - for photosynthesis. H. polysperma transports HCO3 - into the leaf by a DIDS-sensitive HCO3 - transporter and converted to CO2 by carbonic anhydrase. Additionally, proteome analysis revealed that submerged leaves accumulated fewer proteins associated with C4 photosynthesis compared with terrestrial leaves. This finding suggested that H. polysperma is capable of C4 and C3 photosynthesis in the terrestrial and submerged leaves, respectively. The ratio of phosphoenol pyruvate carboxylase to ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in the submerged leaves was less than that in the terrestrial leaves. Upon anatomical observation, the terrestrial leaves exhibited a phenotype similar to the Kranz anatomy found among C4 plants; however, chloroplasts in the bundle sheath cells were not located adjacent to the vascular bundles, and the typical Kranz anatomy was absent in submerged leaves. These results suggest that H. polysperma performs proto-Kranz type photosynthesis in a terrestrial environment and shifts from a proto-Kranz type in terrestrial leaves to a HCO3 - use photosynthesis in the submerged environments.

Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry

The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase, an enzyme that catalyzes one of the key reactions in the C₄ pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C₄ trait much earlier. By comparing the enzyme kinetics, we show that native isoforms with few amino acid replacements have substrate K_M values similar to the non-C₄ ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C₄ isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.

A low CO2-responsive mutant of Setaria viridis reveals that reduced carbonic anhydrase limits C4 photosynthesis

In C4 species, β-carbonic anhydrase (CA), localized to the cytosol of the mesophyll cells, accelerates the interconversion of CO2 to HCO3-, the substrate used by phosphoenolpyruvate carboxylase (PEPC) in the first step of C4 photosynthesis. Here we describe the identification and characterization of low CO2-responsive mutant 1 (lcr1) isolated from an N-nitroso-N-methylurea- (NMU) treated Setaria viridis mutant population. Forward genetic investigation revealed that the mutated gene Sevir.5G247800 of lcr1 possessed a single nucleotide transition from cytosine to thymine in a β-CA gene causing an amino acid change from leucine to phenylalanine. This resulted in severe reduction in growth and photosynthesis in the mutant. Both the CO2 compensation point and carbon isotope discrimination values of the mutant were significantly increased. Growth of the mutants was stunted when grown under ambient pCO2 but recovered at elevated pCO2. Further bioinformatics analyses revealed that the mutation has led to functional changes in one of the conserved residues of the protein, situated near the catalytic site. CA transcript accumulation in the mutant was 80% lower, CA protein accumulation 30% lower, and CA activity ~98% lower compared with the wild type. Changes in the abundance of other primary C4 pathway enzymes were observed; accumulation of PEPC protein was significantly increased and accumulation of malate dehydrogenase and malic enzyme decreased. The reduction of CA protein activity and abundance in lcr1 restricts the supply of bicarbonate to PEPC, limiting C4 photosynthesis and growth. This study establishes Sevir.5G247800 as the major CA allele in Setaria for C4 photosynthesis and provides important insights into the function of CA in C4 photosynthesis that would be required to generate a rice plant with a functional C4 biochemical pathway.

Stress-Related Changes in the Expression and Activity of Plant Carbonic Anhydrases

The data on stress-related changes in the expression and activity of plant carbonic anhydrases (CAs) suggest that they are generally upregulated at moderate stress severity. This indicates probable involvement of CAs in adaptation to drought, high salinity, heat, high light, C_i deficit, and excess bicarbonate. The changes in CA levels under cold stress are less studied and generally represented by the downregulation of CAs excepting βCA2. Excess Cd²⁺ and deficit of Zn²⁺ specifically reduce CA activity and reduce its synthesis. Probable roles of βCAs in stress adaptation include stomatal closure, ROS scavenging and partial compensation for decreased mesophyll CO₂ conductance. βCAs play contrasting roles in pathogen responses, interacting with phytohormone signaling networks. Their role can be either negative or positive, probably depending on the host-pathogen system, pathogen initial titer, and levels of ·NO and ROS. It is still not clear why CAs are suppressed under severe stress levels. It should be noted, that the role of βCAs in the facilitation of CO₂ diffusion and their involvement in redox signaling or ROS detoxication are potentially antagonistic, as they are inactivated by oxidation or nitrosylation. Interestingly, some chloroplastic βCAs may be relocated to the cytoplasm under stress conditions, but the physiological meaning of this effect remains to be studied.

Retrospective analysis of biochemical limitations to photosynthesis in 49 species: C4 crops appear still adapted to pre-industrial atmospheric [CO2 ]

Leaf CO₂ uptake (A) in C₄ photosynthesis is limited by the maximum apparent rate of PEPc carboxylation (V_pmax ) at low intercellular [CO₂ ] (c_i ) with a sharp transition to a c_i -saturated rate (V_max ) due to co-limitation by ribulose-1:5-bisphosphate carboxylase/oxygenase (Rubisco) and regeneration of PEP. The response of A to c_i has been widely used to determine these two parameters. V_max and V_pmax depend on different enzymes but draw on a shared pool of leaf resources, such that resource distribution is optimized, and A maximized, when V_max and V_pmax are co-limiting. We collected published A/c_i curves in 49 C₄ species and assessed variation in photosynthetic traits between phylogenetic groups, and as a function of atmospheric [CO₂ ]. The balance of V_max -V_pmax varied among evolutionary lineages and C₄ subtypes. Operating A was strongly V_max -limited, such that re-allocation of resources from V_pmax towards V_max was predicted to improve A by 12% in C₄ crops. This would not require additional inputs but rather altered partitioning of existing leaf nutrients, resulting in increased water and nutrient-use efficiency. Optimal partitioning was achieved only in plants grown at pre-industrial atmospheric [CO₂ ], suggesting C₄ crops have not adjusted to the rapid increase in atmospheric [CO₂ ] of the past few decades.

Mesophyll CO2 conductance and leakiness are not responsive to short- and long-term soil water limitations in the C4 plant Sorghum bicolor

Breeding economically important C₄ crops for enhanced whole-plant water-use efficiency (WUE_plant ) is needed for sustainable agriculture. WUE_plant is a complex trait and an efficient phenotyping method that reports on components of WUE_plant , such as intrinsic water-use efficiency (WUE_i , the rate of leaf CO₂ assimilation relative to water loss via stomatal conductance), is needed. In C₄ plants, theoretical models suggest that leaf carbon isotope composition (δ¹³ C), when the efficiency of the CO₂ -concentrating mechanism (leakiness, ϕ) remains constant, can be used to screen for WUE_i . The limited information about how ϕ responds to water limitations confines the application of δ¹³ C for WUE_i screening of C₄ crops. The current research aimed to test the response of ϕ to short- or long-term moderate water limitations, and the relationship of δ¹³ C with WUE_i and WUE_plant , by addressing potential mesophyll CO₂ conductance (g_m ) and biochemical limitations in the C₄ plant Sorghum bicolor. We demonstrate that g_m and ϕ are not responsive to short- or long-term water limitations. Additionally, δ¹³ C was not correlated with gas-exchange estimates of WUE_i under short- and long-term water limitations, but showed a significant negative relationship with WUE_plant . The observed association between the δ¹³ C and WUE_plant suggests an intrinsic link of δ¹³ C with WUE_i in this C₄ plant, and can potentially be used as a screening tool for WUE_plant in sorghum.

Functional redundancy and divergence of β-carbonic anhydrases in Physcomitrella patens

β-carbonic anhydrases, which function in regulating plant growth, C/N status, and stomata number, showed functional redundancy and divergence in Physcomitrella patens. Carbonic anhydrases (CAs) catalyze the interconversion of CO₂ and HCO₃^-. Plants have three evolutionarily unrelated CA families: α-, β-, and γ-CAs. βCAs are abundant in plants and are involved in CO₂ assimilation, stress responses, and stomata formation. Recent studies of βCAs have mainly examined C₃ or C₄ plants, whereas their functions in non-vascular plants are mostly unknown. In this study, phylogenetic analysis revealed that the evolution of βCAs were conserved between subaerial green algae and bryophytes after terrestrialization event, and βCAs from some cyanobacteria might begin evolving for the adaptation of terrestrial environment/habitat. In addition, we investigated the physiological roles of βCAs in the basal land plant Physcomitrella patens. High PpβCA expression levels in different tissues suggest that PpβCAs play important roles in development in P. patens. Plants treated with 1-10 mM NaHCO₃ had higher fresh and dry weight, PpβCA expression, total CA activity, and photosynthetic yield (Fv/Fm) compared with water-treated plants. However, treatment with 10 mM NaHCO₃ influenced the C/N status. Further study of six Ppβca single-gene mutants revealed that PpβCAs have functional redundancy and divergence in regulating the C/N ratio of plants and stomatal formation. This study provides new insight into the physiological roles of βCAs in basal land plants.

Regulation and Evolution of C4 Photosynthesis

C₄ photosynthesis evolved multiple times independently from ancestral C₃ photosynthesis in a broad range of flowering land plant families and in both monocots and dicots. The evolution of C₄ photosynthesis entails the recruitment of enzyme activities that are not involved in photosynthetic carbon fixation in C₃ plants to photosynthesis. This requires a different regulation of gene expression as well as a different regulation of enzyme activities in comparison to the C₃ context. Further, C₄ photosynthesis relies on a distinct leaf anatomy that differs from that of C₃, requiring a differential regulation of leaf development in C₄. We summarize recent progress in the understanding of C₄-specific features in evolution and metabolic regulation in the context of C₄ photosynthesis.

Emerging roles for carbonic anhydrase in mesophyll conductance and photosynthesis

Carbonic anhydrase (CA) is an abundant protein in most photosynthesizing organisms and higher plants. This review paper considers the physiological importance of the more abundant CA isoforms in photosynthesis, through their effects on CO₂ diffusion and other processes in photosynthetic organisms. In plants, CA has multiple isoforms in three different families (α, β and γ) and is mainly known to catalyze the CO₂↔HCO3- equilibrium. This reversible conversion has a clear role in photosynthesis, primarily through sustaining the CO₂ concentration at the site of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Despite showing the same major reaction mechanism, the three main CA families are evolutionarily distinct. For different CA isoforms, cellular localization and total gene expression as a function of developmental stage are predicted to determine the role of each family in relation to the net assimilation rate. Reaction-diffusion modeling and observational evidence support a role for CA activity in reducing resistance to CO₂ diffusion inside mesophyll cells by facilitating CO₂ transfer in both gas and liquid phases. In addition, physical and/or biochemical interactions between CAs and other membrane-bound compartments, for example aquaporins, are suggested to trigger a CO₂ -sensing response by stomatal movement. In response to environmental stresses, changes in the expression level of CAs and/or stimulated deactivation of CAs may correspond with lower photosynthetic capacity. We suggest that further studies should focus on the dynamics of the relationship between the activity of CAs (with different subcellular localization, abundance and gene expression) and limitations due to CO₂ diffusivity through the mesophyll and supply of CO₂ to photosynthetic reactions.

Translocation of Drought-Responsive Proteins from the Chloroplasts

Some chloroplast proteins are known to serve as messengers to transmit retrograde signals from chloroplasts to the nuclei in response to environmental stresses. However, whether particular chloroplast proteins respond to drought stress and serve as messengers for retrograde signal transduction are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) to monitor the proteomic changes in tobacco (Nicotiana benthamiana) treated with drought stress/re-watering. We identified 3936 and 1087 differentially accumulated total leaf and chloroplast proteins, respectively, which were grouped into 16 categories. Among these, one particular category of proteins, that includes carbonic anhydrase 1 (CA1), exhibited a great decline in chloroplasts, but a remarkable increase in leaves under drought stress. The subcellular localizations of CA1 proteins from moss (Physcomitrella patens), Arabidopsis thaliana and rice (Oryza sativa) in P. patens protoplasts consistently showed that CA1 proteins gradually diminished within chloroplasts but increasingly accumulated in the cytosol under osmotic stress treatment, suggesting that they could be translocated from chloroplasts to the cytosol and act as a signal messenger from the chloroplast. Our results thus highlight the potential importance of chloroplast proteins in retrograde signaling pathways and provide a set of candidate proteins for further research.

Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands

Little is known on maize germplasm adapted to the African highland agro-ecologies. In this study, we analyzed high-density genotyping by sequencing (GBS) data of 298 African highland adapted maize inbred lines to (i) assess the extent of genetic purity, genetic relatedness, and population structure, and (ii) identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to highland environments. Nearly 91% of the pairs of inbred lines differed by 30-36% of the scored alleles, but only 32% of the pairs of the inbred lines had relative kinship coefficient <0.050, which suggests the presence of substantial redundancy in allelic composition that may be due to repeated use of fewer genetic backgrounds (source germplasm) during line development. Results from different genetic relatedness and population structure analyses revealed three different groups, which generally agrees with pedigree information and breeding history, but less so by heterotic groups and endosperm modification. We identified 944 single nucleotide polymorphic (SNP) markers that fell within 22 selective sweeps that harbored 265 protein-coding candidate genes of which some of the candidate genes had known functions. Details of the candidate genes with known functions and differences in nucleotide diversity among groups predicted based on multivariate methods have been discussed.

Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album

Plants with facultative crassulacean acid metabolism (CAM) maximize performance through utilizing C3 or C4 photosynthesis under ideal conditions while temporally switching to CAM under water stress (drought). While genome-scale analyses of constitutive CAM plants suggest that time of day networks are shifted, or phased to the evening compared to C3, little is known for how the shift from C3 to CAM networks is modulated in drought induced CAM. Here we generate a draft genome for the drought-induced CAM-cycling species Sedum album. Through parallel sampling in well-watered (C3) and drought (CAM) conditions, we uncover a massive rewiring of time of day expression and a CAM and stress-specific network. The core circadian genes are expanded in S. album and under CAM induction, core clock genes either change phase or amplitude. While the core clock cis-elements are conserved in S. album, we uncover a set of novel CAM and stress specific cis-elements consistent with our finding of rewired co-expression networks. We identified shared elements between constitutive CAM and CAM-cycling species and expression patterns unique to CAM-cycling S. album. Together these results demonstrate that drought induced CAM-cycling photosynthesis evolved through the mobilization of a stress-specific, time of day network, and not solely the phasing of existing C3 networks. These results will inform efforts to engineer water use efficiency into crop plants for growth on marginal land.

Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO2

BACKGROUND

Carbonic anhydrase (CA) catalyzes the hydration of CO2 in the first biochemical step of C4 photosynthesis, and has been considered a potentially rate-limiting step when CO2 availability within a leaf is low. Previous work in Zea mays (maize) with a double knockout of the two highest-expressed β-CA genes, CA1 and CA2, reduced total leaf CA activity to less than 3% of wild-type. Surprisingly, this did not limit photosynthesis in maize at ambient or higher CO2concentrations. However, the ca1ca2 mutants exhibited reduced rates of photosynthesis at sub-ambient CO2, and accumulated less biomass when grown under sub-ambient CO2 (9.2 Pa). To further clarify the importance of CA for C4 photosynthesis, we assessed gene expression changes in wild-type, ca1 and ca1ca2 mutants in response to changes in pCO2 from 920 to 9.2 Pa.

RESULTS

Leaf samples from each genotype were collected for RNA-seq analysis at high CO2 and at two time points after the low CO2 transition, in order to identify early and longer-term responses to CO2 deprivation. Despite the existence of multiple isoforms of CA, no other CA genes were upregulated in CA mutants. Although photosynthetic genes were downregulated in response to low CO2, differential expression was not observed between genotypes. However, multiple indicators of carbon starvation were present in the mutants, including amino acid synthesis, carbohydrate metabolism, and sugar signaling. In particular, multiple genes previously implicated in low carbon stress such as asparagine synthetase, amino acid transporters, trehalose-6-phosphate synthase, as well as many transcription factors, were strongly upregulated. Furthermore, genes in the CO2 stomatal signaling pathway were differentially expressed in the CA mutants under low CO2.

CONCLUSIONS

Using a transcriptomic approach, we showed that carbonic anhydrase mutants do not compensate for the lack of CA activity by upregulating other CA or photosynthetic genes, but rather experienced extreme carbon stress when grown under low CO2. Our results also support a role for CA in the CO2 stomatal signaling pathway. This study provides insight into the importance of CA for C4 photosynthesis and its role in stomatal signaling.

The molecular evolution of C4 photosynthesis: opportunities for understanding and improving the world's most productive plants

C4 photosynthesis is a convergent evolutionary trait that enhances photosynthetic efficiency in a variety of environmental conditions. It has evolved repeatedly following a fall in atmospheric CO2 concentration such that there is up to a 30 million year difference in the amount of time that natural selection has had to improve C4 function between the oldest and youngest C4 lineages. This large difference in time, coupled with the phylogenetic distance between lineages, has resulted in a large disparity in anatomy, physiology, and biochemistry between extant C4 species. This review summarizes the myriad of molecular sequence changes that have been linked to the evolution of C4 photosynthesis. These range from single nucleotide changes to duplication of entire genes, and provide a roadmap for how natural selection has adapted enzymes and pathways for enhanced C4 function. Finally, this review discusses how this molecular diversity can provide opportunities for understanding and improving photosynthesis for multiple important C4 food, feed, and bioenergy crops.

Estimating Mesophyll Conductance from Measurements of C18OO Photosynthetic Discrimination and Carbonic Anhydrase Activity

Carbonic anhydrase (CA) activity in leaves catalyzes the ¹⁸O exchange between CO₂ and water during photosynthesis. This feature has been used to estimate the mesophyll conductance to CO₂ (g _m) from measurements of online C¹⁸OO photosynthetic discrimination (∆¹⁸O). Based on CA assays on leaf extracts, it has been argued that CO₂ in mesophyll cells should be in isotopic equilibrium with water in most C₃ species as well as many C₄ dicot species. However, this seems incompatible with ∆¹⁸O data that would indicate a much lower degree of equilibration, especially in C₄ plants under high light intensity. This apparent contradiction is resolved here using a new model of C₃ and C₄ photosynthetic discrimination that includes competition between CO₂ hydration and carboxylation and the contribution of respiratory fluxes. This new modeling framework is used to revisit previously published data sets on C₃ and C₄ species, including CA-deficient plants. We conclude that (1) newly ∆¹⁸O-derived g _m values are usually close but significantly higher (typically 20% and up to 50%) than those derived assuming full equilibration and (2) despite the uncertainty associated with the respiration rate in light, or the water isotope gradient between mesophyll and bundle sheath cells, robust estimates of ∆¹⁸O-derived g _m can be achieved in both C₃ and C₄ plants.

Characterization of maize leaf pyruvate orthophosphate dikinase using high throughput sequencing

In C₄ photosynthesis, pyruvate orthophosphate dikinase (PPDK) catalyzes the regeneration of phosphoenolpyruvate in the carbon shuttle pathway. Although the biochemical function of PPDK in maize is well characterized, a genetic analysis of PPDK has not been reported. In this study, we use the maize transposable elements Mutator and Ds to generate multiple mutant alleles of PPDK. Loss-of-function mutants are seedling lethal, even when plants were grown under 2% CO₂ , and they show very low capacity for CO₂ assimilation, indicating C₄ photosynthesis is essential in maize. Using RNA-seq and GC-MS technologies, we examined the transcriptional and metabolic responses to a deficiency in PPDK activity. These results indicate loss of PPDK results in downregulation of gene expression of enzymes of the C₄ cycle, the Calvin cycle, and components of photochemistry. Furthermore, the loss of PPDK did not change Kranz anatomy, indicating that this metabolic defect in the C₄ cycle did not impinge on the morphological differentiation of C₄ characters. However, sugar metabolism and nitrogen utilization were altered in the mutants. An interaction between light intensity and genotype was also detected from transcriptome profiling, suggesting altered transcriptional and metabolic responses to environmental and endogenous signals in the PPDK mutants.

Carbonic Anhydrase Mutants in Zea mays Have Altered Stomatal Responses to Environmental Signals

Stomata regulate transpirational water loss and CO2 uptake for photosynthesis in response to changing environmental conditions. Research investigating stomatal movement has mostly been conducted in C3 eudicot species, which have very different CO2 requirements for photosynthesis relative to C4 grasses. Carbonic anhydrase (CA) catalyzes the hydration of CO2, and its activity has been linked to stomatal aperture regulation in eudicots. The number of Ca genes and their evolutionary history differ between monocots and dicots, and many questions remain unanswered about potential neofunctionalization and subfunctionalization of grass Ca paralogs and their roles in photosynthesis and stomatal conductance. To investigate the roles of different Ca genes in maize (Zea mays), we examined stomatal responses in ca1 and ca2 single mutants as well as a ca1ca2 double mutant. The ca1 and ca2 single mutants had 10% and 87% of the CA activity exhibited by the wild type, respectively, while ca1ca2 had less than 5% of wild-type CA activity. The ca mutants had higher stomatal conductance than the wild type and slower stomatal closure in response to increases in CO2 partial pressure. Contrary to previous reports in eudicots, ca mutants showed slowed stomatal closure in response to the light-dark transition and did not show differences in stomatal density compared with the wild type. These results implicate CA-mediated signaling in the control of stomatal movement but not stomatal development. Drought experiments with ca1ca2 mutant plants suggest a role for CA in water-use efficiency and reveal that Z. mays is not optimized for water-use efficiency under well-watered conditions.

Mesophyll conductance in Zea mays responds transiently to CO2 availability: implications for transpiration efficiency in C4 crops

Mesophyll conductance (g_m ) describes the movement of CO₂ from the intercellular air spaces below the stomata to the site of initial carboxylation in the mesophyll. In contrast with C₃ -g_m , little is currently known about the intraspecific variation in C₄ -g_m or its responsiveness to environmental stimuli. To address these questions, g_m was measured on five maize (Zea mays) lines in response to CO₂ , employing three different estimates of g_m . Each of the methods indicated a significant response of g_m to CO₂ . Estimates of g_m were similar between methods at ambient and higher CO₂ , but diverged significantly at low partial pressures of CO₂ . These differences are probably driven by incomplete chemical and isotopic equilibrium between CO₂ and bicarbonate under these conditions. Carbonic anhydrase and phosphoenolpyruvate carboxylase in vitro activity varied significantly despite similar values of g_m and leaf anatomical traits. These results provide strong support for a CO₂ response of g_m in Z. mays, and indicate that g_m in maize is probably driven by anatomical constraints rather than by biochemical limitations. The CO₂ response of g_m indicates a potential role for facilitated diffusion in C₄ -g_m . These results also suggest that water-use efficiency could be enhanced in C₄ species by targeting g_m .

Carbonic Anhydrases Function in Anther Cell Differentiation Downstream of the Receptor-Like Kinase EMS1

Plants extensively employ leucine-rich repeat receptor-like kinases (LRR-RLKs), the largest family of RLKs, to control a wide range of growth and developmental processes as well as defense responses. To date, only a few direct downstream effectors for LRR-RLKs have been identified. We previously showed that the LRR-RLK EMS1 (EXCESS MICROSPOROCYTES1) and its ligand TPD1 (TAPETUM DETERMINANT1) are required for the differentiation of somatic tapetal cells and reproductive microsporocytes during early anther development in Arabidopsis thaliana Here, we report the identification of β-carbonic anhydrases (βCAs) as the direct downstream targets of EMS1. EMS1 biochemically interacts with βCA proteins. Loss of function of βCA genes caused defective tapetal cell differentiation, while overexpression of βCA1 led to the formation of extra tapetal cells. EMS1 phosphorylates βCA1 at four sites, resulting in increased βCA1 activity. Furthermore, phosphorylation-blocking mutations impaired the function of βCA1 in tapetal cell differentiation; however, a phosphorylation mimic mutation promoted the formation of tapetal cells. βCAs are also involved in pH regulation in tapetal cells. Our findings highlight the role of βCA in controlling cell differentiation and provide insights into the posttranslational modification of carbonic anhydrases via receptor-like kinase-mediated phosphorylation.

Real-Time Determination of Photosynthesis, Transpiration, Water-Use Efficiency and Gene Expression of Two Sorghum bicolor (Moench) Genotypes Subjected to Dry-Down

Plant growth and productivity are strongly affected by limited water availability in drought prone environments. The current climate change scenario, characterized by long periods without precipitations followed by short but intense rainfall, forces plants to implement different strategies to cope with drought stress. Understanding how plants use water during periods of limited water availability is of primary importance to identify and select the best adapted genotypes to a certain environment. Two sorghum genotypes IS22330 and IS20351, previously characterized as drought tolerant and drought sensitive genotypes, were subjected to progressive drought stress through a dry-down experiment. A whole-canopy multi-chamber system was used to determine the in vivo water use efficiency (WUE). This system records whole-canopy net photosynthetic and transpiration rate of 12 chambers five times per hour allowing the calculation of whole-canopy instantaneous WUE daily trends. Daily net photosynthesis and transpiration rates were coupled with gene expression dynamics of five drought related genes. Under drought stress, the tolerant genotype increased expression level for all the genes analyzed, whilst the opposite trend was highlighted by the drought sensitive genotype. Correlation between gene expression dynamics and gas exchange measurements allowed to identify three genes as valuable candidate to assess drought tolerance in sorghum.

Temperature response of mesophyll conductance in three C4 species calculated with two methods: 18 O discrimination and in vitro Vpmax

Mesophyll conductance (g_m ) is an important factor limiting rates of C₃ photosynthesis. However, its role in C₄ photosynthesis is poorly understood because it has been historically difficult to estimate. We use two methods to derive the temperature responses of g_m in C₄ species. The first (Δ¹⁸ O) combines measurements of gas exchange with models and measurements of ¹⁸ O discrimination. The second method (in vitro V_pmax ) derives g_m by retrofitting models of C₄ photosynthesis and ¹³ C discrimination with gas exchange, kinetic constants and in vitro V_pmax measurements. The two methods produced similar g_m for Setaria viridis and Zea mays. Additionally, we present the first temperature response (10-40°C) of C₄ g_m in S. viridis, Z. mays and Miscanthus × giganteus. Values for g_m at 25°C ranged from 2.90 to 7.85 μmol m^-2  s^-1  Pa^-1 . Our study demonstrated that: the two described methods are suitable to calculate g_m in C₄ species; g_m values in C₄ are similar to high-end values reported for C₃ species; and g_m increases with temperature analogous to reports for C₃ species and the response is species specific. These results improve our mechanistic understanding of C₄ photosynthesis.

Absence of OsβCA1 causes a CO2 deficit and affects leaf photosynthesis and the stomatal response to CO2 in rice

Plants always adjust the opening of stomatal pores to adapt to the environment, for example CO₂ concentration ([CO₂ ]), humidity and temperature. Low [CO₂ ] will trigger the opening of stomatal pores to absorb extra CO₂ . However, little is known about how CO₂ supply affects the carbon fixation and opening of stomatal pores in rice. Here, a chloroplast-located gene coding for β-carbonic anhydrase (βCA) was found to be involved in carbon assimilation and the CO₂ -mediated stomatal pore response in rice. OsβCA1 was constitutively expressed in all tissues and its transcripts were induced by high [CO₂ ] in leaves. Both T-DNA mutant and RNA interference lines showed phenotypes of lower biomass and CA activities. Knockout of OsβCA1 obviously decreased photosynthetic capacity, as demonstrated by the increased CO₂ compensation point and decreased light saturation point in the mutant, while knockout increased the opening ratio of stomatal pores and the rate of water loss. Moreover, the mutant showed a delayed response to low [CO₂ ], and stomatal pores could not be closed to the same degree as those of wild type even though the stomatal pores could rapidly respond to high [CO₂ ]. Genome-wide gene expression analysis via RNA sequencing demonstrated that the transcript abundance of genes related to Rubisco, photosystem compounds and the opening of stomatal pores was globally upregulated in the mutant. Taken together, the inadequate CO₂ supply caused by the absence of OsβCA1 reduces photosynthetic efficiency, triggers the opening of stomatal pores and finally decreases their sensitivity to CO₂ fluctuation.

The multifunctional face of plant carbonic anhydrase

Although most studies on the ubiquitous enzyme carbonic anhydrase (CA) have indicated its significant role in plants to facilitate the diffusion of CO₂ to the site of inorganic carbon fixation, it is becoming increasingly likely that carbonic anhydrase isoforms also have diverse unexplored functions in plant cells. This review lays emphasis on additional roles of CA associated with many physiological, biochemical and structural changes in plant metabolism. The presented findings have revealed essential functions of CA isoforms in plant adjustment to both abiotic and biotic agents and developmental stimuli. However, sometimes it is difficult to separate the non-photosynthetic from the photosynthetic-related role of CAs during post-stress impaired metabolism, and the preventive CA outcome might be due to the effect of these enzymes on improvement of photosynthetic capacity. Finally, taking into account the experimental evidence, the direct and indirect functional roles of CAs in mitigating negative effects of environmental conditions are presented.

Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles

Carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the interconversion of CO2 and HCO3- and are ubiquitous in nature. Higher plants contain three evolutionarily distinct CA families, αCAs, βCAs, and γCAs, where each family is represented by multiple isoforms in all species. Alternative splicing of CA transcripts appears common; consequently, the number of functional CA isoforms in a species may exceed the number of genes. CAs are expressed in numerous plant tissues and in different cellular locations. The most prevalent CAs are those in the chloroplast, cytosol, and mitochondria. This diversity in location is paralleled in the many physiological and biochemical roles that CAs play in plants. In this review, the number and types of CAs in C3, C4, and crassulacean acid metabolism (CAM) plants are considered, and the roles of the α and γCAs are briefly discussed. The remainder of the review focuses on plant βCAs and includes the identification of homologs between species using phylogenetic approaches, a consideration of the inter- and intracellular localization of the proteins, along with the evidence for alternative splice forms. Current understanding of βCA tissue-specific expression patterns and what controls them are reviewed, and the physiological roles for which βCAs have been implicated are presented.

C4 photosynthesis in C3 rice: a theoretical analysis of biochemical and anatomical factors

Engineering C₄ photosynthesis into rice has been considered a promising strategy to increase photosynthesis and yield. A question that remains to be answered is whether expressing a C₄ metabolic cycle into a C₃ leaf structure and without removing the C₃ background metabolism improves photosynthetic efficiency. To explore this question, we developed a 3D reaction diffusion model of bundle-sheath and connected mesophyll cells in a C₃ rice leaf. Our results show that integrating a C₄ metabolic pathway into rice leaves with a C₃ metabolism and mesophyll structure may lead to an improved photosynthesis under current ambient CO₂ concentration. We analysed a number of physiological factors that influence the CO₂ uptake rate, which include the chloroplast surface area exposed to intercellular air space, bundle-sheath cell wall thickness, bundle-sheath chloroplast envelope permeability, Rubisco concentration and the energy partitioning between C₃ and C₄ cycles. Among these, partitioning of energy between C₃ and C₄ photosynthesis and the partitioning of Rubisco between mesophyll and bundle-sheath cells are decisive factors controlling photosynthetic efficiency in an engineered C₃ -C₄ leaf. The implications of the results for the sequence of C₄ evolution are also discussed.

Cross species selection scans identify components of C4 photosynthesis in the grasses

C4 photosynthesis is perhaps one of the best examples of convergent adaptive evolution with over 25 independent origins in the grasses (Poaceae) alone. The availability of high quality grass genome sequences presents new opportunities to explore the mechanisms underlying this complex trait using evolutionary biology-based approaches. In this study, we performed genome-wide cross-species selection scans in C4 lineages to facilitate discovery of C4 genes. The study was enabled by the well conserved collinearity of grass genomes and the recently sequenced genome of a C3 panicoid grass, Dichanthelium oligosanthes This method, in contrast to previous studies, does not rely on any a priori knowledge of the genes that contribute to biochemical or anatomical innovations associated with C4 photosynthesis. We identified a list of 88 candidate genes that include both known and potentially novel components of the C4 pathway. This set includes the carbon shuttle enzymes pyruvate, phosphate dikinase, phosphoenolpyruvate carboxylase and NADP malic enzyme as well as several predicted transporter proteins that likely play an essential role in promoting the flux of metabolites between the bundle sheath and mesophyll cells. Importantly, this approach demonstrates the application of fundamental molecular evolution principles to dissect the genetic basis of a complex photosynthetic adaptation in plants. Furthermore, we demonstrate how the output of the selection scans can be combined with expression data to provide additional power to prioritize candidate gene lists and suggest novel opportunities for pathway engineering.

Effects of reduced carbonic anhydrase activity on CO2 assimilation rates in Setaria viridis: a transgenic analysis

In C4 species, the major β-carbonic anhydrase (β-CA) localized in the mesophyll cytosol catalyses the hydration of CO2 to HCO3-, which phosphoenolpyruvate carboxylase uses in the first step of C4 photosynthesis. To address the role of CA in C4 photosynthesis, we generated transgenic Setaria viridis depleted in β-CA. Independent lines were identified with as little as 13% of wild-type CA. No photosynthetic defect was observed in the transformed lines at ambient CO2 partial pressure (pCO2). At low pCO2, a strong correlation between CO2 assimilation rates and CA hydration rates was observed. C18O16O isotope discrimination was used to estimate the mesophyll conductance to CO2 diffusion from the intercellular air space to the mesophyll cytosol (gm) in control plants, which allowed us to calculate CA activities in the mesophyll cytosol (Cm). This revealed a strong relationship between the initial slope of the response of the CO2 assimilation rate to cytosolic pCO2 (ACm) and cytosolic CA activity. However, the relationship between the initial slope of the response of CO2 assimilation to intercellular pCO2 (ACi) and cytosolic CA activity was curvilinear. This indicated that in S. viridis, mesophyll conductance may be a contributing limiting factor alongside CA activity to CO2 assimilation rates at low pCO2.