C4 photosynthesis evolution: the conditional Mt. Fuji

Tribulus (Zygophyllaceae) as a case study for the evolution of C2 and C4 photosynthesis

C2 photosynthesis is a photosynthetic pathway in which photorespiratory CO2 release and refixation are enhanced in leaf bundle sheath (BS) tissues. The evolution of C2 photosynthesis has been hypothesized to be a major step in the origin of C4 photosynthesis, highlighting the importance of studying C2 evolution. In this study, physiological, anatomical, ultrastructural, and immunohistochemical properties of leaf photosynthetic tissues were investigated in six non-C4 Tribulus species and four C4 Tribulus species. At 42°C, T. cristatus exhibited a photosynthetic CO2 compensation point in the absence of respiration (C*) of 21 µmol mol-1, below the C3 mean C* of 73 µmol mol-1. Tribulus astrocarpus had a C* value at 42°C of 55 µmol mol-1, intermediate between the C3 species and the C2 T. cristatus. Glycine decarboxylase (GDC) allocation to BS tissues was associated with lower C*. Tribulus cristatus and T. astrocarpus allocated 86% and 30% of their GDC to the BS tissues, respectively, well above the C3 mean of 11%. Tribulus astrocarpus thus exhibits a weaker C2 (termed sub-C2) phenotype. Increased allocation of mitochondria to the BS and decreased length-to-width ratios of BS cells, were present in non-C4 species, indicating a potential role in C2 and C4 evolution.

Meeting in the Middle: Lessons and Opportunities from Studying C3-C4 Intermediates

The discovery of C₃-C₄ intermediate species nearly 50 years ago opened up a new avenue for studying the evolution of photosynthetic pathways. Intermediate species exhibit anatomical, biochemical, and physiological traits that range from C₃ to C₄. A key feature of C₃-C₄ intermediates that utilize C₂ photosynthesis is the improvement in photosynthetic efficiency compared with C₃ species. Although the recruitment of some core enzymes is shared across lineages, there is significant variability in gene expression patterns, consistent with models that suggest numerous evolutionary paths from C₃ to C₄ photosynthesis. Despite the many evolutionary trajectories, the recruitment of glycine decarboxylase for C₂ photosynthesis is likely required. As technologies enable high-throughput genotyping and phenotyping, the discovery of new C₃-C₄ intermediates species will enrich comparisons between evolutionary lineages. The investigation of C₃-C₄ intermediate species will enhance our understanding of photosynthetic mechanisms and evolutionary processes and will potentially aid in crop improvement.

Upregulation of C4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass

C₄ photosynthesis is thought to have evolved via intermediate stages, with changes towards the C₄ phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C₄ components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding study system since it includes C₄ and non-C₄ populations. Here, we analyse F1 hybrids between C₃ and C₄ , and C₃ +C₄ and C₄ genotypes to determine whether the acquisition of C₄ characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C₄ gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C₄ cycle coexists with C₃ carbon fixation in the hybrids. This partial C₄ phenotype is associated with C₄ -like photosynthetic efficiency in C₃ +C₄  × C₄ , but not in C₃  × C₄ hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C₄ characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C₄ components is thus constrained, with C₃ +C₄ species providing an essential step for C₄ evolution.

Upregulation of C4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass

C₄ photosynthesis is thought to have evolved via intermediate stages, with changes towards the C₄ phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C₄ components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding study system since it includes C₄ and non-C₄ populations. Here, we analyse F1 hybrids between C₃ and C₄ , and C₃ +C₄ and C₄ genotypes to determine whether the acquisition of C₄ characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C₄ gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C₄ cycle coexists with C₃ carbon fixation in the hybrids. This partial C₄ phenotype is associated with C₄ -like photosynthetic efficiency in C₃ +C₄  × C₄ , but not in C₃  × C₄ hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C₄ characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C₄ components is thus constrained, with C₃ +C₄ species providing an essential step for C₄ evolution.

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

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

Evolutionary History of Plant Metabolism

Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO₂ and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.

Facultative crassulacean acid metabolism in a C3-C4 intermediate

The Portulacaceae enable the study of the evolutionary relationship between C4 and crassulacean acid metabolism (CAM) photosynthesis. Shoots of well-watered plants of the C3-C4 intermediate species Portulaca cryptopetala Speg. exhibit net uptake of CO2 solely during the light. CO2 fixation is primarily via the C3 pathway as indicated by a strong stimulation of CO2 uptake when shoots were provided with air containing 2% O2. When plants were subjected to water stress, daytime CO2 uptake was reduced and CAM-type net CO2 uptake in the dark occurred. This was accompanied by nocturnal accumulation of acid in both leaves and stems, also a defining characteristic of CAM. Following rewatering, net CO2 uptake in the dark ceased in shoots, as did nocturnal acidification of the leaves and stems. With this unequivocal demonstration of stress-related reversible, i.e. facultative, induction of CAM, P. cryptopetala becomes the first C3-C4 intermediate species reported to exhibit CAM. Portulaca molokiniensis Hobdy, a C4 species, also exhibited CAM only when subjected to water stress. Facultative CAM has now been demonstrated in all investigated species of Portulaca, which are well sampled from across the phylogeny. This strongly suggests that in Portulaca, a lineage in which species engage predominately in C4 photosynthesis, facultative CAM is ancestral to C4. In a broader context, it has now been demonstrated that CAM can co-exist in leaves that exhibit any of the other types of photosynthesis known in terrestrial plants: C3, C4 and C3-C4 intermediate.

Mind the gap: the evolutionary engagement of the C4 metabolic cycle in support of net carbon assimilation

C₄ photosynthesis evolved dozens of times, with a critical step being the engagement of a C₄ metabolic cycle to concentrate CO₂ into a bundle sheath-like compartment. While C₃-C₄ intermediate species show a progressive increase in the activity of a C₄ metabolic cycle, the integration of the C₄ and C₃ biochemical cycles in enhancing photosynthetic carbon gain occurs in a punctuated manner, at an initial C₄ cycle activity near 60%. Punctuated integration of the C₄ cycle could result from the evolutionary acquisition of traits that coordinate the C₃ and C₄ biochemical cycles (for example, an enzymatic, regulatory or transport function) or from a sudden reduction in the mesophyll C₃ cycle. Alternatively, a punctuated pattern could be an artifact of low numbers of C₃-C₄ intermediates in the evolutionary space where C₄ cycle engagement occurs, due to incomplete sampling of natural diversity or evolutionary dynamics rendering such intermediates unstable. Understanding how the C₄ cycle becomes integrated with the C₃ cycle could reveal new avenues for engineering the C₄ pathway into C₃ plants. Such efforts would be facilitated by the generation of hybrids, or the discovery of additional intermediates, that span the transition from low to high C₄ cycle engagement.

Metabolite profiles reveal interspecific variation in operation of the Calvin-Benson cycle in both C4 and C3 plants

Low atmospheric CO2 in recent geological time led to the evolution of carbon-concentrating mechanisms (CCMs) such as C4 photosynthesis in >65 terrestrial plant lineages. We know little about the impact of low CO2 on the Calvin-Benson cycle (CBC) in C3 species that did not evolve CCMs, representing >90% of terrestrial plant species. Metabolite profiling provides a top-down strategy to investigate the operational balance in a pathway. We profiled CBC intermediates in a panel of C4 (Zea mays, Setaria viridis, Flaveria bidentis, and F. trinervia) and C3 species (Oryza sativa, Triticium aestivum, Arabidopsis thaliana, Nicotiana tabacum, and Manihot esculenta). Principal component analysis revealed differences between C4 and C3 species that were driven by many metabolites, including lower ribulose 1,5-bisphosphate in C4 species. Strikingly, there was also considerable variation between C3 species. This was partly due to different chlorophyll and protein contents, but mainly to differences in relative levels of metabolites. Correlation analysis indicated that one contributory factor was the balance between fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, phosphoribulokinase, and Rubisco. Our results point to the CBC having experienced different evolutionary trajectories in C3 species since the ancestors of modern plant lineages diverged. They underline the need to understand CBC operation in a wide range of species.

A Resurrected Scenario: Single Gain and Massive Loss of Nitrogen-Fixing Nodulation

Root nodule endosymbiosis with nitrogen-fixing bacteria provides plants with unlimited access to fixed nitrogen, but at a significant energetic cost. Nodulation is generally considered to have originated in parallel in different lineages, but this hypothesis downplays the genetic complexity of nodulation and requires independent recruitment of many common features across lineages. Recent phylogenomic studies revealed that genes that function in establishing or maintaining nitrogen-fixing nodules are independently lost in non-nodulating relatives of nitrogen-fixing plants. In our opinion, these data are best explained by a scenario of a single gain followed by massively parallel loss of nitrogen-fixing root nodules triggered by events at geological scale.

Evolutionary Diversification of Primary Metabolism and Its Contribution to Plant Chemical Diversity

Plants produce a diverse array of lineage-specific specialized (secondary) metabolites, which are synthesized from primary metabolites. Plant specialized metabolites play crucial roles in plant adaptation as well as in human nutrition and medicine. Unlike well-documented diversification of plant specialized metabolic enzymes, primary metabolism that provides essential compounds for cellular homeostasis is under strong selection pressure and generally assumed to be conserved across the plant kingdom. Yet, some alterations in primary metabolic pathways have been reported in plants. The biosynthetic pathways of certain amino acids and lipids have been altered in specific plant lineages. Also, two alternative pathways exist in plants for synthesizing primary precursors of the two major classes of plant specialized metabolites, terpenoids and phenylpropanoids. Such primary metabolic diversities likely underlie major evolutionary changes in plant metabolism and chemical diversity by acting as enabling or associated traits for the evolution of specialized metabolic pathways.

Lessons from Cleomaceae, the Sister of Crucifers

Cleomaceae is a diverse group well-suited to addressing fundamental genomic and evolutionary questions as the sister group to Brassicaceae, facilitating transfer of knowledge from the model Arabidopsis thaliana. Phylogenetic and taxonomic revisions provide a framework for examining the evolution of substantive morphological and physiology diversity in Cleomaceae, but not necessarily in Brassicaceae. The investigation of both nested and contrasting whole-genome duplications (WGDs) between Cleomaceae and Brassicaceae allows comparisons of independently duplicated genes and investigation of whether they may be drivers of the observed innovations. Further, a wealth of outstanding genetic research has provided insight into how the important alternative carbon fixation pathway, C₄ photosynthesis, has evolved via differential expression of a suite of genes, of which the underlying mechanisms are being elucidated.

Some like it hot: the physiological ecology of C4 plant evolution

The evolution of C₄ photosynthesis requires an intermediate phase where photorespiratory glycine produced in the mesophyll cells must flow to the vascular sheath cells for metabolism by glycine decarboxylase. This glycine flux concentrates photorespired CO₂ within the sheath cells, allowing it to be efficiently refixed by sheath Rubisco. A modest C₄ biochemical cycle is then upregulated, possibly to support the refixation of photorespired ammonia in sheath cells, with subsequent increases in C₄ metabolism providing incremental benefits until an optimized C₄ pathway is established. 'Why' C₄ photosynthesis evolved is largely explained by ancestral C₃ species exploiting photorespiratory CO₂ to improve carbon gain and thus enhance fitness. While photorespiration depresses C₃ performance, it produces a resource (photorespired CO₂) that can be exploited to build an evolutionary bridge to C₄ photosynthesis. 'Where' C₄ evolved is indicated by the habitat of species branching near C₃-to-C₄ transitions on phylogenetic trees. Consistent with the photorespiratory bridge hypothesis, transitional species show that the large majority of > 60 C₄ lineages arose in hot, dry, and/or saline regions where photorespiratory potential is high. 'When' C₄ evolved has been clarified by molecular clock analyses using phylogenetic data, coupled with isotopic signatures from fossils. Nearly all C₄ lineages arose after 25 Ma when atmospheric CO₂ levels had fallen to near current values. This reduction in CO₂, coupled with persistent high temperature at low-to-mid-latitudes, met a precondition where photorespiration was elevated, thus facilitating the evolutionary selection pressure that led to C₄ photosynthesis.

Gene duplication and dosage effects during the early emergence of C4 photosynthesis in the grass genus Alloteropsis

The importance of gene duplication for evolutionary diversification has been mainly discussed in terms of genetic redundancy allowing neofunctionalization. In the case of C4 photosynthesis, which evolved via the co-option of multiple enzymes to boost carbon fixation in tropical conditions, the importance of genetic redundancy has not been consistently supported by genomic studies. Here, we test for a different role for gene duplication in the early evolution of C4 photosynthesis, via dosage effects creating rapid step changes in expression levels. Using genome-wide data for accessions of the grass genus Alloteropsis that recently diversified into different photosynthetic types, we estimate gene copy numbers and demonstrate that recurrent duplications in two important families of C4 genes coincided with increases in transcript abundance along the phylogeny, in some cases via a pure dosage effect. While increased gene copy number during the initial emergence of C4 photosynthesis probably offered a rapid route to enhanced expression, we also find losses of duplicates following the acquisition of genes encoding better-suited isoforms. The dosage effect of gene duplication might therefore act as a transient process during the evolution of a C4 biochemistry, rendered obsolete by the fixation of regulatory mutations increasing expression levels.

Photosynthesis in C3-C4 intermediate Moricandia species

Evolution of C4 photosynthesis is not distributed evenly in the plant kingdom. Particularly interesting is the situation in the Brassicaceae, because the family contains no C4 species, but several C3-C4 intermediates, mainly in the genus Moricandia Investigation of leaf anatomy, gas exchange parameters, the metabolome, and the transcriptome of two C3-C4 intermediate Moricandia species, M. arvensis and M. suffruticosa, and their close C3 relative M. moricandioides enabled us to unravel the specific C3-C4 characteristics in these Moricandia lines. Reduced CO2 compensation points in these lines were accompanied by anatomical adjustments, such as centripetal concentration of organelles in the bundle sheath, and metabolic adjustments, such as the balancing of C and N metabolism between mesophyll and bundle sheath cells by multiple pathways. Evolution from C3 to C3-C4 intermediacy was probably facilitated first by loss of one copy of the glycine decarboxylase P-protein, followed by dominant activity of a bundle sheath-specific element in its promoter. In contrast to recent models, installation of the C3-C4 pathway was not accompanied by enhanced activity of the C4 cycle. Our results indicate that metabolic limitations connected to N metabolism or anatomical limitations connected to vein density could have constrained evolution of C4 in Moricandia.

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

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