Using evolution as a guide to engineer kranz-type c4 photosynthesis

Comparative characteristics of oat doubled haploids and oat × maize addition lines: Anatomical features of the leaves, chlorophyll a fluorescence and yield parameters

As a result of oat (Avena sativa L.) × maize (Zea mays L.) crossing, maize chromosomes may not be completely eliminated at the early stages of embryogenesis, leading to the oat × maize addition (OMA) lines development. Introgression of maize chromosomes into oat genome can cause morphological and physiological modifications. The aim of the research was to evaluate the leaves' anatomy, chlorophyll a fluorescence, and yield parameter of oat doubled haploid (DH) and OMA lines obtained by oat × maize crossing. The present study examined two DH and two disomic OMA lines and revealed that they differ significantly in the majority of studied traits, apart from: the number of cells of the outer bundle sheath; light energy absorption; excitation energy trapped in PSII reaction centers; and energy dissipated from PSII. The OMA II line was characterized by larger size of single cells in the outer bundle sheath and greater number of seeds per plant among tested lines.

C4 rice engineering, beyond installing a C4 cycle

C4 photosynthesis in higher plants is carried out by two distinct cell types: mesophyll cells and bundle sheath cells, as a result highly concentrated carbon dioxide is released surrounding RuBisCo in chloroplasts of bundle sheath cells and the photosynthetic efficiency is significantly higher than that of C3 plants. The evolution of the dual-cell C4 cycle involved complex modifications to leaf anatomy and cell ultra-structures. These include an increase in leaf venation, the formation of Kranz anatomy, changes in chloroplast morphology in bundle sheath cells, and increases in the density of plasmodesmata at interfaces between the bundle sheath and mesophyll cells. It is predicted that cereals will be in severe worldwide shortage at the mid-term of this century. Rice is a staple food that feeds more than half of the world's population. If rice can be engineered to perform C4 photosynthesis, it is estimated that rice yield will be increased by at least 50% due to enhanced photosynthesis. Thus, the Second Green Revolution has been launched on this principle by genetically installing C4 photosynthesis into C3 crops. The studies on molecular mechanisms underlying the changes in leaf morphoanatomy involved in C4 photosynthesis have made great progress in recent years. As there are plenty of reviews discussing the installment of the C4 cycle, we focus on the current progress and challenges posed to the research regarding leaf anatomy and cell ultra-structure modifications made towards the development of C4 rice.

SHORT ROOT and INDETERMINATE DOMAIN family members govern PIN-FORMED expression to regulate minor vein differentiation in rice

C3 and C4 grasses directly and indirectly provide the vast majority of calories to the human diet, yet our understanding of the molecular mechanisms driving photosynthetic productivity in grasses is largely unexplored. Ground meristem cells divide to form mesophyll or vascular initial cells early in leaf development in C3 and C4 grasses. Here we define a genetic circuit composed of SHORT ROOT (SHR), INDETERMINATE DOMAIN (IDD), and PIN-FORMED (PIN) family members that specifies vascular identify and ground cell proliferation in leaves of both C3 and C4 grasses. Ectopic expression and loss-of-function mutant studies of SHR paralogs in the C3 plant Oryza sativa (rice) and the C4 plant Setaria viridis (green millet) revealed the roles of these genes in both minor vein formation and ground cell differentiation. Genetic and in vitro studies further suggested that SHR regulates this process through its interactions with IDD12 and 13. We also revealed direct interactions of these IDD proteins with a putative regulatory element within the auxin transporter gene PIN5c. Collectively, these findings indicate that a SHR-IDD regulatory circuit mediates auxin transport by negatively regulating PIN expression to modulate minor vein patterning in the grasses.

In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici-a comparative study across C3, C4, CAM, and SCC4 model plants

Single-cell C₄ (SCC₄) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC₄ photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C₃, C₄, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC₄ plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC₄ species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC₄ plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC₄ system in comparison with other C₃, C₄, and CAM model plants.

(Don't) Look Up!: Is short-root just a short-root plant?

SHORT-ROOT (SHR) is a mobile transcription factor that plays important roles in ground tissue patterning, stem cell niche specification and maintenance, and vascular development in Arabidopsis roots. Although mRNA and protein of SHR are also found in hypocotyls, inflorescence stems, and leaves, its role in the above-ground organs has been less explored. In most developmental cases, SHR, together with its partner SCARECROW (SCR), regulates the expression of downstream target genes in controlling formative and proliferative cell divisions. Accumulating evidence on the regulatory role of SHR in shoots suggests that SHR may also play key roles in the above-ground organs. Interestingly, recent work has provided new evidence that SHR is also required for cell elongation in the hypocotyl of the etiolated seedling. This suggests that the novel roles of SHR and SHR-mediated regulatory networks can be found in shoots. Furthermore, comparative research on SHR function in roots and shoots will broaden and deepen our understanding of plant growth and development.

Insights into Regulation of C2 and C4 Photosynthesis in Amaranthaceae/Chenopodiaceae Using RNA-Seq

Amaranthaceae (incl. Chenopodiaceae) shows an immense diversity of C₄ syndromes. More than 15 independent origins of C₄ photosynthesis, and the largest number of C₄ species in eudicots signify the importance of this angiosperm lineage in C₄ evolution. Here, we conduct RNA-Seq followed by comparative transcriptome analysis of three species from Camphorosmeae representing related clades with different photosynthetic types: Threlkeldia diffusa (C₃), Sedobassia sedoides (C₂), and Bassia prostrata (C₄). Results show that B. prostrata belongs to the NADP-ME type and core genes encoding for C₄ cycle are significantly upregulated when compared with Sed. sedoides and T. diffusa. Sedobassia sedoides and B. prostrata share a number of upregulated C₄-related genes; however, two C₄ transporters (DIT and TPT) are found significantly upregulated only in Sed. sedoides. Combined analysis of transcription factors (TFs) of the closely related lineages (Camphorosmeae and Salsoleae) revealed that no C₃-specific TFs are higher in C₂ species compared with C₄ species; instead, the C₂ species show their own set of upregulated TFs. Taken together, our study indicates that the hypothesis of the C₂ photosynthesis as a proxy towards C₄ photosynthesis is questionable in Sed. sedoides and more in favour of an independent evolutionary stable state.

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.

Finding the C4 sweet spot: cellular compartmentation of carbohydrate metabolism in C4 photosynthesis

The two-cell type C4 photosynthetic pathway requires both anatomical and biochemical specialization to achieve a functional CO2-concentrating mechanism. While a great deal of research has been done on Kranz anatomy and cell-specific expression and activity of enzymes in the C4 pathway, less attention has been paid to partitioning of carbohydrate synthesis between the cell types of C4 leaves. As early as the 1970s it became apparent that, in the small number of species examined at the time, sucrose was predominantly synthesized in the mesophyll cells and starch in the bundle sheath cells. Here we discuss how this partitioning is achieved in C4 plants and explore whether this is a consequence of C4 metabolism or indeed a requirement for its evolution and efficient operation.

Finding the C4 sweet spot: cellular compartmentation of carbohydrate metabolism in C4 photosynthesis

The two-cell type C4 photosynthetic pathway requires both anatomical and biochemical specialization to achieve a functional CO2-concentrating mechanism. While a great deal of research has been done on Kranz anatomy and cell-specific expression and activity of enzymes in the C4 pathway, less attention has been paid to partitioning of carbohydrate synthesis between the cell types of C4 leaves. As early as the 1970s it became apparent that, in the small number of species examined at the time, sucrose was predominantly synthesized in the mesophyll cells and starch in the bundle sheath cells. Here we discuss how this partitioning is achieved in C4 plants and explore whether this is a consequence of C4 metabolism or indeed a requirement for its evolution and efficient operation.

grasviq: an image analysis framework for automatically quantifying vein number and morphology in grass leaves

Beyond facilitating transport and providing mechanical support to the leaf, veins have important roles in the performance and productivity of plants and the ecosystem. In recent decades, computational image analysis has accelerated the extraction and quantification of vein traits, benefiting fields of research from agriculture to climatology. However, most of the existing leaf vein image analysis programs have been developed for the reticulate venation found in dicots. Despite the agroeconomic importance of cereal grass crops, like Oryza sativa (rice) and Zea mays (maize), a dedicated image analysis program for the parallel venation found in monocots has yet to be developed. To address the need for an image-based vein phenotyping tool for model and agronomic grass species, we developed the grass vein image quantification (grasviq) framework. Designed specifically for parallel venation, this framework automatically segments and quantifies vein patterns from images of cleared leaf pieces using classical computer vision techniques. Using image data sets from maize inbred lines and auxin biosynthesis and transport mutants in maize, we demonstrate the utility of grasviq for quantifying important vein traits, including vein density, vein width and interveinal distance. Furthermore, we show that the framework can resolve quantitative differences and identify vein patterning defects, which is advantageous for genetic experiments and mutant screens. We report that grasviq can perform high-throughput vein quantification, with precision on a par with that of manual quantification. Therefore, we envision that grasviq will be adopted for vein phenomics in maize and other grass species.

Redundant SCARECROW genes pattern distinct cell layers in roots and leaves of maize

The highly efficient C₄ photosynthetic pathway is facilitated by ‘Kranz’ leaf anatomy. In Kranz leaves, closely spaced veins are encircled by concentric layers of photosynthetic bundle sheath (inner) and mesophyll (outer) cells. Here, we demonstrate that, in the C₄ monocot maize, Kranz patterning is regulated by redundant function of SCARECROW 1 (ZmSCR1) and a previously uncharacterized homeologue: ZmSCR1h. ZmSCR1 and ZmSCR1h transcripts accumulate in ground meristem cells of developing leaf primordia and in Zmscr1;Zmscr1h mutant leaves, most veins are separated by one rather than two mesophyll cells; many veins have sclerenchyma above and/or below instead of mesophyll cells; and supernumerary bundle sheath cells develop. The mutant defects are unified by compromised mesophyll cell development. In addition to Kranz defects, Zmscr1;Zmscr1h mutants fail to form an organized endodermal layer in the root. Collectively, these data indicate that ZmSCR1 and ZmSCR1h redundantly regulate cell-type patterning in both the leaves and roots of maize. Leaf and root pathways are distinguished, however, by the cell layer in which they operate – mesophyll at a two-cell distance from leaf veins versus endodermis immediately adjacent to root vasculature.

Summary: Two duplicated maize SCARECROW genes control the development of the endodermis in roots and the mesophyll in leaves.

Reporter-based forward genetic screen to identify bundle sheath anatomy mutants in A. thaliana

The evolution of C₄ photosynthesis proceeded stepwise with each small step increasing the fitness of the plant. An important pre-condition for the introduction of a functional C₄ cycle is the photosynthetic activation of the C₃ bundle sheath by increasing its volume and organelle number. Therefore, to engineer C₄ photosynthesis into existing C₃ crops, information about genes that control the bundle sheath cell size and organelle content is needed. However, very little information is known about the genes that could be manipulated to create a more C₄ -like bundle sheath. To this end, an ethylmethanesulfonate (EMS)-based forward genetic screen was established in the Brassicaceae C₃  species Arabidopsis thaliana. To ensure a high-throughput primary screen, the bundle sheath cells of A. thaliana were labeled using a luciferase (LUC68) or by a chloroplast-targeted green fluorescent protein (sGFP) reporter using a bundle sheath specific promoter. The signal strengths of the reporter genes were used as a proxy to search for mutants with altered bundle sheath anatomy. Here, we show that our genetic screen predominantly identified mutants that were primarily affected in the architecture of the vascular bundle, and led to an increase in bundle sheath volume. By using a mapping-by-sequencing approach the genomic segments that contained mutated candidate genes were identified.

Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes

Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light-dark cycles and under total darkness and obtained eight time-ordered gene coexpression networks (TO-GCNs), which can be used to predict upstream regulators of any genes in the GCNs. One of the eight TO-GCNs is light-independent and likely includes all genes involved in the development of Kranz anatomy, which is a structure crucial for the high efficiency of photosynthesis in C₄ plants. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade upstream of SHORTROOT1, a key Kranz anatomy regulator. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of maize C₄ enzyme genes and RUBISCO SMALL SUBUNIT2 Our study provides not only a powerful method but also novel insights into the regulatory networks underlying Kranz anatomy development and C₄ photosynthesis.

Getting closer: vein density in C4 leaves

Contents Summary 1260 I. Introduction 1260 II. Molecular and genetic mechanisms of C₄ leaf venation 1262 III. Conclusions and future perspectives 1266 Acknowledgements 1266 References 1266 SUMMARY: C₄ grasses are major contributors to the world's food supply. Their highly efficient method of carbon fixation is a unique adaptation that combines close vein spacing and distinct photosynthetic cell types. Despite its importance, the molecular genetic basis of C₄ leaf development is still poorly understood. Here we summarize current knowledge of leaf venation and review recent progress in understanding molecular and genetic regulation of vascular patterning events in C₄ plants. Evidence points to the interplay of auxin, brassinosteroids, SHORTROOT/SCARECROW and INDETERMINATE DOMAIN transcription factors. Identification and functional characterization of candidate regulators acting early in vascular development will be essential for further progress in understanding the precise regulation of these processes.

Screening of Mutants Related to the C4 Photosynthetic Kranz Structure in Foxtail Millet

C₄ plants exhibit significantly higher photosynthetic, water and nutrient use efficiency compared with C₃ plants. Kranz anatomy is associated with many C₄ plants in which bundle sheath cells surround the veins and are themselves surrounded by mesophyll cells. This specialized Kranz anatomy is elucidated as an important contributor to C₄ photosynthetic activities in C₄ plant. Characterizing the molecular basis of Kranz structure formation has become a key objective for studies of C₄ photosynthesis. However, severe mutants that specifically disrupt Kranz anatomy have not been identified. In this study, we detected 549 stable ethyl methane sulfonate-induced foxtail millet (cultivar Yugu1) mutants related to leaf development and photosynthesis among 2,709 mutants screened (M₃/M₄ generation). The identified mutants included 52 that had abnormal leaf veins (with abnormal starch accumulation based on iodine staining). Each of the 52 mutants was characterized through an analysis of leaf morphology, and through microscopic observations of leaf tissue sections embedded in resin and paraffin. In total, 14 mutants were identified with abnormal Kranz structures exemplified by small bundle sheath cell size. Additional phenotypes of the mutants included poorly differentiated mesophyll and bundle sheath cells, increased vein density and the absence of chloroplasts in the bundle sheath cells. Kranz structure mutations were accompanied by varying leaf thickness, implying these mutations induced complex effects. We identified mutations related to Kranz structure development in this trial, which may be useful for the mapping and cloning of genes responsible for mediating Kranz structure development.

Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants

The INDETERMINATE DOMAIN (IDD) family of transcriptional regulators controls a diversity of processes in a variety of plant tissues and organs and at different stages of plant development. Several recent reports describe the genetic characterization of IDD family members, including those that are likely to regulate C₄ kranz anatomy, with implications for the engineering of C₄ traits into C₃ crops. In this review we summarize the reported functions of IDD members in the regulation of metabolic sensing and leaf, root, seed, and inflorescence development. We also provide an IDD phylogeny for the grasses and suggest future directions and strategies to define the function of IDDs in C₄ photosynthesis and other developmental processes.

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.

Shared characteristics underpinning C4 leaf maturation derived from analysis of multiple C3 and C4 species of Flaveria

Most terrestrial plants use C3 photosynthesis to fix carbon. In multiple plant lineages a modified system known as C4 photosynthesis has evolved. To better understand the molecular patterns associated with induction of C4 photosynthesis, the genus Flaveria that contains C3 and C4 species was used. A base to tip maturation gradient of leaf anatomy was defined, and RNA sequencing was undertaken along this gradient for two C3 and two C4 Flaveria species. Key C4 traits including vein density, mesophyll and bundle sheath cross-sectional area, chloroplast ultrastructure, and abundance of transcripts encoding proteins of C4 photosynthesis were quantified. Candidate genes underlying each of these C4 characteristics were identified. Principal components analysis indicated that leaf maturation and the photosynthetic pathway were responsible for the greatest amount of variation in transcript abundance. Photosynthesis genes were over-represented for a prolonged period in the C4 species. Through comparison with publicly available data sets, we identify a small number of transcriptional regulators that have been up-regulated in diverse C4 species. The analysis identifies similar patterns of expression in independent C4 lineages and so indicates that the complex C4 pathway is associated with parallel as well as convergent evolution.

Sucrose Transporter ZmSut1 Expression and Localization Uncover New Insights into Sucrose Phloem Loading

Sucrose transporters (SUTs) translocate sucrose (Suc) across cellular membranes, and in eudicots, multiple SUTs are known to function in Suc phloem loading in leaves. In maize (Zea mays), the Sucrose Transporter1 (ZmSut1) gene has been implicated in Suc phloem loading based upon RNA expression in leaves, electrophysiological experiments, and phenotypic analysis of zmsut1 mutant plants. However, no previous studies have examined the cellular expression of ZmSut1 RNA or the subcellular localization of the ZmSUT1 protein to assess the gene's hypothesized function in Suc phloem loading or to evaluate its potential roles, such as phloem unloading, in nonphotosynthetic tissues. To this end, we performed RNA in situ hybridization experiments, promoter-reporter gene analyses, and ZmSUT1 localization studies to elucidate the cellular expression pattern of the ZmSut1 transcript and protein. These data showed that ZmSut1 was expressed in multiple cell types throughout the plant and indicated that it functions in phloem companion cells to load Suc and also in other cell types to retrieve Suc from the apoplasm to prevent its accumulation and loss to the transpiration stream. Additionally, by comparing a phloem-mobile tracer with ZmSut1 expression, we determined that developing maize leaves dynamically switch from symplasmic to apoplasmic phloem unloading, reconciling previously conflicting reports, and suggest that ZmSut1 does not have an apparent function in either unloading process. A model for the dual roles for ZmSut1 function (phloem loading and apoplasmic recycling), Sut1 evolution, and its possible use to enhance Suc export from leaves in engineering C3 grasses for C4 photosynthesis is discussed.

Modelling metabolic evolution on phenotypic fitness landscapes: a case study on C4 photosynthesis

How did the complex metabolic systems we observe today evolve through adaptive evolution? The fitness landscape is the theoretical framework to answer this question. Since experimental data on natural fitness landscapes is scarce, computational models are a valuable tool to predict landscape topologies and evolutionary trajectories. Careful assumptions about the genetic and phenotypic features of the system under study can simplify the design of such models significantly. The analysis of C4 photosynthesis evolution provides an example for accurate predictions based on the phenotypic fitness landscape of a complex metabolic trait. The C4 pathway evolved multiple times from the ancestral C3 pathway and models predict a smooth 'Mount Fuji' landscape accordingly. The modelled phenotypic landscape implies evolutionary trajectories that agree with data on modern intermediate species, indicating that evolution can be predicted based on the phenotypic fitness landscape. Future directions will have to include structural changes of metabolic fitness landscape structure with changing environments. This will not only answer important evolutionary questions about reversibility of metabolic traits, but also suggest strategies to increase crop yields by engineering the C4 pathway into C3 plants.

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.

Finding the genes to build C4 rice

Rice, a C3 crop, is a staple food for more than half of the world's population, with most consumers living in developing countries. Engineering C4 photosynthetic traits into rice is increasingly suggested as a way to meet the 50% yield increase that is predicted to be needed by 2050. Advances in genome-wide deep-sequencing, gene discovery and genome editing platforms have brought the possibility of engineering a C3 to C4 conversion closer than ever before. Because C4 plants have evolved independently multiple times from C3 origins, it is probably that key genes and gene regulatory networks that regulate C4 were recruited from C3 ancestors. In the past five years there have been over 20 comparative transcriptomic studies published that aimed to identify these recruited C4 genes and regulatory mechanisms. Here we present an overview of what we have learned so far and preview the efforts still needed to provide a practical blueprint for building C4 rice.

Starch Accumulation in the Bundle Sheaths of C3 Plants: A Possible Pre-Condition for C4 Photosynthesis

C4 plants have evolved >60 times from their C3 ancestors. C4 photosynthesis requires a set of closely co-ordinated anatomical and biochemical characteristics. However, it is now recognized that the evolution of C4 plants requires fewer changes than had ever been considered, because of the genetic, biochemical and anatomical pre-conditions of C3 ancestors that were recruited into C4 photosynthesis. Therefore, the pre-conditions in C3 plants are now being actively investigated to clarify the evolutionary trajectory from C3 to C4 plants and to engineer C4 traits efficiently into C3 crops. In the present mini review, the anatomical characteristics of C3 and C4 plants are briefly reviewed and the importance of the bundle sheath for the evolution of C4 photosynthesis is described. For example, while the bundle sheath of C3 rice plants accumulates large amounts of starch in the developing leaf blade and at the lamina joint of the mature leaf, the starch sheath function is also observed during leaf development in starch accumulator grasses regardless of photosynthetic type. The starch sheath function of C3 plants is therefore also implicated as a possible pre-condition for the evolution of C4 photosynthesis. The phylogenetic relationships between the types of storage carbohydrates and of photosynthesis need to be clarified in the future.

Insights into the regulation of C4 leaf development from comparative transcriptomic analysis

C4 photosynthesis is more efficient than C3 photosynthesis for two reasons. First, C4 plants have evolved a repertoire of C4 enzymes to enhance CO2 fixation. Second, C4 leaves have Kranz anatomy with a high vein density in which the veins are surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. The BS and M cells are not only functionally well differentiated, but also well-coordinated for rapid transport of photo-assimilates between the two types of photosynthetic cells. Recent comparative transcriptomic and anatomical analyses of C3 and C4 leaves have revealed early onset of C4-related processes in leaf development, suggesting that delayed mesophyll differentiation contributes to higher C4 vein density, and have identified some candidate regulators for the higher vein density in C4 leaves. Moreover, comparative transcriptomics of maize husk (C3) and foliar leaves (C4) has identified a cohort of candidate regulators of Kranz anatomy development. In addition, there has been major progress in the identification of transcription factor binding sites, greatly increasing our knowledge of gene regulation in plants.

C4 Photosynthesis in the Rice Paddy: Insights from the Noxious Weed Echinochloa glabrescens

The C4 pathway is a highly complex trait that increases photosynthetic efficiency in more than 60 plant lineages. Although the majority of C4 plants occupy disturbed, arid, and nutrient-poor habitats, some grow in high-nutrient, waterlogged conditions. One such example is Echinochloa glabrescens, which is an aggressive weed of rice paddies. We generated comprehensive transcriptome datasets for C4 E. glabrescens and C3 rice to identify genes associated with adaption to waterlogged, nutrient-replete conditions, but also used the data to better understand how C4 photosynthesis operates in these conditions. Leaves of E. glabrescens exhibited classical Kranz anatomy with lightly lobed mesophyll cells having low chloroplast coverage. As with rice and other hygrophytic C3 species, leaves of E. glabrescens accumulated a chloroplastic phosphoenolpyruvate carboxylase protein, albeit at reduced amounts relative to rice. The arid-grown species Setaria italica (C4) and Brachypodium distachyon (C3) were also found to accumulate chloroplastic phosphoenolpyruvate carboxylase. We identified a molecular signature associated with C4 photosynthesis in nutrient-replete, waterlogged conditions that is highly similar to those previously reported from C4 plants that grow in more arid conditions. We also identified a cohort of genes that have been subjected to a selective sweep associated with growth in paddy conditions. Overall, this approach highlights the value of using wild species such as weeds to identify adaptions to specific conditions associated with high-yielding crops in agriculture.

Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species

C(4) photosynthesis outperforms the ancestral C(3) state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C(3) backgrounds. However, the genetic architecture of C(4) photosynthesis remains largely unknown. To define the divergence in gene expression modules between C(3) and C(4) photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C(4)) and Tarenaya hassleriana (C(3)), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C(3) and C(4) species. We found that known C(4) genes were recruited to photosynthesis from different expression domains in C(3), including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C(3) root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C(4) bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C(4) leaf.

From proto-Kranz to C4 Kranz: building the bridge to C4 photosynthesis

In this review, we examine how the specialized "Kranz" anatomy of C4 photosynthesis evolved from C3 ancestors. Kranz anatomy refers to the wreath-like structural traits that compartmentalize the biochemistry of C4 photosynthesis and enables the concentration of CO2 around Rubisco. A simplified version of Kranz anatomy is also present in the species that utilize C2 photosynthesis, where a photorespiratory glycine shuttle concentrates CO2 into an inner bundle-sheath-like compartment surrounding the vascular tissue. C2 Kranz is considered to be an intermediate stage in the evolutionary development of C4 Kranz, based on the intermediate branching position of C2 species in 14 evolutionary lineages of C4 photosynthesis. In the best-supported model of C4 evolution, Kranz anatomy in C2 species evolved from C3 ancestors with enlarged bundle sheath cells and high vein density. Four independent lineages have been identified where C3 sister species of C2 plants exhibit an increase in organelle numbers in the bundle sheath and enlarged bundle sheath cells. Notably, in all of these species, there is a pronounced shift of mitochondria to the inner bundle sheath wall, forming an incipient version of the C2 type of Kranz anatomy. This incipient version of C2 Kranz anatomy is termed proto-Kranz, and is proposed to scavenge photorespiratory CO2. By doing so, it may provide fitness benefits in hot environments, and thus represent a critical first stage of the evolution of both the C2 and C4 forms of Kranz anatomy.

Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes

The comparison of the cell-specific transcriptomes of bundle sheath (BS) and mesophyll (M) cells from successive developmental stages of maize (Zea mays) leaves reveals that the number of genes preferentially transcribed in one cell type or the other varies considerably from the sink-source transition to mature photosynthetic stages. The number of differentially expressed (DE) genes is maximal at a stage well before full maturity, including those that encode key functions for C4 photosynthesis. The developmental dynamics of BS/M differential expression can be used to identify candidates for other C4-related functions and to simplify the identification of specific pathways members from otherwise complex gene families. A significant portion of the candidates for C4-related transcription factors identified with this developmental DE strategy overlap with those identified in studies using alternative strategies, thus providing independent support for their potential importance.

Photosynthesis at the forefront of a sustainable life

The development of a sustainable bio-based economy has drawn much attention in recent years, and research to find smart solutions to the many inherent challenges has intensified. In nature, perhaps the best example of an authentic sustainable system is oxygenic photosynthesis. The biochemistry of this intricate process is empowered by solar radiation influx and performed by hierarchically organized complexes composed by photoreceptors, inorganic catalysts, and enzymes which define specific niches for optimizing light-to-energy conversion. The success of this process relies on its capability to exploit the almost inexhaustible reservoirs of sunlight, water, and carbon dioxide to transform photonic energy into chemical energy such as stored in adenosine triphosphate. Oxygenic photosynthesis is responsible for most of the oxygen, fossil fuels, and biomass on our planet. So, even after a few billion years of evolution, this process unceasingly supports life on earth, and probably soon also in outer-space, and inspires the development of enabling technologies for a sustainable global economy and ecosystem. The following review covers some of the major milestones reached in photosynthesis research, each reflecting lasting routes of innovation in agriculture, environmental protection, and clean energy production.

Can the cyanobacterial carbon-concentrating mechanism increase photosynthesis in crop species? A theoretical analysis

Experimental elevation of [CO₂] around C₃ crops in the field has been shown to increase yields by suppressing the Rubisco oxygenase reaction and, in turn, photorespiration. Bioengineering a cyanobacterial carbon-concentrating mechanism (CCM) into C₃ crop species provides a potential means of elevating [CO₂] at Rubisco, thereby decreasing photorespiration and increasing photosynthetic efficiency and yield. The cyanobacterial CCM is an attractive alternative relative to other CCMs, because its features do not require anatomical changes to leaf tissue. However, the potential benefits of engineering the entire CCM into a C₃ leaf are unexamined. Here, a CO₂ and HCO₃⁻ diffusion-reaction model is developed to examine how components of the cyanobacterial CCM affect leaf light-saturated CO₂ uptake (A(sat)) and to determine whether a different Rubisco isoform would perform better in a leaf with a cyanobacterial CCM. The results show that the addition of carboxysomes without other CCM components substantially decreases A(sat) and that the best first step is the addition of HCO₃⁻ transporters, as a single HCO₃⁻ transporter increased modeled A(sat) by 9%. Addition of all major CCM components increased A(sat) from 24 to 38 µmol m⁻² s⁻¹. Several Rubisco isoforms were compared in the model, and increasing ribulose bisphosphate regeneration rate will allow for further improvements by using a Rubisco isoform adapted to high [CO₂]. Results from field studies that artificially raise [CO₂] suggest that this 60% increase in A(sat) could result in a 36% to 60% increase in yield.

Regulatory modules controlling maize inflorescence architecture

Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures.