Plastid transport and metabolism of C3 and C4 plants--comparative analysis and possible biotechnological exploitation

Fast dehydration reduces bundle sheath conductance in C4 maize and sorghum

In the face of anthropogenic warming, drought poses an escalating threat to food production. C4 plants offer promise in addressing this threat. C4 leaves operate a biochemical CO2 concentrating mechanism that exchanges metabolites between two partially isolated compartments (mesophyll and bundle sheath), which confers high-productivity potential in hot climates boosting water use efficiency. However, when C4 leaves experience dehydration, photosynthesis plummets. This paper explores the physiological mechanisms behind this decline. In a fast dehydration experiment, we measured the fluxes and isotopic composition of water and CO2 in the gas exchanged by leaves, and we interpreted results using a novel biochemical model and analysis of elasticity. Our findings show that, while CO2 supply to the mesophyll and to the bundle sheath persisted during dehydration, there was a decrease in CO2 conductance at the bundle sheath-mesophyll interface. We interpret this as causing a slowdown of intercellular metabolite exchange - an essential feature of C4 photosynthesis. This would impede the supply of reducing power to the bundle sheath, leading to phosphoglycerate accumulation and feedback inhibition of Rubisco carboxylation. The interplay between this rapid sensitivity and the effectiveness of coping strategies that C4 plants deploy may be an overlooked driver of their competitive performance.

Chloroplast NADH dehydrogenase-like complex-mediated cyclic electron flow is the main electron transport route in C4 bundle sheath cells

The superior productivity of C4 plants is achieved via a metabolic C4 cycle which acts as a CO2 pump across mesophyll and bundle sheath (BS) cells and requires an additional input of energy in the form of ATP. The importance of chloroplast NADH dehydrogenase-like complex (NDH) operating cyclic electron flow (CEF) around Photosystem I (PSI) for C4 photosynthesis has been shown in reverse genetics studies but the contribution of CEF and NDH to cell-level electron fluxes remained unknown. We have created gene-edited Setaria viridis with null ndhO alleles lacking functional NDH and developed methods for quantification of electron flow through NDH in BS and mesophyll cells. We show that CEF accounts for 84% of electrons reducing PSI in BS cells and most of those electrons are delivered through NDH while the contribution of the complex to electron transport in mesophyll cells is minimal. A decreased leaf CO2 assimilation rate and growth of plants lacking NDH cannot be rescued by supplying additional CO2. Our results indicate that NDH-mediated CEF is the primary electron transport route in BS chloroplasts highlighting the essential role of NDH in generating ATP required for CO2 fixation by the C3 cycle in BS cells.

Understanding grain development in the Poaceae family by comparing conserved and distinctive pathways through omics studies in wheat and maize

The Poaceae family, commonly known as the grass family, encompasses a diverse group of crops that play an essential role in providing food, fodder, biofuels, environmental conservation, and cultural value for both human and environmental well-being. Crops in Poaceae family are deeply intertwined with human societies, economies, and ecosystems, making it one of the most significant plant families in the world. As the major reservoirs of essential nutrients, seed grain of these crops has garnered substantial attention from researchers. Understanding the molecular and genetic processes that controls seed formation, development and maturation can provide insights for improving crop yield, nutritional quality, and stress tolerance. The diversity in photosynthetic pathways between C3 and C4 plants introduces intriguing variations in their physiological and biochemical processes, potentially affecting seed development. In this review, we explore recent studies performed with omics technologies, such as genomics, transcriptomics, proteomics and metabolomics that shed light on the mechanisms underlying seed development in wheat and maize, as representatives of C3 and C4 plants respectively, providing insights into their unique adaptations and strategies for reproductive success.

Transcriptional and metabolic profiling of sulfur starvation response in two monocots

BACKGROUND

Sulfur (S) is a mineral nutrient essential for plant growth and development, which is incorporated into diverse molecules fundamental for primary and secondary metabolism, plant defense, signaling, and maintaining cellular homeostasis. Although, S starvation response is well documented in the dicot model Arabidopsis thaliana, it is not clear if the same transcriptional networks control the response also in the monocots.

RESULTS

We performed series of physiological, expression, and metabolite analyses in two model monocot species, one representing the C3 plants, Oryza sativa cv. kitaake, and second representing the C4 plants, Setaria viridis. Our comprehensive transcriptomic analysis revealed twice as many differentially expressed genes (DEGs) in S. viridis than in O. sativa under S-deficiency, consistent with a greater loss of sulfur and S-containing metabolites under these conditions. Surprisingly, most of the DEGs and enriched gene ontology terms were species-specific, with an intersect of only 58 common DEGs. The transcriptional networks were different in roots and shoots of both species, in particular no genes were down-regulated by S-deficiency in the roots of both species.

CONCLUSIONS

Our analysis shows that S-deficiency seems to have different physiological consequences in the two monocot species and their nutrient homeostasis might be under distinct control mechanisms.

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.

13CO2 labeling kinetics in maize reveal impaired efficiency of C4 photosynthesis under low irradiance

C4 photosynthesis allows faster photosynthetic rates and higher water and nitrogen use efficiency than C3 photosynthesis, but at the cost of lower quantum yield due to the energy requirement of its biochemical carbon concentration mechanism. It has also been suspected that its operation may be impaired in low irradiance. To investigate fluxes under moderate and low irradiance, maize (Zea mays) was grown at 550 µmol photons m-2 s-l and 13CO2 pulse-labeling was performed at growth irradiance or several hours after transfer to 160 µmol photons m-2 s-1. Analysis by liquid chromatography/tandem mass spectrometry or gas chromatography/mass spectrometry provided information about pool size and labeling kinetics for 32 metabolites and allowed estimation of flux at many steps in C4 photosynthesis. The results highlighted several sources of inefficiency in low light. These included excess flux at phosphoenolpyruvate carboxylase, restriction of decarboxylation by NADP-malic enzyme, and a shift to increased CO2 incorporation into aspartate, less effective use of metabolite pools to drive intercellular shuttles, and higher relative and absolute rates of photorespiration. The latter provides evidence for a lower bundle sheath CO2 concentration in low irradiance, implying that operation of the CO2 concentration mechanism is impaired in this condition. The analyses also revealed rapid exchange of carbon between the Calvin-Benson cycle and the CO2-concentration shuttle, which allows rapid adjustment of the balance between CO2 concentration and assimilation, and accumulation of large amounts of photorespiratory intermediates in low light that provides a major carbon reservoir to build up C4 metabolite pools when irradiance increases.

Metabolic profiles in C3, C3-C4 intermediate, C4-like, and C4 species in the genus Flaveria

C4 photosynthesis concentrates CO2 around Rubisco in the bundle sheath, favouring carboxylation over oxygenation and decreasing photorespiration. This complex trait evolved independently in >60 angiosperm lineages. Its evolution can be investigated in genera such as Flaveria (Asteraceae) that contain species representing intermediate stages between C3 and C4 photosynthesis. Previous studies have indicated that the first major change in metabolism probably involved relocation of glycine decarboxylase and photorespiratory CO2 release to the bundle sheath and establishment of intercellular shuttles to maintain nitrogen stoichiometry. This was followed by selection for a CO2-concentrating cycle between phosphoenolpyruvate carboxylase in the mesophyll and decarboxylases in the bundle sheath, and relocation of Rubisco to the latter. We have profiled 52 metabolites in nine Flaveria species and analysed 13CO2 labelling patterns for four species. Our results point to operation of multiple shuttles, including movement of aspartate in C3-C4 intermediates and a switch towards a malate/pyruvate shuttle in C4-like species. The malate/pyruvate shuttle increases from C4-like to complete C4 species, accompanied by a rise in ancillary organic acid pools. Our findings support current models and uncover further modifications of metabolism along the evolutionary path to C4 photosynthesis in the genus Flaveria.

High light and temperature reduce photosynthetic efficiency through different mechanisms in the C4 model Setaria viridis

C₄ plants frequently experience high light and high temperature conditions in the field, which reduce growth and yield. However, the mechanisms underlying these stress responses in C₄ plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C₄ model plant Setaria viridis responded to a four-hour high light or high temperature treatment at photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in high light or high temperature treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to high light and high temperature. We provide a systematic analysis of high light and high temperature responses in S. viridis, reveal different acclimation strategies to these two stresses in C₄ plants, discover unique light/temperature responses in C₄ plants in comparison to C₃ plants, and identify potential targets to improve abiotic stress tolerance in C₄ crops.

Challenges and Approaches to Crop Improvement Through C3-to-C4 Engineering

With a rapidly growing world population and dwindling natural resources, we are now facing the enormous challenge of increasing crop yields while simultaneously improving the efficiency of resource utilization. Introduction of C4 photosynthesis into C3 crops is widely accepted as a key strategy to meet this challenge because C4 plants are more efficient than C3 plants in photosynthesis and resource usage, particularly in hot climates, where the potential for productivity is high. Lending support to the feasibility of this C3-to-C4 engineering, evidence indicates that C4 photosynthesis has evolved from C3 photosynthesis in multiple lineages. Nevertheless, C3-to-C4 engineering is not an easy task, as several features essential to C4 photosynthesis must be introduced into C3 plants. One such feature is the spatial separation of the two phases of photosynthesis (CO₂ fixation and carbohydrate synthesis) into the mesophyll and bundle sheath cells, respectively. Another feature is the Kranz anatomy, characterized by a close association between the mesophyll and bundle sheath (BS) cells (1:1 ratio). These anatomical features, along with a C4-specific carbon fixation enzyme (PEPC), form a CO₂-concentration mechanism that ensures a high photosynthetic efficiency. Much effort has been taken in the past to introduce the C4 mechanism into C3 plants, but none of these attempts has met with success, which is in my opinion due to a lack of system-level understanding and manipulation of the C3 and C4 pathways. As a prerequisite for the C3-to-C4 engineering, I propose that not only the mechanisms that control the Kranz anatomy and cell-type-specific expression in C3 and C4 plants must be elucidated, but also a good understanding of the gene regulatory network underlying C3 and C4 photosynthesis must be achieved. In this review, I first describe the past and current efforts to increase photosynthetic efficiency in C3 plants and their limitations; I then discuss a systems approach to tackling down this challenge, some practical issues, and recent technical innovations that would help us to solve these problems.

Comparative Transcriptome Profiling of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) in Response to Light of Different Wavelengths and Carbon Dioxide Enrichment

Rhodophyta (red algae) comprises over 6000 species, however, there have only been a few comparative transcriptomic studies due to their under-representation in genomic databases. Kappaphycus alvarezii, a Gigartinales algae, is a valuable source of carrageenan and is extensively cultivated in many countries. The majority of seaweed farming in Southeast Asia is done in intertidal zones under varying light (i.e., spectra and irradiance) and carbon dioxide (CO₂) conditions, which affects the rate of photosynthesis. This study conducted transcriptome profiling to investigate the photosynthetic mechanisms in K. alvarezii exposed to different wavelengths of light (i.e., blue, green, and red light, in comparison to white light) and CO₂ availability. We analyzed the responses of photosynthetic protein complexes to light and observed that light of different wavelengths regulates a similar set of photosynthetic apparatuses. Under CO₂ enrichment, genes encoding C₃ and C₄ enzymes were found to be actively transcribed, suggesting the likely shift in the carbon metabolism pathway or the involvement of these genes in adaptive physiological processes. This study contributes to the understanding of the regulatory mechanisms of photosynthetic carbon metabolism in red algae and has implications for the culture and commercial production of these economically valuable macroalgae.

Upregulation of bundle sheath electron transport capacity under limiting light in C4 Setaria viridis

C₄ photosynthesis is a biochemical pathway that operates across mesophyll and bundle sheath (BS) cells to increase CO₂ concentration at the site of CO₂ fixation. C₄ plants benefit from high irradiance but their efficiency decreases under shade, causing a loss of productivity in crop canopies. We investigated shade acclimation responses of Setaria viridis, a model monocot of NADP-dependent malic enzyme subtype, focussing on cell-specific electron transport capacity. Plants grown under low light (LL) maintained CO₂ assimilation rates similar to high light plants but had an increased chlorophyll and light-harvesting-protein content, predominantly in BS cells. Photosystem II (PSII) protein abundance, oxygen-evolving activity and the PSII/PSI ratio were enhanced in LL BS cells, indicating a higher capacity for linear electron flow. Abundances of PSI, ATP synthase, Cytochrome b₆ f and the chloroplast NAD(P)H dehydrogenase complex, which constitute the BS cyclic electron flow machinery, were also increased in LL plants. A decline in PEP carboxylase activity in mesophyll cells and a consequent shortage of reducing power in BS chloroplasts were associated with a more oxidised plastoquinone pool in LL plants and the formation of PSII - light-harvesting complex II supercomplexes with an increased oxygen evolution rate. Our results suggest that the supramolecular composition of PSII in BS cells is adjusted according to the redox state of the plastoquinone pool. This discovery contributes to the understanding of the acclimation of PSII activity in C₄ plants and will support the development of strategies for crop improvement, including the engineering of C₄ photosynthesis into C₃ plants.

Transport Proteins Enabling Plant Photorespiratory Metabolism

Photorespiration (PR) is a metabolic repair pathway that acts in oxygenic photosynthetic organisms to degrade a toxic product of oxygen fixation generated by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase. Within the metabolic pathway, energy is consumed and carbon dioxide released. Consequently, PR is seen as a wasteful process making it a promising target for engineering to enhance plant productivity. Transport and channel proteins connect the organelles accomplishing the PR pathway-chloroplast, peroxisome, and mitochondrion-and thus enable efficient flux of PR metabolites. Although the pathway and the enzymes catalyzing the biochemical reactions have been the focus of research for the last several decades, the knowledge about transport proteins involved in PR is still limited. This review presents a timely state of knowledge with regard to metabolite channeling in PR and the participating proteins. The significance of transporters for implementation of synthetic bypasses to PR is highlighted. As an excursion, the physiological contribution of transport proteins that are involved in C₄ metabolism is discussed.

C3 and C4 plant systems respond differently to the concurrent challenges of mercuric oxide nanoparticles and future climate CO2

Future climate CO₂ (eCO₂) and contamination with nano-sized heavy metals (HM-NPs) represent concurrent challenges threatening plants. The interaction between eCO₂ and HM-NPs is rarely investigated, and no study has addressed their synchronous impact on the metabolism of the multifunctional stress-related metabolites, such as sugars and amino acids. Moreover, the characteristic responses of C3 and C4 plant systems to the concurrent impact of eCO₂ and HM-NPs are poorly understood. Herein, we have assessed the impact of eCO₂ (620 ppm) and/or HgO-NPs (100 mg/Kg soil) on growth, physiology and metabolism of sugars and amino acids, particularly proline, in C3 (wheat) and C4 (maize) plant systems. Under Hg-free conditions, eCO₂ treatment markedly improved the growth and photosynthesis and induced sugars levels and metabolism (glucose, fructose, sucrose, starch, sucrose P synthase and starch synthase) in wheat (C3) only. In contrast, HgO-NPs induced the uptake, accumulation and translocation of Hg in wheat and to less extend in maize plants. Particularly in wheat, this induced significant decreases in growth and photosynthesis and increases in photorespiration, dark respiration and levels of tricarboxylic acid cycle organic acids. Interestingly, the co-application of eCO₂ reduced the accumulation of Hg and recovered the HgO-NPs-induced effects on growth and metabolism in both plants. At stress defense level, HgO-NPs induced the accumulation of sucrose and proline, more in maize, via upregulation of sucrose P synthase, ornithine amino transferase, ∆¹-pyrroline-5-carboxylate (P5C) synthetase and P5C reductase. The co-existence of eCO₂ favored reduced sucrose biosynthesis and induced proline catabolism, which provide high energy to resume plant growth. Overall, despite the difference in their response to eCO₂ under normal conditions, eCO₂ induced similar metabolic events in C3 and C4 plants under stressful conditions, which trigger stress recovery.

What Matters for C4 Transporters: Evolutionary Changes of Phosphoenolpyruvate Transporter for C4 Photosynthesis

C4 photosynthesis is a complex trait that evolved from its ancestral C3 photosynthesis by recruiting pre-existing genes. These co-opted genes were changed in many aspects compared to their counterparts in C3 species. Most of the evolutionary changes of the C4 shuttle enzymes are well characterized, however, evolutionary changes for the recruited metabolite transporters are less studied. Here we analyzed the evolutionary changes of the shuttle enzyme phosphoenolpyruvate (PEP) transporter (PPT) during its recruitment from C3 to C4 photosynthesis. Our analysis showed that among the two PPT paralogs PPT1 and PPT2, PPT1 was the copy recruited for C4 photosynthesis in multiple C4 lineages. During C4 evolution, PPT1 gained increased transcript abundance, shifted its expression from predominantly in root to in leaf and from bundle sheath cell to mesophyll cell, and gained more rapid and long-lasting responsiveness to light. Modifications occurred in both regulatory and coding regions in C4 PPT1 as compared to C3 PPT1, however, the PEP transporting function of PPT1 remained. We found that PPT1 of a Flaveria C4 species recruited a MEM1 B submodule in the promoter region, which might be related to the increased transcript abundance of PPT1 in C4 mesophyll cells. The case study of PPT further suggested that high transcript abundance in a proper location is of high priority for PPT to support C4 function.

Carbon fixation gene expression in Skeletonema marinoi in nitrogen-, phosphate-, silicate-starvation, and low-temperature stress exposure

Diatoms are unicellular algae with a set of extraordinary genes, metabolic pathways, and physiological functions acquired by secondary endosymbiosis, especially for their efficient photosynthetic carbon fixation mechanisms, which can be a reason for their successful environmental adaptation and great contribution to primary production. Based on the available genomic information, the expression patterns of carbon fixation genes were analyzed using transcriptomic sequencing and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in Skeletonema marinoi. Meanwhile, suitable reference genes applying to specific experimental treatments were selected. In our results, carbon fixation genes were standardized by actin and TATA box-binding protein-coding genes in growth phase samples and stress conditions, respectively. It was found that a series of carbon fixation genes, such as the pyruvate orthophosphate dikinase (PPDK)-coding gene, had significantly up-regulated expression in nitrogen-starvation, phosphate-starvation, and low-temperature conditions, but consistently down-regulated in silicate-starvation treatment. These carbon fixation genes exhibited variable expression levels in different conditions and will be useful for investigating gene expression mechanisms in S. marinoi and improve our understanding of diatom carbon fixation pathways.

Ectopic expression of C4 photosynthetic pathway genes improves carbon assimilation and alleviate stress tolerance for future climate change

Alteration in atmospheric carbon dioxide concentration and other environmental factors are the significant cues of global climate change. Environmental factors affect the most fundamental biological process including photosynthesis and different metabolic pathways. The feeding of the rapidly growing world population is another challenge which imposes pressure to improve productivity and quality of the existing crops. C₄ plants are considered the most productive, containing lower photorespiration, and higher water-use & N-assimilation efficiencies, compared to C₃ plants. Besides, the C₄-photosynthetic genes not only play an important role in carbon assimilation but also modulate abiotic stresses. In this review, fundamental three metabolic processes (C₄, C₃, and CAM) of carbon dioxide assimilation, the evolution of C₄-photosynthetic genes, effect of elevated CO₂ on photosynthesis, and overexpression of C₄-photosynthetic genes for higher photosynthesis were discussed. Kranz-anatomy is considered an essential prerequisite for the terrestrial C₄ carbon assimilation, but single-celled C₄ plant species changed this well-established paradigm. C₄ plants are insensitive to an elevated CO₂ stress condition but performed better under stress conditions. Overexpression of essential C₄-photosynthetic genes such as PEPC, PPDK, and NADP-ME in C₃ plants like Arabidopsis, tobacco, rice, wheat, and potato not only improved photosynthesis but also provided tolerance to various environmental stresses, especially drought. The review provides useful information for sustainable productivity and yield under elevated CO₂ environment, which to be explored further for CO₂ assimilation and also abiotic stress tolerance. Additionally, it provides a better understanding to explore C₄-photosynthetic gene(s) to cope with global warming and prospective adverse climatic changes.

A Partial C4 Photosynthetic Biochemical Pathway in Rice

Introduction of a C₄ photosynthetic pathway into C₃ rice (Oryza sativa) requires installation of a biochemical pump that concentrates CO₂ at the site of carboxylation in modified bundle sheath cells. To investigate the feasibility of this, we generated a quadruple line that simultaneously accumulates four of the core C₄ photosynthetic enzymes from the NADP-malic enzyme subtype, phosphoenolpyruvate carboxylase (ZmPEPC), NADP-malate dehydrogenase (ZmNADP-MDH), NADP-malic enzyme (ZmNADP-ME), and pyruvate phosphate dikinase (ZmPPDK). This led to enhanced enzyme activity and mild phenotypic perturbations but was largely neutral in its effects on photosynthetic rate. Measurements of the flux of ¹³CO₂ through photosynthetic metabolism revealed a significant increase in the incorporation of ¹³C into malate, consistent with increased fixation of ¹³CO₂ via PEP carboxylase in lines expressing the maize PEPC enzyme. However, there was no significant differences in labeling of 3-phosphoglycerate (3PGA) indicating that there was no carbon flux through NADP-ME into the Calvin-Benson cycle. There was also no significant difference in labeling of phosphoenolpyruvate (PEP) indicating that there was no carbon flux through PPDK. Crossing the quadruple line with a line with reduced glycine decarboxylase H-protein (OsGDCH) abundance led to a photosynthetic phenotype characteristic of the reduced OsGDCH line and higher labeling of malate, aspartate and citrate than in the quintuple line. There was evidence of ¹³C labeling of aspartate indicating ¹³CO₂ fixation into oxaloacetate by PEPC and conversion to aspartate by the endogenous aspartate aminotransferase activity. While Kranz anatomy or other anatomical modifications have not yet been installed in these plants to enable a fully functional C₄ cycle, these results demonstrate for the first-time a partial flux through the carboxylation phase of NADP-ME C₄ metabolism in transgenic rice containing two of the key metabolic steps in the C₄ pathway.

Transgenic maize phosphoenolpyruvate carboxylase alters leaf-atmosphere CO2 and 13CO2 exchanges in Oryza sativa

The engineering process of C4 photosynthesis into C3 plants requires an increased activity of phosphoenolpyruvate carboxylase (PEPC) in the cytosol of leaf mesophyll cells. The literature varies on the physiological effect of transgenic maize (Zea mays) PEPC (ZmPEPC) leaf expression in Oryza sativa (rice). Therefore, to address this issue, leaf-atmosphere CO2 and 13CO2 exchanges were measured, both in the light (at atmospheric O2 partial pressure of 1.84 kPa and at different CO2 levels) and in the dark, in transgenic rice expressing ZmPEPC and wild-type (WT) plants. The in vitro PEPC activity was 25 times higher in the PEPC overexpressing (PEPC-OE) plants (~20% of maize) compared to the negligible activity in WT. In the PEPC-OE plants, the estimated fraction of carboxylation by PEPC (β) was ~6% and leaf net biochemical discrimination against 13CO2[Formula: see text] was ~ 2‰ lower than in WT. However, there were no differences in leaf net CO2 assimilation rates (A) between genotypes, while the leaf dark respiration rates (Rd) over three hours after light-dark transition were enhanced (~ 30%) and with a higher 13C composition [Formula: see text] in the PEPC-OE plants compared to WT. These data indicate that ZmPEPC in the PEPC-OE rice plants contributes to leaf carbon metabolism in both the light and in the dark. However, there are some factors, potentially posttranslational regulation and PEP availability, which reduce ZmPEPC activity in vivo.

Exploring natural variation of photosynthesis in a site-specific manner: evolution, progress, and prospects

Site-specific changes of photosynthesis, a relatively new concept, can be used to improve the productivity of critical food crops to mitigate the foreseen food crisis. Global food security is threatened by an increasing population and the effects of climate change. Large yield improvements were achieved in major cereal crops between the 1950s and 1980s through the Green Revolution. However, we are currently experiencing a significant decline in yield progress. Of the many approaches to improved cereal yields, exploitation of the mode of photosynthesis has been intensely studied. Even though the C₄ pathway is considered the most efficient, mainly because of the carbon concentrating mechanisms around the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase, which minimize photorespiration, much is still unknown about the specific gene regulation of this mode of photosynthesis. Most of the critical cereal crops, including wheat and rice, are categorized as C₃ plants based on the photosynthesis of major photosynthetic organs. However, recent findings raise the possibility of different modes of photosynthesis occurring at different sites in the same plant and/or in plants grown in different habitats. That is, it seems possible that efficient photosynthetic traits may be expressed in specific organs, even though the major photosynthetic pathway is C₃. Knowledge of site-specific differences in photosynthesis, coupled with site-specific regulation of gene expression, may therefore hold a potential to enhance the yields of economically important C₃ crops.

A leaf-level biochemical model simulating the introduction of C2 and C4 photosynthesis in C3 rice: gains, losses and metabolite fluxes

This work aims at developing an adequate theoretical basis for comparing assimilation of the ancestral C₃ pathway with CO₂ concentrating mechanisms (CCM) that have evolved to reduce photorespiratory yield losses. We present a novel model for C₃ , C₂ , C₂  + C₄ and C₄ photosynthesis simulating assimilatory metabolism, energetics and metabolite traffic at the leaf level. It integrates a mechanistic description of light reactions to simulate ATP and NADPH production, and a variable engagement of cyclic electron flow. The analytical solutions are compact and thus suitable for larger scale simulations. Inputs were derived with a comprehensive gas-exchange experiment. We show trade-offs in the operation of C₄ that are in line with ecophysiological data. C₄ has the potential to increase assimilation over C₃ at high temperatures and light intensities, but this benefit is reversed under low temperatures and light. We apply the model to simulate the introduction of progressively complex levels of CCM into C₃ rice, which feeds > 3.5 billion people. Increasing assimilation will require considerable modifications such as expressing the NAD(P)H Dehydrogenase-like complex and upregulating cyclic electron flow, enlarging the bundle sheath, and expressing suitable transporters to allow adequate metabolite traffic. The simpler C₂ rice may be a desirable alternative.

Efficient 2-phosphoglycolate degradation is required to maintain carbon assimilation and allocation in the C4 plant Flaveria bidentis

Photorespiration is indispensable for oxygenic photosynthesis since it detoxifies and recycles 2-phosphoglycolate (2PG), which is the primary oxygenation product of Rubisco. However, C4 plant species typically display very low rates of photorespiration due to their efficient biochemical carbon-concentrating mechanism. Thus, the broader relevance of photorespiration in these organisms remains unclear. In this study, we assessed the importance of a functional photorespiratory pathway in the C4 plant Flaveria bidentis using knockdown of the first enzymatic step, namely 2PG phosphatase (PGLP). The isolated RNAi lines showed strongly reduced amounts of PGLP protein, but distinct signs of the photorespiratory phenotype only emerged below 5% residual PGLP protein. Lines with this characteristic were stunted in growth, had strongly increased 2PG content, exhibited accelerated leaf senescence, and accumulated high amounts of branched-chain and aromatic amino acids, which are both characteristics of incipient carbon starvation. Oxygen-dependent gas-exchange measurements consistently suggested the cumulative impairment of ribulose-1,5-bisphosphate regeneration with increased photorespiratory pressure. Our results indicate that photorespiration is essential for maintaining high rates of C4 photosynthesis by preventing the 2PG-mediated inhibition of carbon utilization efficiency. However, considerably higher 2PG accumulation can be tolerated compared to equivalent lines of C3 plants due to the differential distribution of specific enzymatic steps between the mesophyll and bundle sheath cells.

Impact of Arbuscular Mycorrhizal Fungi on Photosynthesis, Water Status, and Gas Exchange of Plants Under Salt Stress-A Meta-Analysis

Soil salinization is one of the most serious abiotic stress factors affecting plant productivity through reduction of soil water potential, decreasing the absorptive capacity of the roots for water and nutrients. A weighted meta-analysis was conducted to study the effects of arbuscular mycorrhizal fungi (AMF) inoculation in alleviating salt stress in C₃ and C₄ plants. We analyzed the salt stress influence on seven independent variables such as chlorophyll, leaf area, photosynthetic rate (Amax), stomatal conductance (Gs), transpiration rate (E), relative water content (RWC), and water use efficiency (WUE) on AMF inoculated plants. Responses were compared between C₃ and C₄ plants, AMF species, plant functional groups, level of salinity, and environmental conditions. Our results showed that AMF inoculated plants had a positive impact on gas exchange and water status under salt stress. The total chlorophyll contents of C₃ plants were higher than C₄ plants. However, C₃ plants responses regarding Gs, Amax, and E were more positive compared to C₄ plants. The increase in G _s mainly maintained E and it explains the increase in Amax and increase in E. When the two major AMF species (Rhizophagus intraradices and Funnelliformis mosseae) were considered, the effect sizes of RWC and WUE in R. intraradices were lower than those in F. mosseae indicating that F. mosseae inoculated plants performed better under salt stress. In terms of C₃ and C₄ plant photosynthetic pathways, the effect size of C₄ was lower than C₃ plants indicating that AMF inoculation more effectively alleviated salt stress in C₃ compared to C₄ plants.

Uncovering C4-like photosynthesis in C3 vascular cells

In C4 plants, the vascularization of the leaf is extended to include a ring of photosynthetic bundle sheath cells, which have essential and specific functions. In contrast to the substantial knowledge of photosynthesis in C4 plants, relatively little is known about photosynthesis in C3 plant veins, which differs substantially from that in C3 mesophyll cells. In this review we highlight the specific photosynthetic machinery present in C3 vascular cells, which likely evolved prior to the divergence between C3 and C4 plants. The associated primary processes of carbon recapture, nitrogen transport, and antioxidant metabolism are discussed. This review of the basal C4 photosynthesis in C3 plants is significant in the context of promoting the potential for biotechnological development of C4-transgenic rice crops.

Ion and metabolite transport in the chloroplast of algae: lessons from land plants

Chloroplasts are endosymbiotic organelles and play crucial roles in energy supply and metabolism of eukaryotic photosynthetic organisms (algae and land plants). They harbor channels and transporters in the envelope and thylakoid membranes, mediating the exchange of ions and metabolites with the cytosol and the chloroplast stroma and between the different chloroplast subcompartments. In secondarily evolved algae, three or four envelope membranes surround the chloroplast, making more complex the exchange of ions and metabolites. Despite the importance of transport proteins for the optimal functioning of the chloroplast in algae, and that many land plant homologues have been predicted, experimental evidence and molecular characterization are missing in most cases. Here, we provide an overview of the current knowledge about ion and metabolite transport in the chloroplast from algae. The main aspects reviewed are localization and activity of the transport proteins from algae and/or of homologues from other organisms including land plants. Most chloroplast transporters were identified in the green alga Chlamydomonas reinhardtii, reside in the envelope and participate in carbon acquisition and metabolism. Only a few identified algal transporters are located in the thylakoid membrane and play role in ion transport. The presence of genes for putative transporters in green algae, red algae, diatoms, glaucophytes and cryptophytes is discussed, and roles in the chloroplast are suggested. A deep knowledge in this field is required because algae represent a potential source of biomass and valuable metabolites for industry, medicine and agriculture.

Multiple mechanisms for enhanced plasmodesmata density in disparate subtypes of C4 grasses

Proliferation of plasmodesmata (PD) connections between bundle sheath (BS) and mesophyll (M) cells has been proposed as a key step in the evolution of two-cell C4 photosynthesis; However, a lack of quantitative data has hampered further exploration and validation of this hypothesis. In this study, we quantified leaf anatomical traits associated with metabolite transport in 18 species of BEP and PACMAD grasses encompassing four origins of C4 photosynthesis and all three C4 subtypes (NADP-ME, NAD-ME, and PCK). We demonstrate that C4 leaves have greater PD density between M and BS cells than C3 leaves. We show that this greater PD density is achieved by increasing either the pit field (cluster of PD) area or the number of PD per pit field area. NAD-ME species had greater pit field area per M-BS interface than NADP-ME or PCK species. In contrast, NADP-ME and PCK species had lower pit field area with increased number of PD per pit field area than NAD-ME species. Overall, PD density per M-BS cell interface was greatest in NAD-ME species while PD density in PCK species exhibited the largest variability. Finally, the only other anatomical characteristic that clearly distinguished C4 from C3 species was their greater Sb value, the BS surface area to subtending leaf area ratio. In contrast, BS cell volume was comparable between the C3 and C4 grass species examined.

Walking the C4 pathway: past, present, and future

The year 2016 marks 50 years since the publication of the seminal paper by Hatch and Slack describing the biochemical pathway we now know as C₄ photosynthesis. This review provides insight into the initial discovery of this pathway, the clues which led Hatch and Slack and others to these definitive experiments, some of the intrigue which surrounds the international activities which led up to the discovery, and personal insights into the future of this research field. While the biochemical understanding of the basic pathways came quickly, the role of the bundle sheath intermediate CO₂ pool was not understood for a number of years, and the nature of C₄ as a biochemical CO₂ pump then linked the unique Kranz anatomy of C₄ plants to their biochemical specialization. Decades of "grind and find biochemistry" and leaf physiology fleshed out the regulation of the pathway and the differences in physiological response to the environment between C₃ and C₄ plants. The more recent advent of plant transformation then high-throughput RNA and DNA sequencing and synthetic biology has allowed us both to carry out biochemical experiments and test hypotheses in planta and to better understand the evolution-driven molecular and genetic changes which occurred in the genomes of plants in the transition from C₃ to C₄ Now we are using this knowledge in attempts to engineer C₄ rice and improve the C₄ engine itself for enhanced food security and to provide novel biofuel feedstocks. The next 50 years of photosynthesis will no doubt be challenging, stimulating, and a drawcard for the best young minds in plant biology.

Metabolite pools and carbon flow during C4 photosynthesis in maize: 13CO2 labeling kinetics and cell type fractionation

Worldwide efforts to engineer C4 photosynthesis into C3 crops require a deep understanding of how this complex pathway operates. CO2 is incorporated into four-carbon metabolites in the mesophyll, which move to the bundle sheath where they are decarboxylated to concentrate CO2 around RuBisCO. We performed dynamic 13CO2 labeling in maize to analyze C flow in C4 photosynthesis. The overall labeling kinetics reflected the topology of C4 photosynthesis. Analyses of cell-specific labeling patterns after fractionation to enrich bundle sheath and mesophyll cells revealed concentration gradients to drive intercellular diffusion of malate, but not pyruvate, in the major CO2-concentrating shuttle. They also revealed intercellular concentration gradients of aspartate, alanine, and phosphenolpyruvate to drive a second phosphoenolpyruvate carboxykinase (PEPCK)-type shuttle, which carries 10-14% of the carbon into the bundle sheath. Gradients also exist to drive intercellular exchange of 3-phosphoglycerate and triose-phosphate. There is rapid carbon exchange between the Calvin-Benson cycle and the CO2-concentrating shuttle, equivalent to ~10% of carbon gain. In contrast, very little C leaks from the large pools of metabolites in the C concentration shuttle into respiratory metabolism. We postulate that the presence of multiple shuttles, alongside carbon transfer between them and the Calvin-Benson cycle, confers great flexibility in C4 photosynthesis.

C3 cotyledons are followed by C4 leaves: intra-individual transcriptome analysis of Salsola soda (Chenopodiaceae)

Some species of Salsoleae (Chenopodiaceae) convert from C₃ photosynthesis during the seedling stage to the C₄ pathway in adult leaves. This unique developmental transition of photosynthetic pathways offers the exceptional opportunity to follow the development of the derived C₄ syndrome from the C₃ condition within individual plants, avoiding phylogenetic noise. Here we investigate Salsola soda, a little-studied species from tribe Salsoleae, using an ontogenetic approach. Anatomical sections, carbon isotope (δ¹³C) values, transcriptome analysis by means of mRNA sequencing, and protein levels of the key C₄ enzyme phosphoenolpyruvate carboxylase (PEPC) were examined from seed to adult plant stages. Despite a previous report, our results based on δ¹³C values, anatomy and transcriptomics clearly indicate a C₃ phase during the cotyledon stage. During this stage, the entire transcriptional repertoire of the C₄ NADP-malic enzyme type is detected at low levels compared to a significant increase in true leaves. In contrast, abundance of transcripts encoding most of the major photorespiratory enzymes is not significantly decreased in leaves compared to cotyledons. PEPC polypeptide was detected only in leaves, correlating with increased PEPC transcript abundance from the cotyledon to leaf stage.

The Differences between NAD-ME and NADP-ME Subtypes of C4 Photosynthesis: More than Decarboxylating Enzymes

As an adaptation to changing climatic conditions that caused high rates of photorespiration, C4 plants have evolved to display higher photosynthetic efficiency than C3 plants under elevated temperature, high light intensities, and drought. The C4 plants independently evolved more than 60 times in 19 families of angiosperms to establish similar but not uniform C4 mechanisms to concentrate CO2 around the carboxylating enzyme Rubisco (ribulose bisphosphate carboxylase oxygenase). C4 photosynthesis is divided into at least two basic biochemical subtypes based on the primary decarboxylating enzymes, NAD-dependent malic enzyme (NAD-ME) and NADP-dependent malic enzyme (NADP-ME). The multiple polygenetic origins of these subtypes raise questions about the association of C4 variation between biochemical subtypes and diverse lineages. This review addresses the differences in evolutionary scenario, leaf anatomy, and especially C4 metabolic flow, C4 transporters, and cell-specific function deduced from recently reported cell-specific transcriptomic, proteomic, and metabolic analyses of NAD-ME and NADP-ME subtypes. Current omic analysis has revealed the extent to which component abundances differ between the two biochemical subtypes, leading to a better understanding of C4 photosynthetic mechanisms in NAD-ME and NADP-ME subtypes.

Walking the C4 pathway: past, present, and future

The year 2016 marks 50 years since the publication of the seminal paper by Hatch and Slack describing the biochemical pathway we now know as C4 photosynthesis. This review provides insight into the initial discovery of this pathway, the clues which led Hatch and Slack and others to these definitive experiments, some of the intrigue which surrounds the international activities which led up to the discovery, and personal insights into the future of this research field. While the biochemical understanding of the basic pathways came quickly, the role of the bundle sheath intermediate CO2 pool was not understood for a number of years, and the nature of C4 as a biochemical CO2 pump then linked the unique Kranz anatomy of C4 plants to their biochemical specialization. Decades of "grind and find biochemistry" and leaf physiology fleshed out the regulation of the pathway and the differences in physiological response to the environment between C3 and C4 plants. The more recent advent of plant transformation then high-throughput RNA and DNA sequencing and synthetic biology has allowed us both to carry out biochemical experiments and test hypotheses in planta and to better understand the evolution-driven molecular and genetic changes which occurred in the genomes of plants in the transition from C3 to C4 Now we are using this knowledge in attempts to engineer C4 rice and improve the C4 engine itself for enhanced food security and to provide novel biofuel feedstocks. The next 50 years of photosynthesis will no doubt be challenging, stimulating, and a drawcard for the best young minds in plant biology.

Engineering C4 photosynthesis into C3 chassis in the synthetic biology age

C4 photosynthetic plants outperform C3 plants in hot and arid climates. By concentrating carbon dioxide around Rubisco C4 plants drastically reduce photorespiration. The frequency with which plants evolved C4 photosynthesis independently challenges researchers to unravel the genetic mechanisms underlying this convergent evolutionary switch. The conversion of C3 crops, such as rice, towards C4 photosynthesis is a long-standing goal. Nevertheless, at the present time, in the age of synthetic biology, this still remains a monumental task, partially because the C4 carbon-concentrating biochemical cycle spans two cell types and thus requires specialized anatomy. Here we review the advances in understanding the molecular basis and the evolution of the C4 trait, advances in the last decades that were driven by systems biology methods. In this review we emphasise essential genetic engineering tools needed to translate our theoretical knowledge into engineering approaches. With our current molecular understanding of the biochemical C4 pathway, we propose a simplified rational engineering model exclusively built with known C4 metabolic components. Moreover, we discuss an alternative approach to the progressing international engineering attempts that would combine targeted mutagenesis and directed evolution.

Roles and Transport of Sodium and Potassium in Plants

The two alkali cations Na(+) and K(+) have similar relative abundances in the earth crust but display very different distributions in the biosphere. In all living organisms, K(+) is the major inorganic cation in the cytoplasm, where its concentration (ca. 0.1 M) is usually several times higher than that of Na(+). Accumulation of Na(+) at high concentrations in the cytoplasm results in deleterious effects on cell metabolism, e.g., on photosynthetic activity in plants. Thus, Na(+) is compartmentalized outside the cytoplasm. In plants, it can be accumulated at high concentrations in vacuoles, where it is used as osmoticum. Na(+) is not an essential element in most plants, except in some halophytes. On the other hand, it can be a beneficial element, by replacing K(+) as vacuolar osmoticum for instance. In contrast, K(+) is an essential element. It is involved in electrical neutralization of inorganic and organic anions and macromolecules, pH homeostasis, control of membrane electrical potential, and the regulation of cell osmotic pressure. Through the latter function in plants, it plays a role in turgor-driven cell and organ movements. It is also involved in the activation of enzymes, protein synthesis, cell metabolism, and photosynthesis. Thus, plant growth requires large quantities of K(+) ions that are taken up by roots from the soil solution, and then distributed throughout the plant. The availability of K(+) ions in the soil solution, slowly released by soil particles and clays, is often limiting for optimal growth in most natural ecosystems. In contrast, due to natural salinity or irrigation with poor quality water, detrimental Na(+) concentrations, toxic for all crop species, are present in many soils, representing 6 % to 10 % of the earth's land area. Three families of ion channels (Shaker, TPK/KCO, and TPC) and 3 families of transporters (HAK, HKT, and CPA) have been identified so far as contributing to K(+) and Na(+) transport across the plasmalemma and internal membranes, with high or low ionic selectivity. In the model plant Arabidopsis thaliana, these families gather at least 70 members. Coordination of the activities of these systems, at the cell and whole plant levels, ensures plant K(+) nutrition, use of Na(+) as a beneficial element, and adaptation to saline conditions.

Understanding metabolite transport and metabolism in C4 plants through RNA-seq

RNA-seq, the measurement of steady-state RNA levels by next generation sequencing, has enabled quantitative transcriptome analyses of complex traits in many species without requiring the parallel sequencing of their genomes. The complex trait of C4 photosynthesis, which increases photosynthetic efficiency via a biochemical pump that concentrates CO2 around RubisCO, has evolved convergently multiple times. Due to these interesting properties, C4 photosynthesis has been analyzed in a series of comparative RNA-seq projects. These projects compared both species with and without the C4 trait and different tissues or organs within a C4 plant. The RNA-seq studies were evaluated by comparing to earlier single gene studies. The studies confirmed the marked changes expected for C4 signature genes, but also revealed numerous new players in C4 metabolism showing that the C4 cycle is more complex than previously thought, and suggesting modes of integration into the underlying C3 metabolism.

Strategies for improving C4 photosynthesis

Recent activities to improve photosynthetic performance in crop plants has focused mainly on C3 photosynthesis where there are clear identified targets such as improving Rubisco kinetics, installation of a CO2 concentrating mechanism and alleviating limitations in chloroplast electron transport. Here we address strategies to improve photosynthetic performance in C4 plants, which utilize a CO2 concentrating mechanism, having evolved a complex blend of anatomy and biochemistry to achieve this. While the limitations to photosynthetic flux are not as well studied in C4 plants, work in transgenic Flaveria bidentis, a transformable model C4 dicot, and recent transcriptional analysis of leaves from diverse C4 plants, provides several gene candidates for improvement of carbon metabolism (such as pyruvate orthophosphate dikinase, phosphoenolpyruvate carboxylase and Rubisco) and for access of CO2 to phosphoenolpyruvate carboxylase in the mesophyll cells (such as carbonic anhydrase and CO2 porins). Chloroplast electron transport in C4 plants is shared between the two cell types, providing opportunities not only to alleviate limitations to flux through intersystem electron transport by targeting nuclear encoded proteins in the cytochrome (Cyt) b6/f complex, but in better sharing the harvesting of light energy between mesophyll and bundle sheath chloroplasts. Gene candidates for improvement of C4 photosynthesis could be utilized either through transgenic approaches or via mining natural allelic variation in sequenced populations of crop species.

Pyruvate transport systems in organelles: future directions in C4 biology research

Pyruvate is a central metabolite that must be imported into organelles for specific metabolic processes, including C4 photosynthesis. Plastidial and mitochondrial pyruvate transporter molecules were recently identified: the former was found based on C4 photosynthesis transcriptome analysis and the latter using a bioinformatics approach in yeast. The transport activities of these molecules were recently investigated in heterologous expression systems: Escherichia coli and Lactococcus lactis, respectively. These studies demonstrated the important roles of the NHD1/Bass2-protein coupling function and the mitochondria pyruvate carrier protein complex in pyruvate uptake. Here, I summarize the approaches used to isolate these proteins and the issues that remain to be investigated.

A two-dimensional microscale model of gas exchange during photosynthesis in maize (Zea mays L.) leaves

CO2 exchange in leaves of maize (Zea mays L.) was examined using a microscale model of combined gas diffusion and C4 photosynthesis kinetics at the leaf tissue level. Based on a generalized scheme of photosynthesis in NADP-malic enzyme type C4 plants, the model accounted for CO2 diffusion in a leaf tissue, CO2 hydration and assimilation in mesophyll cells, CO2 release from decarboxylation of C4 acids, CO2 fixation in bundle sheath cells and CO2 retro-diffusion from bundle sheath cells. The transport equations were solved over a realistic 2-D geometry of the Kranz anatomy obtained from light microscopy images. The predicted responses of photosynthesis rate to changes in ambient CO2 and irradiance compared well with those obtained from gas exchange measurements. A sensitivity analysis showed that the CO2 permeability of the mesophyll-bundle sheath and airspace-mesophyll interfaces strongly affected the rate of photosynthesis and bundle sheath conductance. Carbonic anhydrase influenced the rate of photosynthesis, especially at low intercellular CO2 levels. In addition, the suberin layer at the exposed surface of the bundle sheath cells was found beneficial in reducing the retro-diffusion. The model may serve as a tool to investigate CO2 diffusion further in relation to the Kranz anatomy in C4 plants.

Most photorespiratory genes are preferentially expressed in the bundle sheath cells of the C4 grass Sorghum bicolor

One of the hallmarks of C4 plants is the division of labor between two different photosynthetic cell types, the mesophyll and the bundle sheath cells. C4 plants are of polyphyletic origin and, during the evolution of C4 photosynthesis, the expression of thousands of genes was altered and many genes acquired a cell type-specific or preferential expression pattern. Several lines of evidence, including computational modeling and physiological and phylogenetic analyses, indicate that alterations in the expression of a key photorespiration-related gene, encoding the glycine decarboxylase P subunit, was an early and important step during C4 evolution. Restricting the expression of this gene to the bundle sheath led to the establishment of a photorespiratory CO2 pump. We were interested in whether the expression of genes related to photorespiration remains bundle sheath specific in a fully optimized C4 species. Therefore we analyzed the expression of photorespiratory and C4 cycle genes using RNA in situ hybridization and transcriptome analysis of isolated mesophyll and bundle sheath cells in the C4 grass Sorghum bicolor It turns out that the C4 metabolism of Sorghum is based solely on the NADP-dependent malic enzyme pathway. The majority of photorespiratory gene expression, with some important exceptions, is restricted to the bundle sheath.

Transcriptome comparisons shed light on the pre-condition and potential barrier for C4 photosynthesis evolution in eudicots

C4 photosynthesis evolved independently from C3 photosynthesis in more than 60 lineages. Most of the C4 lineages are clustered together in the order Poales and the order Caryophyllales while many other angiosperm orders do not have C4 species, suggesting the existence of biological pre-conditions in the ancestral C3 species that facilitate the evolution of C4 photosynthesis in these lineages. To explore pre-adaptations for C4 photosynthesis evolution, we classified C4 lineages into the C4-poor and the C4-rich groups based on the percentage of C4 species in different genera and conducted a comprehensive comparison on the transcriptomic changes between the non-C4 species from the C4-poor and the C4-rich groups. Results show that species in the C4-rich group showed higher expression of genes related to oxidoreductase activity, light reaction components, terpene synthesis, secondary cell synthesis, C4 cycle related genes and genes related to nucleotide metabolism and senescence. In contrast, C4-poor group showed up-regulation of a PEP/Pi translocator, genes related to signaling pathway, stress response, defense response and plant hormone metabolism (ethylene and brassinosteroid). The implications of these transcriptomic differences between the C4-rich and C4-poor groups to C4 evolution are discussed.

Comparative cell-specific transcriptomics reveals differentiation of C4 photosynthesis pathways in switchgrass and other C4 lineages

Almost all C4 plants require the co-ordination of the adjacent and fully differentiated cell types, mesophyll (M) and bundle sheath (BS). The C4 photosynthetic pathway operates through two distinct subtypes based on how malate is decarboxylated in BS cells; through NAD-malic enzyme (NAD-ME) or NADP-malic enzyme (NADP-ME). The diverse or unique cell-specific molecular features of M and BS cells from separate C4 subtypes of independent lineages remain to be determined. We here provide an M/BS cell type-specific transcriptome data set from the monocot NAD-ME subtype switchgrass (Panicum virgatum). A comparative transcriptomics approach was then applied to compare the M/BS mRNA profiles of switchgrass, monocot NADP-ME subtype C4 plants maize and Setaria viridis, and dicot NAD-ME subtype Cleome gynandra. We evaluated the convergence in the transcript abundance of core components in C4 photosynthesis and transcription factors to establish Kranz anatomy, as well as gene distribution of biological functions, in these four independent C4 lineages. We also estimated the divergence between NAD-ME and NADP-ME subtypes of C4 photosynthesis in the two cell types within C4 species, including differences in genes encoding decarboxylating enzymes, aminotransferases, and metabolite transporters, and differences in the cell-specific functional enrichment of RNA regulation and protein biogenesis/homeostasis. We suggest that C4 plants of independent lineages in both monocots and dicots underwent convergent evolution to establish C4 photosynthesis, while distinct C4 subtypes also underwent divergent processes for the optimization of M and BS cell co-ordination. The comprehensive data sets in our study provide a basis for further research on evolution of C4 species.

Metabolic response of maize plants to multi-factorial abiotic stresses

Clarification of the metabolic mechanisms underlying multi-stress responses in plants will allow further optimisation of crop breeding and cultivation to obtain high yields in an increasingly variable environment. Using NMR metabolomic techniques, we examined the metabolic responses of maize plants grown under different conditions: soil drought, soil salinity, heat and multiple concurrent stresses. A detailed time-course metabolic profile was also performed on maize plants sampled 1, 3 and 7 days after initiation of soil drought and heat stress. The metabolic profile of maize plants subjected to soil drought was more similar to plants exposed to salt stress than to heat-stressed plants. Drought-stressed maize plants subjected to salt or heat stress showed distinct integrated metabolic profiles compared with those exposed to either stressor individually. These differences show the considerable metabolic plasticity of maize in response to different growth conditions. Moreover, glucose, fructose, malate, citrate, proline, alanine, aspartate, asparagine, threonine and one unknown compound fluctuated obviously between maize plants grown in controlled growth cabinet and a natural regime. These changes were associated with the TCA cycle and core nitrogen metabolism, and could be related to their multiple functions during plant growth. The evident stress-induced trajectory of metabolic changes in maize indicated that the primary metabolic responses to soil drought, heat and combined drought and heat stresses occurred in a time-dependent manner. Plasticity at the metabolic level may allow maize plants to acclimatise their metabolic ranges in response to changing environmental conditions.

Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species

Leaves of C4 crops usually have higher radiation, water and nitrogen use efficiencies compared to the C3 species. Engineering C4 traits into C3 crops has been proposed as one of the most promising ways to repeal the biomass yield ceiling. To better understand the function of C4 photosynthesis, and to identify candidate genes that are associated with the C4 pathways, a comparative transcription network analysis was conducted on leaf developmental gradients of three C4 species including maize, green foxtail and sorghum and one C3 species, rice. By combining the methods of gene co-expression and differentially co-expression networks, we identified a total of 128 C4 specific genes. Besides the classic C4 shuttle genes, a new set of genes associated with light reaction, starch and sucrose metabolism, metabolites transportation, as well as transcription regulation, were identified as involved in C4 photosynthesis. These findings will provide important insights into the differential gene regulation between C3 and C4 species, and a good genetic resource for establishing C4 pathways in C3 crops.

Major alterations in transcript profiles between C3-C4 and C4 photosynthesis of an amphibious species Eleocharis baldwinii

Engineering C4 photosynthetic metabolism into C3 crops is regarded as a major strategy to increase crop productivity, and clarification of the evolutionary processes of C4 photosynthesis can help the better use of this strategy. Here, Eleocharis baldwinii, a species in which C4 photosynthesis can be induced from a C3-C4 state under either environmental or ABA treatments, was used to identify the major transcriptional modifications during the process from C3-C4 to C4. The transcriptomic comparison suggested that in addition to the major differences in C4 core pathway, the pathways of glycolysis, citrate acid metabolism and protein synthesis were dramatically modified during the inducement of C4 photosynthetic states. Transcripts of many transporters, including not only metabolite transporters but also ion transporters, were dramatically increased in C4 photosynthetic state. Many candidate regulatory genes with unidentified functions were differentially expressed in C3-C4 and C4 photosynthetic states. Finally, it was indicated that ABA, auxin signaling and DNA methylation play critical roles in the regulation of C4 photosynthesis. In summary, by studying the different photosynthetic states of the same species, this work provides the major transcriptional differences between C3-C4 and C4 photosynthesis, and many of the transcriptional differences are potentially related to C4 development and therefore are the potential targets for reverse genetics studies.

Transplastomic integration of a cyanobacterial bicarbonate transporter into tobacco chloroplasts

Improving global yields of agricultural crops is a complex challenge with evidence indicating benefits in productivity are achieved by enhancing photosynthetic carbon assimilation. Towards improving rates of CO2 capture within leaf chloroplasts, this study shows the versatility of plastome transformation for expressing the Synechococcus PCC7002 BicA bicarbonate transporter within tobacco plastids. Fractionation of chloroplast membranes from transplastomic tob(BicA) lines showed that ~75% of the BicA localized to the thylakoid membranes and ~25% to the chloroplast envelope. BicA levels were highest in young emerging tob(BicA) leaves (0.12 μmol m(-2), ≈7mg m(-2)) accounting for ~0.1% (w/w) of the leaf protein. In these leaves, the molar amount of BicA was 16-fold lower than the abundant thylakoid photosystem II D1 protein (~1.9 μmol m(-2)) which was comparable to the 9:1 molar ratio of D1:BicA measured in air-grown Synechococcus PCC7002 cells. The BicA produced had no discernible effect on chloroplast ultrastructure, photosynthetic CO2-assimilation rates, carbon isotope discrimination, or growth of the tob(BicA) plants, implying that the bicarbonate transporter had little or no activity. These findings demonstrate the utility of plastome transformation for targeting bicarbonate transporter proteins into the chloroplast membranes without impeding growth or plastid ultrastructure. This study establishes the span of experimental measurements required to verify heterologous bicarbonate transporter function and location in chloroplasts and underscores the need for more detailed understanding of BicA structure and function to identify solutions for enabling its activation and operation in leaf chloroplasts.

The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria

C4 photosynthesis represents a most remarkable case of convergent evolution of a complex trait, which includes the reprogramming of the expression patterns of thousands of genes. Anatomical, physiological, and phylogenetic and analyses as well as computational modeling indicate that the establishment of a photorespiratory carbon pump (termed C2 photosynthesis) is a prerequisite for the evolution of C4. However, a mechanistic model explaining the tight connection between the evolution of C4 and C2 photosynthesis is currently lacking. Here we address this question through comparative transcriptomic and biochemical analyses of closely related C3, C3-C4, and C4 species, combined with Flux Balance Analysis constrained through a mechanistic model of carbon fixation. We show that C2 photosynthesis creates a misbalance in nitrogen metabolism between bundle sheath and mesophyll cells. Rebalancing nitrogen metabolism requires anaplerotic reactions that resemble at least parts of a basic C4 cycle. Our findings thus show how C2 photosynthesis represents a pre-adaptation for the C4 system, where the evolution of the C2 system establishes important C4 components as a side effect.

Elements required for an efficient NADP-malic enzyme type C4 photosynthesis

C4 photosynthesis has higher light, nitrogen, and water use efficiencies than C3 photosynthesis. Although the basic anatomical, cellular, and biochemical features of C4 photosynthesis are well understood, the quantitative significance of each element of C4 photosynthesis to the high photosynthetic efficiency are not well defined. Here, we addressed this question by developing and using a systems model of C4 photosynthesis, which includes not only the Calvin-Benson cycle, starch synthesis, sucrose synthesis, C4 shuttle, and CO₂ leakage, but also photorespiration and metabolite transport between the bundle sheath cells and mesophyll cells. The model effectively simulated the CO₂ uptake rates, and the changes of metabolite concentrations under varied CO₂ and light levels. Analyses show that triose phosphate transport and CO₂ leakage can help maintain a high photosynthetic rate by balancing ATP and NADPH amounts in bundle sheath cells and mesophyll cells. Finally, we used the model to define the optimal enzyme properties and a blueprint for C4 engineering. As such, this model provides a theoretical framework for guiding C4 engineering and studying C4 photosynthesis in general.

Genome-scale models of plant metabolism

A genome-scale model (GSM) is an in silico metabolic model comprising hundreds or thousands of chemical reactions that constitute the metabolic inventory of a cell, tissue, or organism. A complete, accurate GSM, in conjunction with a simulation technique such as flux balance analysis (FBA), can be used to comprehensively predict cellular metabolic flux distributions for a given genotype and given environmental conditions. Apart from enabling a user to quantitatively visualize carbon flow through metabolic pathways, these flux predictions also facilitate the hypothesis of new network properties. By simulating the impacts of environmental stresses or genetic interventions on metabolism, GSMs can aid the formulation of nontrivial metabolic engineering strategies. GSMs for plants and other eukaryotes are significantly more complicated than those for prokaryotes due to their extensive compartmentalization and size. The reconstruction of a GSM involves creating an initial model, curating the model, and then rendering the model ready for FBA. Model reconstruction involves obtaining organism-specific reactions from the annotated genome sequence or organism-specific databases. Model curation involves determining metabolite protonation status or charge, ensuring that reactions are stoichiometrically balanced, assigning reactions to appropriate subcellular compartments, deleting generic reactions or creating specific versions of them, linking dead-end metabolites, and filling of pathway gaps to complete the model. Subsequently, the model requires the addition of transport, exchange, and biomass synthesis reactions to make it FBA-ready. This cycle of editing, refining, and curation has to be performed iteratively to obtain an accurate model. This chapter outlines the reconstruction and curation of GSMs with a focus on models of plant metabolism.

Improvement of photosynthesis in rice (Oryza sativa L.) by inserting the C4 pathway

To boost food production for a rapidly growing global population, crop yields must significantly increase. One of the avenues being recently explored is the improvement of photosynthetic capacity by installing the C4 photosynthetic pathway into C3 crops like rice to drastically increase their yield. Crops with an enhanced photosynthetic mechanism would better utilize the solar radiation that can be translated into yield. This subsequently will help in producing more grain yield, reduce water loss and increase nitrogen use efficiency especially in hot and dry environments. This review provides a summary of the factors that need to be modified in rice so that the C4 pathway can be introduced successfully. It also discusses the differences between the C3 and C4 photosynthetic pathways in terms of anatomy, biochemistry and genetics.

Transcriptomic and Metabolic Changes Associated with Photorespiratory Ammonium Accumulation in the Model Legume Lotus japonicus

The transcriptomic and metabolic consequences of the lack of plastidic glutamine (Gln) synthetase in the model legume Lotus japonicus were investigated. Wild-type and mutant plants lacking the plastidic isoform of Gln synthetase were grown in conditions that suppress photorespiration and then transferred for different lengths of time to photorespiratory conditions. Transcript and metabolite levels were determined at the different time points considered. Under photorespiratory active conditions, the mutant accumulated high levels of ammonium, followed by its subsequent decline. A coordinate repression of the photorespiratory genes was observed in the mutant background. This was part of a greater modulation of the transcriptome, especially in the mutant, that was paralleled by changes in the levels of several key metabolites. The data obtained for the mutant represent the first direct experimental evidence for a coordinate regulation of photorespiratory genes over time. Metabolomic analysis demonstrated that mutant plants under active photorespiratory conditions accumulated high levels of several amino acids and organic acids, including intermediates of the Krebs cycle. An increase in Gln levels was also detected in the mutant, which was paralleled by an increase in cytosolic Gln synthetase1 gene transcription and enzyme activity levels. The global panoramic of the transcripts and metabolites that changed in L. japonicus plants during the transfer from photorespiration-suppressed to photorespiration-active conditions highlighted the link between photorespiration and several other cellular processes, including central carbon metabolism, amino acid metabolism, and secondary metabolism.

Adaptation of maize source leaf metabolism to stress related disturbances in carbon, nitrogen and phosphorus balance

Background

Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses.

Results

To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C₄ metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low P conditions indicated that only low P treated leaves suffered carbon starvation.

Conclusions

Maize employs very different strategies to manage N and P metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C₄ maize leaves were particularly sensitive to P starvation.