On the mechanism of C4 photosynthesis intermediate exchange between Kranz mesophyll and bundle sheath cells in grasses

The operation of PEPCK increases light harvesting plasticity in C4 NAD-ME and NADP-ME photosynthetic subtypes: A theoretical study

The repeated emergence of NADP-malic enzyme (ME), NAD-ME and phosphoenolpyruvate carboxykinase (PEPCK) subtypes of C4 photosynthesis are iconic examples of convergent evolution, which suggests that these biochemistries do not randomly assemble, but are instead specific adaptations resulting from unknown evolutionary drivers. Theoretical studies that are based on the classic biochemical understanding have repeatedly proposed light-use efficiency as a possible benefit of the PEPCK subtype. However, quantum yield measurements do not support this idea. We explore this inconsistency here via an analytical model that features explicit descriptions across a seamless gradient between C4 biochemistries to analyse light harvesting and dark photosynthetic metabolism. Our simulations show that the NADP-ME subtype, operated by the most productive crops, is the most efficient. The NAD-ME subtype has lower efficiency, but has greater light harvesting plasticity (the capacity to assimilate CO2 in the broadest combination of light intensity and spectral qualities). In both NADP-ME and NAD-ME backgrounds, increasing PEPCK activity corresponds to greater light harvesting plasticity but likely imposed a reduction in photosynthetic efficiency. We draw the first mechanistic links between light harvesting and C4 subtypes, providing the theoretical basis for future investigation.

The asymmetric photosynthetic characteristics of the isobilateral sorghum leaves under the illumination of the diffuse light

The difference between photosynthesis on the two leaf sides (dorsoventral asymmetry) of photosynthesis is important for light-use patterns, but the asymmetry is environment dependent. Its role in photosynthetic regulation has been intensively studied, but little is known about the impacts of direct and diffuse light on the asymmetry. Because of the current changing fraction of diffuse light in sky radiation, this study investigated the dorsoventral asymmetry of photosynthetic traits under direct and diffuse light conditions in an important food and energy crop, Sorghum bicolor L. A unique method was used to investigate the specific gas exchange of each leaf surface. Anatomical and morphological traits were different between the two surfaces of sorghum leaves, which might result in photosynthetic asymmetry. The variations in photosynthetic rates and stomatal conductance were significant between the two surfaces in direct and diffuse light, but the degree of dorsoventral asymmetry decreased in diffuse light. The integrated P _N and G _s of the adaxial illumination were significantly higher than that of abaxial illumination both in direct and diffuse light in sorghum leaves, but the ASI of the integrated P _Nwas 2.83 in direct light, while significantly dropped to 1.69 in diffuse light. Significant morphological differences between the two surfaces might cause photosynthetic asymmetry in the sorghum leaves. The variations of specific gas exchange were significant between direct and diffuse light, including in the incident and self-transmitted light. Compared with direct light, diffuse light reduced the stomatal sensitivity, with the degree of decline being greater in the adaxial surface, which caused weak dorsoventral asymmetry in photosynthesis. The specific photosynthetic characteristics in sorghum leaves varied obviously in direct and diffuse light, including in the incident and self-transmitted light, which contributed to the different overall gas exchange. Compared with direct light, the decline of stomatal sensitivity, which showed positive correlation with stomatal density, caused weakened dorsoventral asymmetry in photosynthesis in diffuse light. The findings provide new insights into dorsoventral asymmetry and the impact of diffuse light on photosynthesis in isobilateral leaves.

GmFtsH25 overexpression increases soybean seed yield by enhancing photosynthesis and photosynthates

Increasing plant photosynthetic capacity is a promising approach to boost yields, but it is particularly challenging in C₃ crops, such as soybean (Glycine max (L.) Merr.). Here, we identified GmFtsH25, encoding a member of the filamentation temperature-sensitive protein H protease family, as a major gene involved in soybean photosynthesis, using linkage mapping and a genome-wide association study. Overexpressing GmFtsH25 resulted in more grana thylakoid stacks in chloroplasts and increased photosynthetic efficiency and starch content, while knocking out GmFtsH25 produced the opposite phenotypes. GmFtsH25 interacted with photosystem I light harvesting complex 2 (GmLHCa2), and this interaction may contribute to the observed enhanced photosynthesis. GmFtsH25 overexpression lines had superior yield traits, such as yield per plant, compared to the wild type and knockout lines. Additionally, we identified an elite haplotype of GmFtsH25, generated by natural mutations, which appears to have been selected during soybean domestication. Our study sheds light on the molecular mechanism by which GmFtsH25 modulates photosynthesis and provides a promising strategy for improving the yields of soybean and other crops.

Short-term elevated temperature and CO2 promote photosynthetic induction in the C3 plant Glycine max, but not in the C4 plant Amaranthus tricolor

The continuous increases of atmospheric temperature and CO2 concentration will impact global photosynthesis. However, there are few studies considering the interaction of elevated temperature (eT) and elevated CO2 (eCO2 ) on dynamic photosynthesis, particularly for C4 species. We examine dynamic photosynthesis under four different temperature and [CO2 ] treatments: (1) 400ppm×28°C (CT); (2) 400ppm×33°C (CT+); (3) 800ppm×28°C (C+T); and (4) 800ppm×33°C (C+T+). In Glycine max L., the time required to reach 50% (T 50%A ) and 90% (T 90%A ) of full photosynthetic induction was smaller under the CT+, C+T, and C+T+ treatments than those under the CT treatment. In Amaranthus tricolor L., however, neither T 50%A nor T 90%A was not significantly affected by eT or eCO2 . In comparison with the CT treatment, the achieved carbon gain was increased by 58.3% (CT+), 112% (C+T), and 136.6% (C+T+) in G. max and was increased by 17.1% (CT+), 2.6% (C+T) and 56.9% (C+T+) in A. tricolor . The increases of achieved carbon gain in G. max were attributable to both improved photosynthetic induction efficiency (IE) and enhanced steady-state photosynthesis, whereas those in A. tricolor were attributable to enhanced steady-state photosynthesis.

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.

Elucidating the role of SWEET13 in phloem loading of the C4 grass Setaria viridis

Photosynthetic efficiency and sink demand are tightly correlated with rates of phloem loading, where maintaining low cytosolic sugar concentrations is paramount to prevent the downregulation of photosynthesis. Sugars Will Eventually be Exported Transporters (SWEETs) are thought to have a pivotal role in the apoplastic phloem loading of C₄ grasses. SWEETs have not been well studied in C₄ species, and their investigation is complicated by photosynthesis taking place across two cell types and, therefore, photoassimilate export can occur from either one. SWEET13 homologues in C₄ grasses have been proposed to facilitate apoplastic phloem loading. Here, we provide evidence for this hypothesis using the C₄ grass Setaria viridis. Expression analyses on the leaf gradient of C₄ species Setaria and Sorghum bicolor show abundant transcript levels for SWEET13 homologues. Carbohydrate profiling along the Setaria leaf shows total sugar content to be significantly higher in the mature leaf tip compared with the younger tissue at the base. We present the first known immunolocalization results for SvSWEET13a and SvSWEET13b using novel isoform-specific antisera. These results show localization to the bundle sheath and phloem parenchyma cells of both minor and major veins. We further present the first transport kinetics study of C₄ monocot SWEETs by using a Xenopus laevis oocyte heterologous expression system. We demonstrate that SvSWEET13a and SvSWEET13b are high-capacity transporters of glucose and sucrose, with a higher apparent V_max for sucrose, compared with glucose, typical of clade III SWEETs. Collectively, these results provide evidence for an apoplastic phloem loading pathway in Setaria and possibly other C₄ species.

Why is C4 photosynthesis so rare in trees?

Since C4 photosynthesis was first discovered >50 years ago, researchers have sought to understand how this complex trait evolved from the ancestral C3 photosynthetic machinery on >60 occasions. Despite its repeated emergence across the plant kingdom, C4 photosynthesis is notably rare in trees, with true C4 trees only existing in Euphorbia. Here we consider aspects of the C4 trait that could limit but not preclude the evolution of a C4 tree, including reduced quantum yield, increased energetic demand, reduced adaptive plasticity, evolutionary constraints, and a new theory that the passive symplastic phloem loading mechanism observed in trees, combined with difficulties in maintaining sugar and water transport over a long pathlength, could make C4 photosynthesis largely incompatible with the tree lifeform. We conclude that the transition to a tree habit within C4 lineages as well as the emergence of C4 photosynthesis within pre-existing trees would both face a series of challenges that together explain the global rarity of C4 photosynthesis in trees. The C4 trees in Euphorbia are therefore exceptional in how they have circumvented every potential barrier to the rare C4 tree lifeform.

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.

Photosynthesis capacity diversified by leaf structural and physiological regulation between upland and lowland switchgrass in different growth stages

Understanding and enhancing switchgrass (Panicum virgatum L.) photosynthesis will help to improve yield and quality for bio-industrial applications on cellulosic biofuel production. In the present study, leaf anatomical traits and physiological characteristics related to photosynthetic capacity of both lowland and upland switchgrass were recorded from four varieties across the vegetative, elongation and reproductive growth stages. Compared with the upland varieties, the lowland switchgrass showed 37-59, 22-64 and 27-73% higher performance on height, stem and leaf over all three growth stages. Leaf anatomical traits indicated that the leaves of lowland varieties provided more space for carbon assimilation and transportation caused by enhanced cell proliferation with more bundles sheath cells and larger contact areas between the bundle sheath and mesophyll cells (CAMB), which lead to the 32-72% higher photosynthetic capacity found in the lowland varieties during vegetative and elongation growth. However, photosynthetic capacity became 22-51% higher in the upland varieties during the reproductive stage, which is attributed to more photosynthetic pigment. In conclusion, lowland varieties gain a photosynthetic advantage with enhanced bundle sheath cell proliferation, while the upland varieties preserved more photosynthetic pigments. Our study provides new insights for improving the yield in crops by enhancing photosynthesis with anatomical and physiological strategies.

Physiological and Proteomics Analyses Reveal Low-Phosphorus Stress Affected the Regulation of Photosynthesis in Soybean

Previous studies have revealed a significant genetic relationship between phosphorus (P)-efficiency and photosynthesis-related traits in soybean. In this study, we used proteome profiling in combination with expression analysis, biochemical investigations, and leaf ultrastructural analysis to identify the underlying physiological and molecular responses. The expression analysis and ultrastructural analysis showed that the photosynthesis key genes were decreased at transcript levels and the leaf mesophyll and chloroplast were severely damaged after low-P stress. Approximately 55 protein spots showed changes under low-P condition by mass spectrometry, of which 17 were involved in various photosynthetic processes. Further analysis revealed the depression of photosynthesis caused by low-P stress mainly involves the regulation of leaf structure, adenosine triphosphate (ATP) synthesis, absorption and transportation of CO₂, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. In summary, our findings indicated that the existence of a stringent relationship between P supply and the genomic control of photosynthesis in soybean. As an important strategy to protect soybean photosynthesis, P could maintain the stability of cell structure, up-regulate the enzymes’ activities, recover the process of photosystem II (PSII), and induce the expression of low-P responsive genes and proteins.

Nitrogen supply influences photosynthesis establishment along the sugarcane leaf

Nitrogen (N) is a major component of the photosynthetic apparatus and is widely used as a fertilizer in crops. However, to the best of our knowledge, the dynamic of photosynthesis establishment due to differential N supply in the bioenergy crop sugarcane has not been reported to date. To address this question, we evaluated physiological and metabolic alterations along the sugarcane leaf in two contrasting genotypes, responsive (R) and nonresponsive (NR), grown under high- and low-N conditions. We found that the N supply and the responsiveness of the genotype determined the degree of senescence, the carboxylation process mediated by phosphoenolpyruvate carboxylase (PEPcase) and differential accumulation of soluble sugars. The metabolite profiles indicated that the NR genotype had a higher respiration rate in the youngest tissues after exposure to high N. We observed elevated levels of metabolites related to photosynthesis in almost all leaf segments from the R genotype under high-N conditions, suggesting that N supply and the ability to respond to N influenced photosynthesis. Therefore, we observed that N influence on photosynthesis and other pathways is dependent on the genotype and the leaf region.

Impact of anatomical traits of maize (Zea mays L.) leaf as affected by nitrogen supply and leaf age on bundle sheath conductance

The mechanism of photosynthesis in C₄ crops depends on the archetypal Kranz-anatomy. To examine how the leaf anatomy, as altered by nitrogen supply and leaf age, affects the bundle sheath conductance (g_bs), maize (Zea mays L.) plants were grown under three contrasting nitrogen levels. Combined gas exchange and chlorophyll fluorescence measurements were done on fully grown leaves at two leaf ages. The measured data were analysed using a biochemical model of C₄ photosynthesis to estimate g_bs. The leaf microstructure and ultrastructure were quantified using images obtained from micro-computed tomography and microscopy. There was a strong positive correlation between g_bs and leaf nitrogen content (LNC) while old leaves had lower g_bs than young leaves. Leaf thickness, bundle sheath cell wall thickness and surface area of bundle sheath cells per unit leaf area (S_b) correlated well with g_bs although they were not significantly affected by LNC. As a result, the increase of g_bs with LNC was little explained by the alteration of leaf anatomy. In contrast, the combined effect of LNC and leaf age on S_b was responsible for differences in g_bs between young leaves and old leaves. Future investigations should consider changes at the level of plasmodesmata and membranes along the CO₂ leakage pathway to unravel LNC and age effects further.

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.

A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis

C4 photosynthesis is used by only three percent of all flowering plants, but explains a quarter of global primary production, including some of the worlds' most important cereals and bioenergy grasses. Recent advances in our understanding of C4 development can be attributed to the application of comparative transcriptomics approaches that has been fueled by high throughput sequencing. Global surveys of gene expression conducted between different developmental stages or on phylogenetically closely related C3 and C4 species are providing new insights into C4 function, development and evolution. Importantly, through co-expression analysis and comparative genomics, these studies help define novel candidate genes that transcend traditional genetic screens. In this review, we briefly summarize the major findings from recent transcriptomic studies, compare and contrast these studies to summarize emerging consensus, and suggest new approaches to exploit the data. Finally, we suggest using Setaria viridis as a model system to relieve a major bottleneck in genetic studies of C4 photosynthesis, and discuss the challenges and new opportunities for future comparative transcriptomic studies.

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.

Temperature response of bundle-sheath conductance in maize leaves

A small bundle-sheath conductance (g bs) is essential for the C4 CO2-concentrating mechanism to suppress photorespiration effectively. To predict the productivity of C4 crops accurately under global warming, it is necessary to examine whether and how g bs responds to temperature. We investigated the temperature response of g bs in maize by fitting a C4 photosynthesis model to combined gas exchange and chlorophyll fluorescence measurements of irradiance and CO2 response curves at 21% and 2% O2 within the range of 13.5-39 °C. The analysis was based on reported kinetic constants of C4 Rubisco and phosphoenolpyruvate carboxylase and temperature responses of C3 mesophyll conductance (g m). The estimates of g bs varied greatly with leaf temperature. The temperature response of g bs was well described by the peaked Arrhenius equation, with the optimum temperature being ~34 °C. The assumed temperature responses of g m had only a slight impact on the temperature response of g bs In contrast, using extreme values of some enzyme kinetic constants changed the shape of the response, from the peaked optimum response to the non-peaked Arrhenius pattern. Further studies are needed to confirm such an Arrhenius response pattern from independent measurement techniques and to assess whether it is common across C4 species.

Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model

Maize (Zea mays) is an important C4 plant due to its widespread use as a cereal and energy crop. A second-generation genome-scale metabolic model for the maize leaf was created to capture C4 carbon fixation and investigate nitrogen (N) assimilation by modeling the interactions between the bundle sheath and mesophyll cells. The model contains gene-protein-reaction relationships, elemental and charge-balanced reactions, and incorporates experimental evidence pertaining to the biomass composition, compartmentalization, and flux constraints. Condition-specific biomass descriptions were introduced that account for amino acids, fatty acids, soluble sugars, proteins, chlorophyll, lignocellulose, and nucleic acids as experimentally measured biomass constituents. Compartmentalization of the model is based on proteomic/transcriptomic data and literature evidence. With the incorporation of information from the MetaCrop and MaizeCyc databases, this updated model spans 5,824 genes, 8,525 reactions, and 9,153 metabolites, an increase of approximately 4 times the size of the earlier iRS1563 model. Transcriptomic and proteomic data have also been used to introduce regulatory constraints in the model to simulate an N-limited condition and mutants deficient in glutamine synthetase, gln1-3 and gln1-4. Model-predicted results achieved 90% accuracy when comparing the wild type grown under an N-complete condition with the wild type grown under an N-deficient condition.

Acclimation of C4 metabolism to low light in mature maize leaves could limit energetic losses during progressive shading in a crop canopy

C4 plants have a biochemical carbon-concentrating mechanism that increases CO2 concentration around Rubisco in the bundle sheath. Under low light, the activity of the carbon-concentrating mechanism generally decreases, associated with an increase in leakiness (ϕ), the ratio of CO2 retrodiffusing from the bundle sheath relative to C4 carboxylation. This increase in ϕ had been theoretically associated with a decrease in biochemical operating efficiency (expressed as ATP cost of gross assimilation, ATP/GA) under low light and, because a proportion of canopy photosynthesis is carried out by shaded leaves, potential productivity losses at field scale. Maize plants were grown under light regimes representing the cycle that leaves undergo in the canopy, whereby younger leaves initially developed under high light and were then re-acclimated to low light (600 to 100 μE·m(-2)·s(-1) photosynthetically active radiation) for 3 weeks. Following re-acclimation, leaves reduced rates of light-respiration and reached a status of lower ϕ, effectively optimizing the limited ATP resources available under low photosynthetically active radiation. Direct estimates of respiration in the light, and ATP production rate, allowed an empirical estimate of ATP production rate relative to gross assimilation to be derived. These values were compared to modelled ATP/GA which was predicted using leakiness as the sole proxy for ATP/GA, and, using a novel comprehensive biochemical model, showing that irrespective of whether leaves are acclimated to very low or high light intensity, the biochemical efficiency of the C4 cycle does not decrease at low photosynthetically active radiation.

Bundle sheath suberization in grass leaves: multiple barriers to characterization

High-yielding, stress-tolerant grass crops are essential to meet future food and energy demands. Efforts are underway to engineer improved varieties of the C3 cereal crop rice by introducing NADP-malic enzyme C4 photosynthesis using maize as a model system. However, several modifications to the rice leaf vasculature are potentially necessary, including the introduction of suberin lamellae into the bundle sheath cell walls. Suberized cell walls are ubiquitous in the root endodermis of all grasses, and developmental similarities are apparent between endodermis and bundle sheath cell walls. Nonetheless, there is considerable heterogeneity in sheath cell development and suberin composition both within and between grass taxa. The effect of this variation on physiological function remains ambiguous over forty years after suberin lamellae were initially proposed to regulate solute and photoassimilate fluxes and C4 gas exchange. Interspecies variation has confounded efforts to ascribe physiological differences specifically to the presence or absence of suberin lamellae. Thus, specific perturbation of suberization within a uniform genetic background is needed, but, until recently, the genetic resources to manipulate suberin composition in the grasses were largely unavailable. The recent dissection of the suberin biosynthesis pathway in model dicots and the identification of several promising candidate genes in model grasses will facilitate the characterization of the first suberin biosynthesis genes in a monocot. Much remains to be learned about the role of bundle sheath suberization in leaf physiology, but the stage is set for significant advances in the near future.

Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species

C4 photosynthesis affords higher photosynthetic carbon conversion efficiency than C3 photosynthesis and it therefore represents an attractive target for engineering efforts aiming to improve crop productivity. To this end, blueprints are required that reflect C4 metabolism as closely as possible. Such blueprints have been derived from comparative transcriptome analyses of C3 species with related C4 species belonging to the NAD-malic enzyme (NAD-ME) and NADP-ME subgroups of C4 photosynthesis. However, a comparison between C3 and the phosphoenolpyruvate carboxykinase (PEP-CK) subtype of C4 photosynthesis is still missing. An integrative analysis of all three C4 subtypes has also not been possible to date, since no comparison has been available for closely related C3 and PEP-CK C4 species. To generate the data, the guinea grass Megathyrsus maximus, which represents a PEP-CK species, was analysed in comparison with a closely related C3 sister species, Dichanthelium clandestinum, and with publicly available sets of RNA-Seq data from C4 species belonging to the NAD-ME and NADP-ME subgroups. The data indicate that the core C4 cycle of the PEP-CK grass M. maximus is quite similar to that of NAD-ME species with only a few exceptions, such as the subcellular location of transfer acid production and the degree and pattern of up-regulation of genes encoding C4 enzymes. One additional mitochondrial transporter protein was associated with the core cycle. The broad comparison identified sucrose and starch synthesis, as well as the prevention of leakage of C4 cycle intermediates to other metabolic pathways, as critical components of C4 metabolism. Estimation of intercellular transport fluxes indicated that flux between cells is increased by at least two orders of magnitude in C4 species compared with C3 species. In contrast to NAD-ME and NADP-ME species, the transcription of photosynthetic electron transfer proteins was unchanged in PEP-CK. In summary, the PEP-CK blueprint of M. maximus appears to be simpler than those of NAD-ME and NADP-ME plants.

Bundle-sheath leakiness in C4 photosynthesis: a careful balancing act between CO2 concentration and assimilation

Crop species with the C4 photosynthetic pathway are generally characterized by high productivity, especially in environmental conditions favouring photorespiration. In comparison with the ancestral C3 pathway, the biochemical and anatomical modifications of the C4 pathway allow spatial separation of primary carbon acquisition in mesophyll cells and subsequent assimilation in bundle-sheath cells. The CO2-concentrating C4 cycle has to operate in close coordination with CO2 reduction via the Calvin-Benson-Bassham (CBB) cycle in order to keep the C4 pathway energetically efficient. The gradient in CO2 concentration between bundle-sheath and mesophyll cells facilitates diffusive leakage of CO2. This rate of bundle-sheath CO2 leakage relative to the rate of phosphoenolpyruvate carboxylation (termed leakiness) has been used to probe the balance between C4 carbon acquisition and subsequent reduction as a result of environmental perturbations. When doing so, the correct choice of equations to derive leakiness from stable carbon isotope discrimination (Δ(13)C) during gas exchange is critical to avoid biased results. Leakiness responses to photon flux density, either short-term (during measurements) or long-term (during growth and development), can have important implications for C4 performance in understorey light conditions. However, recent reports show leakiness to be subject to considerable acclimation. Additionally, the recent discovery of two decarboxylating C4 cycles operating in parallel in Zea mays suggests that flexibility in the transported C4 acid and associated decarboxylase could also aid in maintaining C4/CBB balance in a changing environment. In this paper, we review improvements in methodology to estimate leakiness, synthesize reports on bundle-sheath leakiness, discuss different interpretations, and highlight areas where future research is necessary.

Effects of mutual shading on the regulation of photosynthesis in field-grown sorghum

In the field, close planting inevitably causes mutual shading and depression of leaf photosynthesis. To clarify the regulative mechanisms of photosynthesis under these conditions, the effects of planting density on leaf structure, gas exchange and proteomics were carefully studied in field-grown sorghum. In the absence of mineral deficiency, (1) close planting induced a significant decrease in light intensity within populations, which further resulted in much lower stomatal density and other anatomical characteristics associated with shaded leaves; (2) sorghum grown at high planting density had a lower net photosynthetic rate and stomatal conductance than those grown at low planting density; (3) approximately 62 protein spots changed their expression levels under the high planting density conditions, and 22 proteins associated with photosynthesis were identified by mass spectrometry. Further analysis revealed the depression of photosynthesis caused by mutual shading involves the regulation of leaf structure, absorption and transportation of CO2, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. Additionally, heat shock protein and oxygen-evolving enhancer protein play important roles in photoprotection in field-grown sorghum. A model for the regulation of photosynthesis under mutual shading was suggested based on our results.

Acclimation to low light by C4 maize: implications for bundle sheath leakiness

C4 plants have a biochemical carbon concentrating mechanism (CCM) that increases CO2 concentration around ribulose bisphosphate carboxylase oxygenase (Rubisco) in the bundle sheath (BS). Under limiting light, the activity of the CCM generally decreases, causing an increase in leakiness, (Φ), the ratio of CO2 retrodiffusing from the BS relative to C4 carboxylation processes. Maize plants were grown under high and low light regimes (respectively HL, 600 versus LL, 100 μE m(-2)  s(-1) ). Short-term acclimation of Φ was compared from isotopic discrimination (Δ), gas exchange and photochemistry. Direct measurement of respiration in the light, and ATP production rate (JATP ), allowed us use a novel approach to derive Φ, compared with the conventional fitting of measured and predicted Δ. HL grown plants responded to decreasing light intensities with the well-documented increase in Φ. Conversely, LL plants showed a constant Φ, which has not been observed previously. We explain the pattern by two contrasting acclimation strategies: HL plants maintained a high CCM activity at LL, resulting in high CO2 overcycling and increased Φ; LL plants acclimated by down-regulating the CCM, effectively optimizing scarce ATP supply. This surprising plasticity may limit the impact of Φ-dependent carbon losses in leaves becoming shaded within developing canopies.

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.

Molecular evolution of genes recruited into C₄ photosynthesis

The C₄ pathway is found in 62 lineages of land plants. We assess evidence for parallel versus convergent evolution of C₄ photosynthesis from three approaches: (i) studies of specific genes and cis-elements controlling their expression; (ii) phylogenetic analyses of mRNAs and inferred amino acid sequences; and (iii) analysis of C₃ and C₄ genomes and transcriptomes. Evidence suggests that although convergent evolution is common, parallel evolution can underlie both changes to gene expression and amino acid sequence. cis-elements that direct cell specificity in C₄ leaves are present in C₃ orthologues of genes recruited into C₄, probably facilitating this parallel evolution. From this, and genomic data, we propose that gene duplication followed by neofunctionalisation is not necessarily important in the evolution of C₄ biochemistry.

Quantification of plant cell coupling with three-dimensional photoactivation microscopy

Plant cells are directly connected by plasmodesmata that form channels through the cell wall and enable the intercellular movement of cytosolic solutes, membrane lipids and signalling molecules. Transport through plasmodesmata is regulated not only by a fixed size-exclusion limit, but also by physiological and pathological adaptation. To understand plant cell communication, carbon allocation and pathogen attack, the capacities for a specific molecule to pass a specific cell-wall interface is an essential parameter. So far, the degree of cell coupling was derived from frequency and diameter of plasmodesmata in relevant tissues as assessed by electron microscopy of fixed material. However, plasmodesmata functionality and capacity can only be determined in live material, not from electron microscopy, which is static and prone to fixation artefacts. Plasmodesmata functionality was a few times assessed using fluorescent tracers with diffusion properties similar to cytosolic solutes. Here, we used three-dimensional photoactivation microscopy to quantify plasmodesmata-mediated cell-wall permeability between living Cucurbita maxima leaf mesophyll cells with caged fluorescein as tracer. For the first time, all necessary functional and anatomical data were gathered for each individual cell from three-dimensional time series. This approach utilized a confocal microscope equipped with resonant scanner, which provides the high acquisition speed necessary to record optical sections of whole cells and offers time resolution high enough to follow the kinetics of photoactivation. The results were compared to two-dimensional measurements, which are shown to give a good estimate of cell coupling adequate for homogenous tissues. The two-dimensional approach is limited whenever tissues interfaces are studied that couple different cell types with diverse cell geometries.

Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation

We systematically analyzed a developmental gradient of the third maize (Zea mays) leaf from the point of emergence into the light to the tip in 10 continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, and photosynthetic rate measurements showed that the maize leaf undergoes a sink-to-source transition without an intermediate phase of C(3) photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination, showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C(4) photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C(4) photosynthesis. All data sets are included within the publication to serve as a resource for maize leaf systems biology.

Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C(3) and C(4) species

Next-generation sequencing enables the study of species without a sequenced genome at the 'omics' level. Custom transcriptome databases are generated and global expression profiles can be compared. However, the assembly of transcriptome sequence reads into contigs remains a daunting task. In this study, five different assembly programs, both traditional overlap-based, 'read-centric' assemblers and de Bruijn graph data structure-based assemblers, were compared. To this end, artificial read libraries with and without simulated sequencing errors were constructed from Arabidopsis thaliana, based on quantitative profiles of mature leaf tissue. The open source TGICL pipeline and the commercial CLC bio genomics workbench produced the best assemblies in terms of contig length, hybrid assemblies, redundancy reduction, and error tolerance. The mature leaf transcriptomes of the C(3) species Cleome spinosa and the C(4) species Cleome gynandra were assembled and analysed. The pathways and cellular processes tagged in the transcriptome assemblies reflect processes of a mature leaf. The databases are useful for extracting transcripts related to C(4) processes as full-length or nearly full-length sequences.

The grass leaf developmental gradient as a platform for a systems understanding of the anatomical specialization of C(4) leaves

C(4) photosynthesis relies on spatial and quantitative specializations of common features of leaf anatomy, including venation pattern, bundle sheath cell and chloroplast differentiation, plasmodesmatal abundance, and secondary cell wall enhancement. It has thus far been challenging to dissect the molecular basis for these C(4)-specific alterations in spatial and quantitative patterns of regulation. The target downstream networks of genes and protein interactions that produce these fundamental anatomical features in both C(4) and C(3) species are poorly understood. The developing leaves of monocot grasses provide a base-to-tip gradient of developmental stages that can provide the platform for comprehensive molecular and anatomical data that can yield a better understanding both of the regulators and the targets that produce C(4) patterns, through a variety of gene discovery and systems analysis strategies.

Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize

C(4) grasses, such as maize (Zea mays), have high photosynthetic efficiency through combined biochemical and structural adaptations. C(4) photosynthesis is established along the developmental axis of the leaf blade, leading from an undifferentiated leaf base just above the ligule into highly specialized mesophyll cells (MCs) and bundle sheath cells (BSCs) at the tip. To resolve the kinetics of maize leaf development and C(4) differentiation and to obtain a systems-level understanding of maize leaf formation, the accumulation profiles of proteomes of the leaf and the isolated BSCs with their vascular bundle along the developmental gradient were determined using large-scale mass spectrometry. This was complemented by extensive qualitative and quantitative microscopy analysis of structural features (e.g., Kranz anatomy, plasmodesmata, cell wall, and organelles). More than 4300 proteins were identified and functionally annotated. Developmental protein accumulation profiles and hierarchical cluster analysis then determined the kinetics of organelle biogenesis, formation of cellular structures, metabolism, and coexpression patterns. Two main expression clusters were observed, each divided in subclusters, suggesting that a limited number of developmental regulatory networks organize concerted protein accumulation along the leaf gradient. The coexpression with BSC and MC markers provided strong candidates for further analysis of C(4) specialization, in particular transporters and biogenesis factors. Based on the integrated information, we describe five developmental transitions that provide a conceptual and practical template for further analysis. An online protein expression viewer is provided through the Plant Proteome Database.

Can the progressive increase of C₄ bundle sheath leakiness at low PFD be explained by incomplete suppression of photorespiration?

The ability to concentrate CO₂ around Rubisco allows C₄ crops to suppress photorespiration. However, as phosphoenolpyruvate regeneration requires ATP, the energetic efficiency of the C₄ pathway at low photosynthetic flux densities (PFD) becomes a balancing act between primary fixation and concentration of CO₂ in mesophyll (M) cells, and CO₂ reduction in bundle sheath (BS) cells. At low PFD, retro-diffusion of CO₂ from BS cells, relative to the rate of bicarbonate fixation in M cells (termed leakiness φ), is known to increase. This paper investigates whether this increase in ϕ could be explained by incomplete inhibition of photorespiration. The PFD response of φ was measured at various O₂ partial pressures in young Zea mays plants grown at 250 (LL) and 750 µmol m⁻² s⁻¹ PFD (HL). φ increased at low PFD and was positively correlated with O₂ partial pressure. Low PFD during growth caused BS conductance and interveinal distance to be lower in the LL plants, compared to the HL plants, which correlated with lower φ. Model analysis showed that incomplete inhibition of photorespiration, especially in the HL plants, and an increase in the relative contribution of mitochondrial respiration at low PFD could explain the observed increases in φ.

Variations in the dorso-ventral organization of leaf structure and Kranz anatomy coordinate the control of photosynthesis and associated signalling at the whole leaf level in monocotyledonous species

Photosynthesis and associated signalling are influenced by the dorso-ventral properties of leaves. The degree of adaxial/abaxial symmetry in stomatal numbers, photosynthetic regulation with respect to light orientation and the total section areas of the bundle sheath (BS) cells and the surrounding mesophyll (M) cells on the adaxial and abaxial sides of the vascular bundles were compared in two C(4)[Zea mays (maize) and Paspalum dilatatum] and one C(3)[Triticum turgidum (Durum wheat)] monocotyledonous species. The C(3) leaves had a higher degree of dorso-ventral symmetry than the C(4) leaves. Photosynthetic regulation was the same on each side of the wheat leaves, as were stomatal numbers and the section area of the BS relative to that of the M cells (BS/M section area ratio). In contrast, photosynthetic regulation in maize and P. dilatatum leaves showed a marked surface-specific response to light orientation. Compared to the adaxial sides of the C(4) monocotyledonous leaves, the abaxial surfaces had more stomata and the BS/M section area ratio was significantly higher. Differences in dorso-ventral structure, particularly in Kranz anatomy, serve not only to maximize photosynthetic capacity with respect light orientation in C(4) monocotyledonous leaves but also allow adaxial and abaxial-specific signalling from the respective M cells.

Cell-type-specific differentiation of chloroplasts in C4 plants

In leaves of C4 grasses such as maize, photosynthetic activities are partitioned between bundle-sheath and mesophyll cells, leading to increased photosynthetic yield, particularly under stress conditions. As we discuss here, recent comparative chloroplast proteome analyses in maize have shown specific adaptation to C4-cell-specific differentiation of the photosynthetic apparatus, primary and secondary metabolism and metabolite transporters, as well as the chloroplast protein homeostasis machinery. Furthermore, a novel bundle-sheath-enriched 1000-kDa NADPH dehydrogenase 'supercomplex' has been identified, and we discuss its possible role in inorganic carbon concentration. These breakthroughs provide new opportunities to further unravel C4 pathways and to increase crop productivity through metabolic engineering of C4 pathways into C3 plants, such as rice.