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

Alternative transcriptional initiation of OsβCA1 produces three distinct subcellular localization isoforms involved in stomatal response regulation and photosynthesis in rice

Plants adjust the size of their stomatal openings to balance CO2 intake and water loss. Carbonic anhydrases (CAs) facilitate the conversion between CO2 and HCO3 -, and the OsβCA1 mutant in rice (Oryza sativa) shows similar traits in carbon fixation and stomatal response to CO2 as the dual βCA mutants in Arabidopsis thaliana. However, the exact role of OsβCA1 in these processes was unclear. We used gene editing, molecular biology, and plant physiology to study how OsβCA1 contributes to carbon fixation, stomatal opening, and CO2 responses. OsβCA1 produces three isoforms (OsβCA1A, OsβCA1B, and OsβCA1C) through alternative transcriptional initiation, which localize to the chloroplast, cell membrane, and cytosol, respectively. Protein measurements revealed that OsβCA1A/C and OsβCA1B contribute 97 and 3% to OsβCA1, respectively. By creating specific mutants for each isoform, our results found that the chloroplast and cell membrane isoforms independently participate in carbon fixation and regulation of stomatal aperture. Furthermore, the complete knockout of OsβCA1 caused a delayed response to low CO2. Our findings provide new insights into the generation and function of different OsβCA1 isoforms, clarifying their roles in CO2 diffusion, CO2 fixation and stomatal regulation in rice.

The genome of Eleocharis vivipara elucidates the genetics of C3-C4 photosynthetic plasticity and karyotype evolution in the Cyperaceae

Eleocharis vivipara, an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C3 photosynthesis underwater and C4 photosynthesis on land. However, the absence of genomic data has hindered its utility for evolutionary and genetic research. Here, we present a high-quality genome for E. vivipara, representing the first chromosome-level genome for the Eleocharis genus, with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes. Its Hi-C pattern, chromosome clustering results, and one-to-one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n = 4x = 20. Phylogenetic analysis suggests that E. vivipara diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), and underwent a whole-genome duplication (WGD) about 3.5 Mya. Numerous fusion and fission events were identified between the chromosomes of E. vivipara and its close relatives. We demonstrate that E. vivipara has holocentromeres, a chromosomal feature which can maintain the stability of such chromosomal rearrangements. Experimental transplantation and cross-section studies showed its terrestrial culms developed C4 Kranz anatomy with increased number of chloroplasts in the bundle sheath (BS) cells. Gene expression and weighted gene co-expression network analysis (WGCNA) showed overall elevated expression of core genes associated with the C4 pathway, and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency. We found evidence of mixed nicotinamide adenine dinucleotide - malic enzyme and phosphoenolpyruvate carboxykinase type C4 photosynthesis in E. vivipara, and hypothesize that the evolution of C4 photosynthesis predates the WGD event. The mixed type is dominated by subgenome A and supplemented by subgenome B. Collectively, our findings not only shed light on the evolution of E. vivipara and karyotype within the Cyperaceae family, but also provide valuable insights into the transition between C3 and C4 photosynthesis, offering promising avenues for crop improvement and breeding.

Abscisic acid priming confers salt tolerance in maize seedlings by modulating osmotic adjustment, bond energies, ROS homeostasis, and organic acid metabolism

This study aimed at investigating the influence of exogenous abscisic acid (ABA) on salt homeostasis under 100 mM NaCl stress in maize (Zea mays L. cv. Kaveri 50) through 3 and 5 days of exposure. The ratio of Na+ to K+, hydrogen peroxide (H2O2) and superoxide (O2•‒) accumulation, electrolyte leakage were the major determinants for salt sensitivity. Pretreatment with ABA [ABA (+)] had altered the salt sensitivity of plants maximally through 5 days of treatment. Plants controlled well for endogenous ABA level (92% increase) and bond energy minimization of cell wall residues to support salt tolerance proportionately to ABA (+). Salt stress was mitigated through maintenance of relative water content (RWC) (16%), glycine betaine (GB) (26%), proline (28%) and proline biosynthesis enzyme (ΔP5CS) (26%) under the application of ABA (+). Minimization of lipid peroxides (6% decrease), carbonyl content (9% decrease), acid, alkaline phosphatase activities were more tolerated under 100 mM salinity at 5 days duration. Malate metabolism for salt tolerance was dependent on the activity of the malic enzyme, malate dehydrogenase through transcript abundance in real-time manner as a function of ABA (+). Establishment of oxidative stress through days under salinity recorded by NADPH-oxidase activity (39% increase) following ROS generation as detected in tissue specific level. The ABA (+) significantly altered redox homeostasis through ratio of AsA to DHA (21% increase), GSH to GSSG (12% increase) by dehydroascorbate reductase and glutathione reductase respectively, and other enzymes like guaiacol peroxidase, catalase, glutathione reductase activities. The ABA in priming was substantially explained in stress metabolism as biomarker for salinity stress with reference to maize.

Salt stress induces Kranz anatomy and expression of C4 photosynthetic enzymes in the amphibious sedge Eleocharis vivipara

Eleocharis vivipara Link is a unique amphibious leafless plant of the Cyperaceae. The terrestrial form develops culms with Kranz anatomy and C₄-like traits, while the submerged form does culms with non-Kranz anatomy and C₃ traits. The submerged form develops new culms with C₄-like mode when exposed to air or exogenous abscisic acid. In this study, we investigated whether salt stress (0.05-0.3 M NaCl) has a similar effect. When the submerged form was grown for one month in solutions of 0.1 M NaCl and more, culm growth was strongly suppressed. However, these plants slowly developed new culms that had Kranz anatomy with chloroplast-abundant Kranz bundle sheath cells. Although the culms of the submerged form had only few stomata, culms grown in the NaCl solution had many stomata. The NaCl-grown culms also accumulated large amounts of C₄ photosynthetic enzymes (phosphoenolpyruvate carboxylase and pyruvate Pi dikinase), and the cellular localization patterns of these enzymes and ribulose 1,5-bisphosphate carboxylase/oxygenase were similar to those in terrestrial culms. Accumulation of C₄ enzymes increased in mature culms of the submerged form (with non-Kranz anatomy) when exposed to 0.2 M NaCl solution for one week. These results suggest that salt stress induces development of Kranz anatomy and expression of C₄ photosynthetic enzymes in the submerged C₃ form of E. vivipara, whereas the anatomical and biochemical traits of C₄ photosynthesis appear to be regulated independently.

Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize

The efficiencies offered by C4 photosynthesis have motivated efforts to understand its biochemical, genetic, and developmental basis. Reactions underlying C4 traits in most C4 plants are partitioned between two cell types, bundle sheath (BS), and mesophyll (M) cells. RNA-seq has been used to catalog differential gene expression in BS and M cells in maize (Zea mays) and several other C4 species. However, the contribution of translational control to maintaining the distinct proteomes of BS and M cells has not been addressed. In this study, we used ribosome profiling and RNA-seq to describe translatomes, translational efficiencies, and microRNA abundance in BS- and M-enriched fractions of maize seedling leaves. A conservative interpretation of our data revealed 182 genes exhibiting cell type-dependent differences in translational efficiency, 31 of which encode proteins with core roles in C4 photosynthesis. Our results suggest that non-AUG start codons are used preferentially in upstream open reading frames of BS cells, revealed mRNA sequence motifs that correlate with cell type-dependent translation, and identified potential translational regulators that are differentially expressed. In addition, our data expand the set of genes known to be differentially expressed in BS and M cells, including genes encoding transcription factors and microRNAs. These data add to the resources for understanding the evolutionary and developmental basis of C4 photosynthesis and for its engineering into C3 crops.

Gibberellic acid induces non-Kranz anatomy with C4-like biochemical traits in the amphibious sedge Eleocharis vivipara

Gibberellic acid induces photosynthetic tissues with non-Kranz anatomy and C₄-like biochemical traits in terrestrial-form plants of Eleocharis vivipara. This suggests that the structural and biochemical traits are independently regulated. The amphibious leafless sedge, Eleocharis vivipara Link, develops culms (photosynthetic organs) with C₄-like traits and Kranz anatomy under terrestrial conditions, and C₃ traits and non-Kranz anatomy under submerged conditions. The conversion from C₃ mode to C₄-like mode in E. vivipara is reportedly mediated by abscisic acid. Here, we investigated the effects of gibberellic acid (GA) on the differentiation of anatomical and photosynthetic traits because GA is involved in heterophylly in aquatic plants. When 100 µM GA was sprayed on terrestrial plants, the newly developed culms had non-Kranz anatomy in the basal part and Kranz-like anatomy in the upper part. In the basal part, the mesophyll cells were well developed, whereas the Kranz (bundle sheath) cells were reduced and contained few chloroplasts and mitochondria. Stomatal frequency was lower in the basal part than in the upper part. Nevertheless, these tissues had abundant accumulation and high activities of C₄ photosynthetic enzymes and had C₄-like δ¹³C values, as seen in the culms of the terrestrial form. When submerged plants were grown under water containing GA-biosynthesis inhibitors (uniconazole or paclobutrazol), the new culms had Kranz anatomy. The culms developed under paclobutrazol had the C₃ pattern of cellular accumulation of photosynthetic enzymes. These data suggest that GA induces production of photosynthetic tissues with non-Kranz anatomy in terrestrial plants of E. vivipara, without concomitant expression of C₃ biochemical traits. The data also suggest that the differentiation of C₄ structural and biochemical traits is regulated independently.

Regulation and Evolution of C4 Photosynthesis

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

Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata

C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared with C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to detect changes in gene expression associated with different photosynthetic phenotypes. Phylogenetically informed comparative transcriptomics show that intermediates with a weak C4 cycle are separated from the C3 phenotype by increases in the expression of 58 genes (0.22% of genes expressed in the leaves), including those encoding just three core C4 enzymes: aspartate aminotransferase, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate carboxylase. The subsequent transition to full C4 physiology was accompanied by increases in another 15 genes (0.06%), including only the core C4 enzyme pyruvate orthophosphate dikinase. These changes probably created a rudimentary C4 physiology, and isolated populations subsequently improved this emerging C4 physiology, resulting in a patchwork of expression for some C4 accessory genes. Our work shows how C4 assembly in A. semialata happened in incremental steps, each requiring few alterations over the previous step. These create short bridges across adaptive landscapes that probably facilitated the recurrent origins of C4 photosynthesis through a gradual process of evolution.

Accumulation of the components of cyclic electron flow around photosystem I in C4 plants, with respect to the requirements for ATP

By concentrating CO2, C4 photosynthesis can suppress photorespiration and achieve high photosynthetic efficiency, especially under conditions of high light, high temperature, and drought. To concentrate CO2, extra ATP is required, which would also require a change in photosynthetic electron transport in C4 photosynthesis from that in C3 photosynthesis. Several analyses have shown that the accumulation of the components of cyclic electron flow (CEF) around photosystem I, which generates the proton gradient across thylakoid membranes (ΔpH) and functions in ATP production without producing NADPH, is increased in various NAD-malic enzyme and NADP-malic enzyme C4 plants, suggesting that CEF may be enhanced to satisfy the increased need for ATP in C4 photosynthesis. However, in C4 plants, the accumulation patterns of the components of two partially redundant pathways of CEF, NAD(P)H dehydrogenase-like complex and PROTON GRADIENT REGULATION5-PGR5-like1 complex, are not identical, suggesting that these pathways may play different roles in C4 photosynthesis. Accompanying the increase in the amount of NDH, the expression of some genes which encode proteins involved in the assembly of NDH is also increased at the mRNA level in various C4 plants, suggesting that this increase is needed to increase the accumulation of NDH. To better understand the relation between CEF and C4 photosynthesis, a reverse genetic approach to generate C4 transformants with respect to CEF will be necessary.

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.

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.

Loss-of-function mutation of rice SLAC7 decreases chloroplast stability and induces a photoprotection mechanism in rice

Plants absorb sunlight to power the photochemical reactions of photosynthesis, which can potentially damage the photosynthetic machinery. However, the mechanism that protects chloroplasts from the damage remains unclear. In this work, we demonstrated that rice (Oryza sativa L.) SLAC7 is a generally expressed membrane protein. Loss-of-function of SLAC7 caused continuous damage to the chloroplasts of mutant leaves under normal light conditions. Ion leakage indicators related to leaf damage such as H2 O2 and abscisic acid levels were significantly higher in slac7-1 than in the wild type. Consistently, the photosynthesis efficiency and Fv/Fm ratio of slac7-1 were significantly decreased (similar to photoinhibition). In response to chloroplast damage, slac7-1 altered its leaf morphology (curled or fused leaf) by the synergy between plant hormones and transcriptional factors to decrease the absorption of light, suggesting that a photoprotection mechanism for chloroplast damage was activated in slac7-1. When grown in dark conditions, slac7-1 displayed a normal phenotype. SLAC7 under the control of the AtSLAC1 promoter could partially complement the phenotypes of Arabidopsis slac1 mutants, indicating a partial conservation of SLAC protein functions. These results suggest that SLAC7 is essential for maintaining the chloroplast stability in rice.

Insights into C4 metabolism from comparative deep sequencing

C4 photosynthesis suppresses the oxygenation activity of Ribulose Bisphosphate Carboxylase Oxygenase and so limits photorespiration. Although highly complex, it is estimated to have evolved in 66 plant lineages, with the vast majority lacking sequenced genomes. Transcriptomics has recently initiated assessments of the degree to which transcript abundance differs between C3 and C4 leaves, identified novel components of C4 metabolism, and also led to mathematical models explaining the repeated evolution of this complex phenotype. Evidence is accumulating that this complex and convergent phenotype is partly underpinned by parallel evolution of structural genes, but also regulatory elements in both cis and trans. Furthermore, it appears that initial events associated with acquisition of C4 traits likely represent evolutionary exaptations related to non-photosynthetic processes.