The C(4) plant lineages of planet Earth

Evolution of GOLDEN2-LIKE gene function in C(3) and C (4) plants

A pair of GOLDEN2-LIKE transcription factors is required for normal chloroplast development in land plant species that encompass the range from bryophytes to angiosperms. In the C(4) plant maize, compartmentalized function of the two GLK genes in bundle sheath and mesophyll cells regulates dimorphic chloroplast differentiation, whereas in the C(3) plants Physcomitrella patens and Arabidopsis thaliana the genes act redundantly in all photosynthetic cells. To assess whether the cell-specific function of GLK genes is unique to maize, we analyzed gene expression patterns in the C(4) monocot Sorghum bicolor and C(4) eudicot Cleome gynandra. Compartmentalized expression was observed in S. bicolor, consistent with the development of dimorphic chloroplasts in this species, but not in C. gynandra where bundle sheath and mesophyll chloroplasts are morphologically similar. The generation of single and double mutants demonstrated that GLK genes function redundantly in rice, as in other C(3) plants, despite the fact that GLK gene duplication in monocots preceded the speciation of rice, maize and sorghum. Together with phylogenetic analyses of GLK gene sequences, these data have allowed speculation on the evolutionary trajectory of GLK function. Based on current evidence, most species that retain single GLK genes belong to orders that contain only C(3) species. We therefore propose that the ancestral state is a single GLK gene, and hypothesize that GLK gene duplication enabled sub-functionalization, which in turn enabled cell-specific function in C(4) plants with dimorphic chloroplasts. In this scenario, GLK gene duplication preconditioned the evolution of C(4) physiology that is associated with chloroplast dimorphism.

You're so vein: bundle sheath physiology, phylogeny and evolution in C3 and C4 plants

Bundle sheath (BS) anatomy is found in most C4 lineages, associated with low inter-veinal distances (IVD) and high BS:mesophyll ratio (BS:MC). The origins, function and selective advantages of the BS in C3 lineages are relevant for understanding the environmental, molecular and phylogenetic determinants of C4 evolution. Suggested functions for BS have included structural support, hydraulic isolation, storage for water, ions, and carbohydrates, and photorespiratory carbon metabolism; we propose a central role for cavitation repair, consistent with the BS as a control centre on regulating stem and leaf hydraulic continuity. An analysis of BS traits in the phylogenetic lineages giving rise to C4 grasses (the 'PACMAD' clade) shows an initial enhancement in BS:MC ratio in C3 lineages, although IVD is similar to the Pooideae sister group. Using a global database, a well-developed BS in the C3 PACMAD lineages was associated with higher precipitation and temperatures in the habitat of origin on an annual basis, with the C3 to C4 progression defined by the aridity index (AI). Maintaining leaf hydraulic conductance and cavitation repair are consistent with increased evaporative demand and more seasonal precipitation as drivers, first for the C3 BS, and then C4 diversification, under declining CO(2) concentrations in the Palaeogene and Neogene.

Evolution of GOLDEN2-LIKE gene function in C(3) and C (4) plants

A pair of GOLDEN2-LIKE transcription factors is required for normal chloroplast development in land plant species that encompass the range from bryophytes to angiosperms. In the C(4) plant maize, compartmentalized function of the two GLK genes in bundle sheath and mesophyll cells regulates dimorphic chloroplast differentiation, whereas in the C(3) plants Physcomitrella patens and Arabidopsis thaliana the genes act redundantly in all photosynthetic cells. To assess whether the cell-specific function of GLK genes is unique to maize, we analyzed gene expression patterns in the C(4) monocot Sorghum bicolor and C(4) eudicot Cleome gynandra. Compartmentalized expression was observed in S. bicolor, consistent with the development of dimorphic chloroplasts in this species, but not in C. gynandra where bundle sheath and mesophyll chloroplasts are morphologically similar. The generation of single and double mutants demonstrated that GLK genes function redundantly in rice, as in other C(3) plants, despite the fact that GLK gene duplication in monocots preceded the speciation of rice, maize and sorghum. Together with phylogenetic analyses of GLK gene sequences, these data have allowed speculation on the evolutionary trajectory of GLK function. Based on current evidence, most species that retain single GLK genes belong to orders that contain only C(3) species. We therefore propose that the ancestral state is a single GLK gene, and hypothesize that GLK gene duplication enabled sub-functionalization, which in turn enabled cell-specific function in C(4) plants with dimorphic chloroplasts. In this scenario, GLK gene duplication preconditioned the evolution of C(4) physiology that is associated with chloroplast dimorphism.

C3 plants enhance rates of photosynthesis by reassimilating photorespired and respired CO2

Photosynthetic carbon gain in plants using the C(3) photosynthetic pathway is substantially inhibited by photorespiration in warm environments, particularly in atmospheres with low CO(2) concentrations. Unlike C(4) plants, C(3) plants are thought to lack any mechanism to compensate for the loss of photosynthetic productivity caused by photorespiration. Here, for the first time, we demonstrate that the C(3) plants rice and wheat employ a specific mechanism to trap and reassimilate photorespired CO(2) . A continuous layer of chloroplasts covering the portion of the mesophyll cell periphery that is exposed to the intercellular air space creates a diffusion barrier for CO(2) exiting the cell. This facilitates the capture and reassimilation of photorespired CO(2) in the chloroplast stroma. In both species, 24-38% of photorespired and respired CO(2) were reassimilated within the cell, thereby boosting photosynthesis by 8-11% at ambient atmospheric CO(2) concentration and 17-33% at a CO(2) concentration of 200 µmol mol(-1) . Widespread use of this mechanism in tropical and subtropical C(3) plants could explain why the diversity of the world's C(3) flora, and dominance of terrestrial net primary productivity, was maintained during the Pleistocene, when atmospheric CO(2) concentrations fell below 200 µmol mol(-1) .

Parallel recruitment of multiple genes into c4 photosynthesis

During the diversification of living organisms, novel adaptive traits usually evolve through the co-option of preexisting genes. However, most enzymes are encoded by gene families, whose members vary in their expression and catalytic properties. Each may therefore differ in its suitability for recruitment into a novel function. In this work, we test for the presence of such a gene recruitment bias using the example of C4 photosynthesis, a complex trait that evolved recurrently in flowering plants as a response to atmospheric CO2 depletion. We combined the analysis of complete nuclear genomes and high-throughput transcriptome data for three grass species that evolved the C4 trait independently. For five of the seven enzymes analyzed, the same gene lineage was recruited across the independent C4 origins, despite the existence of multiple copies. The analysis of a closely related C3 grass confirmed that C4 expression patterns were not present in the C3 ancestors but were acquired during the evolutionary transition to C4 photosynthesis. The significant bias in gene recruitment indicates that some genes are more suitable for a novel function, probably because the mutations they accumulated brought them closer to the characteristics required for the new function.

Origins and diversity of eukaryotic CO2-concentrating mechanisms: lessons for the future

The importance of the eukaryotic algal CO(2)-concentrating mechanism (CCM) is considered in terms of global productivity as well as molecular phylogeny and diversity. The three major constituents comprising the CCM in the majority of eukaryotes are described. These include: (i) likely plasma- and chloroplast-membrane inorganic carbon transporters; (ii) a suite of carbonic anhydrase enzymes in strategic locations; and usually (iii) a microcompartment in which most Rubisco aggregates (the chloroplast pyrenoid). The molecular diversity of known CCM components are set against the current green algal model for their probable operation. The review then focuses on the kinetic and cystallographic interactions of Rubisco, which permit pyrenoid formation and CCM function. Firstly, we consider observations that surface residues of the Rubisco small subunit directly condition Rubisco aggregation and pyrenoid formation. Secondly, we reanalyse the phylogenetic progression in green Rubisco kinetic properties, and suggest that Rubisco substrate selectivity (the specificity factor, S(rel), and affinity for CO(2), K(c)) demonstrate a systematic relaxation, which directly relates to the origins and effectiveness of a CCM. Finally, we consider the implications of eukaryotic CCM regulation and minimum components needed for introduction into higher plants as a possible means to enhance crop productivity in the future.

Anatomical enablers and the evolution of C4 photosynthesis in grasses

C(4) photosynthesis is a series of anatomical and biochemical modifications to the typical C(3) pathway that increases the productivity of plants in warm, sunny, and dry conditions. Despite its complexity, it evolved more than 62 times independently in flowering plants. However, C(4) origins are absent from most plant lineages and clustered in others, suggesting that some characteristics increase C(4) evolvability in certain phylogenetic groups. The C(4) trait has evolved 22-24 times in grasses, and all origins occurred within the PACMAD clade, whereas the similarly sized BEP clade contains only C(3) taxa. Here, multiple foliar anatomy traits of 157 species from both BEP and PACMAD clades are quantified and analyzed in a phylogenetic framework. Statistical modeling indicates that C(4) evolvability strongly increases when the proportion of vascular bundle sheath (BS) tissue is higher than 15%, which results from a combination of short distance between BS and large BS cells. A reduction in the distance between BS occurred before the split of the BEP and PACMAD clades, but a decrease in BS cell size later occurred in BEP taxa. Therefore, when environmental changes promoted C(4) evolution, suitable anatomy was present only in members of the PACMAD clade, explaining the clustering of C(4) origins in this lineage. These results show that key alterations of foliar anatomy occurring in a C(3) context and preceding the emergence of the C(4) syndrome by millions of years facilitated the repeated evolution of one of the most successful physiological innovations in angiosperm history.

Rubisco evolution in C₄ eudicots: an analysis of Amaranthaceae sensu lato

BACKGROUND

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots.

METHODOLOGY/PRINCIPAL FINDINGS

We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution.

CONCLUSIONS/SIGNIFICANCE

Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.

Multiple photosynthetic transitions, polyploidy, and lateral gene transfer in the grass subtribe Neurachninae

The Neurachninae is the only grass lineage known to contain C(3), C(4), and C(3)-C(4) intermediate species, and as such has been suggested as a model system for studies of photosynthetic pathway evolution in the Poaceae; however, a lack of a robust phylogenetic framework has hindered this possibility. In this study, plastid and nuclear markers were used to reconstruct evolutionary relationships among Neurachninae species. In addition, photosynthetic types were determined with carbon isotope ratios, and genome sizes with flow cytometry. A high frequency of autopolyploidy was found in the Neurachninae, including in Neurachne munroi F.Muell. and Paraneurachne muelleri S.T.Blake, which independently evolved C(4) photosynthesis. Phylogenetic analyses also showed that following their separate C(4) origins, these two taxa exchanged a gene encoding the C(4) form of phosphoenolpyruvate carboxylase. The C(3)-C(4) intermediate Neurachne minor S.T.Blake is phylogenetically distinct from the two C(4) lineages, indicating that intermediacy in this species evolved separately from transitional stages preceding C(4) origins. The Neurachninae shows a substantial capacity to evolve new photosynthetic pathways repeatedly. Enablers of these transitions might include anatomical pre-conditions in the C(3) ancestor, and frequent autopolyploidization. Transfer of key C(4) genetic elements between independently evolved C(4) taxa may have also facilitated a rapid adaptation of photosynthesis in these grasses that had to survive in the harsh climate appearing during the late Pliocene in Australia.

The development of C₄rice: current progress and future challenges

Another "green revolution" is needed for crop yields to meet demands for food. The international C(4) Rice Consortium is working toward introducing a higher-capacity photosynthetic mechanism--the C(4) pathway--into rice to increase yield. The goal is to identify the genes necessary to install C(4) photosynthesis in rice through different approaches, including genomic and transcriptional sequence comparisons and mutant screening.

Phylogeny and photosynthetic pathway distribution in Anticharis Endl. (Scrophulariaceae)

C(4) photosynthesis independently evolved >62 times, with the majority of origins within 16 dicot families. One origin occurs in the poorly studied genus Anticharis Endl. (Scrophulariaceae), which consists of ~10 species from arid regions of Africa and southwest Asia. Here, the photosynthetic pathway of 10 Anticharis species and one species from each of the sister genera Aptosimum and Peliostomum was identified using carbon isotope ratios (δ(13)C). The photosynthetic pathway was then mapped onto an internal transcribed spacer (ITS) phylogeny of Anticharis and its sister genera. Leaf anatomy was examined for nine Anticharis species and plants from Aptosimum and Peliostomum. Leaf ultrastructure, gas exchange, and enzyme distributions were assessed in Anticharis glandulosa collected in SE Iran. The results demonstrate that C(3) photosynthesis is the ancestral condition, with C(4) photosynthesis occurring in one clade containing four species. C(4) Anticharis species exhibit the atriplicoid type of C(4) leaf anatomy and the NAD-malic enzyme biochemical subtype. Six Anticharis species had C(3) or C(3)-C(4) δ(13)C values and branched at phylogenetic nodes that were sister to the C(4) clade. The rest of Anticharis species had enlarged bundle sheath cells, close vein spacing, and clusters of chloroplasts along the centripetal (inner) bundle sheath walls. These traits indicate that basal-branching Anticharis species are evolutionary intermediates between the C(3) and C(4) conditions. Anticharis appears to be an important new group in which to study the dynamics of C(4) evolution.

Historical profiling of maize duplicate genes sheds light on the evolution of C4 photosynthesis in grasses

C4 plants evolved from C3 plants through a series of complex evolutionary steps. On the basis of the evolution of key C4 enzyme genes, the evolution of C4 photosynthesis has been considered a story of gene/genome duplications and subsequent modifications of gene function. If whole-genome duplication has contributed to the evolution of C4 photosynthesis, other genes should have been duplicated together with these C4 genes. However, which genes were co-duplicated with C4 genes and whether they have also played a role in C4 evolution are largely unknown. In this study, we developed a simple method to characterize the historical profile of the paralogs of a gene by tracing back to the most recent common ancestor (MRCA) of the gene and its paralog(s) and then counting the number of paralogs at each MRCA. We clustered the genes into clusters with similar duplication profiles and inferred their functional enrichments. Applying our method to maize, a familiar C4 plant, we identified many genes that show similar duplication profiles with those of the key C4 enzyme genes and found that the functional preferences of the C4 gene clusters are not only similar to those identified by an experimental approach in a recent study but also highly consistent with the functions required for the C4 photosynthesis evolutionary model proposed by S.F. Sage. Some of these genes might have co-evolved with the key C4 enzyme genes to increase the strength of C4 photosynthesis. Moreover, our results suggested that most key C4 enzyme genes had different origins and have undergone a long evolutionary process before the emergence of C4 grasses (Andropogoneae), consistent with the conclusion proposed by previous authors.

A broader model for C₄ photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.)

C(4) photosynthesis is a fascinating example of parallel evolution of a complex trait involving multiple genetic, biochemical and anatomical changes. It is seen as an adaptation to deleteriously high levels of photorespiration. The current scenario for C(4) evolution inferred from grasses is that it originated subsequent to the Oligocene decline in CO(2) levels, is promoted in open habitats, acts as a pre-adaptation to drought resistance, and, once gained, is not subsequently lost. We test the generality of these hypotheses using a dated phylogeny of Amaranthaceae s.l. (including Chenopodiaceae), which includes the largest number of C(4) lineages in eudicots. The oldest chenopod C(4) lineage dates back to the Eocene/Oligocene boundary, representing one of the first origins of C(4) in plants, but still corresponding with the Oligocene decline of atmospheric CO(2). In contrast to grasses, the rate of transitions from C(3) to C(4) is highest in ancestrally drought resistant (salt-tolerant and succulent) lineages, implying that adaptation to dry or saline habitats promoted the evolution of C(4); and possible reversions from C(4) to C(3) are apparent. We conclude that the paradigm established in grasses must be regarded as just one aspect of a more complex system of C(4) evolution in plants in general.

The dicotyledonous NAD malic enzyme C4 plant Cleome gynandra displays age-dependent plasticity of C4 decarboxylation biochemistry

The C(4) photosynthetic pathway enriches carbon dioxide in the vicinity of Rubisco, thereby enabling plants to assimilate carbon more efficiently. Three canonical subtypes of C(4) exist, named after their main decarboxylating enzymes: NAD-dependent malic enzyme type, NADP-dependent malic enzyme type and phosphoenolpyruvate carboxykinase type. Cleome gynandra is known to perform NAD-ME type C(4) photosynthesis. To further assess the mode of C(4) in C. gynandra and its manifestation in leaves of different age, total enzyme activities of eight C(4) -related enzymes and the relative abundance of 31 metabolites were measured. C. spinosa was used as a C(3) control. C. gynandra was confirmed as an NAD-ME type C(4) plant in mid-aged leaves, whereas a mixed NAD-ME and PEPCK type was observed in older leaves. Young leaves showed a C(3) -C(4) intermediate state with respect to enzyme activities and metabolite abundances. Comparative transcriptome analysis of mid-aged leaves of C. gynandra and C. spinosa showed that the transcript of only one aspartate aminotransferase (AspAT) isoform is highly abundant in C. gynandra. However, the canonical model of the NAD-ME pathway requires two AspATs, a mitochondrial and a cytosolic isoform. Surprisingly, our results indicate the existence of only one highly abundant AspAT isoform. Using GFP-fusion, this isozyme was localised exclusively to mitochondria. We propose a revised model of NAD-ME type C(4) photosynthesis in C. gynandra, in which both AspAT catalysed reactions take place in mitochondria and PEPCK catalyses an alternative decarboxylating pathway.

Organic geochemical analysis of archaeological medicine pots from Northern Ghana. The multi-functionality of pottery

Sherds from pots found layered under a granite boulder in the Tong Hills of the Upper East Region of Northern Ghana seem, based on their deposition context to have been used for the preparation of medicines. Organic geochemical and isotopic analyses of these sherds and a modern day analogue reveal an n-alkanoic acid composition that is consistent with their being used in the preparation of plant derived substances. Isotopic analyses of the modern medicine pot indicate a contribution of n-alkanoic acids derived from plants that use C₄ carbon fixation, most likely maize, sorghum and/or millet suggesting that this pot was used for cooking C₄ based plant substances, perhaps, based on current analogy, staple porridge type food. The modern medicine pot could thus have had a prior use. The absence of C₄ plant residues in the archaeological sherds suggests that either staple foodstuffs differed radically to today, or, more likely, were not prepared in vessels that were to be used for medicinal purposes.

A basal carbon concentrating mechanism in plants?

Many photosynthetic organisms have developed inorganic carbon (Ci) concentrating mechanisms (CCMs) that increase the CO₂ concentration within the vicinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Several CCMs, such as four carbon (C4) and crassulacean acid metabolism (CAM), bicarbonate accumulation systems and capsular structures around RubisCO have been described in great detail. These systems are believed to have evolved several times as mechanisms that acclimate organisms to unfavourable growth conditions. Based on recent experimental evidence we propose the occurrence of another more general CCM system present in all plants. This basal CCM (bCCM) is supposed to be composed of mitochondrial carbonic anhydrases (a β-type carbonic anhydrase and the γ-type carbonic anhydrase domain of the mitochondrial NADH dehydrogenase complex) and probably further unknown components. The bCCM is proposed to reduce leakage of CO₂ from plant cells and allow efficient recycling of mitochondrial CO₂ for carbon fixation in chloroplasts.

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.

Atmospheric carbon dioxide: a driver of photosynthetic eukaryote evolution for over a billion years?

Exciting evidence from diverse fields, including physiology, evolutionary biology, palaeontology, geosciences and molecular genetics, is providing an increasingly secure basis for robustly formulating and evaluating hypotheses concerning the role of atmospheric carbon dioxide (CO(2)) in the evolution of photosynthetic eukaryotes. Such studies span over a billion years of evolutionary change, from the origins of eukaryotic algae through to the evolution of our present-day terrestrial floras, and have relevance for plant and ecosystem responses to future global CO(2) increases. The papers in this issue reflect the breadth and depth of approaches being adopted to address this issue. They reveal new discoveries pointing to deep evidence for the role of CO(2) in shaping evolutionary changes in plants and ecosystems, and establish an exciting cross-disciplinary research agenda for uncovering new insights into feedbacks between biology and the Earth system.

Evolution of C4 plants: a new hypothesis for an interaction of CO2 and water relations mediated by plant hydraulics

C(4) photosynthesis has evolved more than 60 times as a carbon-concentrating mechanism to augment the ancestral C(3) photosynthetic pathway. The rate and the efficiency of photosynthesis are greater in the C(4) than C(3) type under atmospheric CO(2) depletion, high light and temperature, suggesting these factors as important selective agents. This hypothesis is consistent with comparative analyses of grasses, which indicate repeated evolutionary transitions from shaded forest to open habitats. However, such environmental transitions also impact strongly on plant-water relations. We hypothesize that excessive demand for water transport associated with low CO(2), high light and temperature would have selected for C(4) photosynthesis not only to increase the efficiency and rate of photosynthesis, but also as a water-conserving mechanism. Our proposal is supported by evidence from the literature and physiological models. The C(4) pathway allows high rates of photosynthesis at low stomatal conductance, even given low atmospheric CO(2). The resultant decrease in transpiration protects the hydraulic system, allowing stomata to remain open and photosynthesis to be sustained for longer under drying atmospheric and soil conditions. The evolution of C(4) photosynthesis therefore simultaneously improved plant carbon and water relations, conferring strong benefits as atmospheric CO(2) declined and ecological demand for water rose.

Engineering C4 photosynthetic regulatory networks

C4 photosynthesis is a complex metabolic pathway responsible for carbon fixation in major feed, food and bioenergy crops. Although many enzymes driving this pathway have been identified, regulatory mechanisms underlying this system remain elusive. C4 photosynthesis contributes to photosynthetic efficiency in major bioenergy crops such as sugarcane, Miscanthus, switchgrass, maize and sorghum, and international efforts are underway to engineer C4 photosynthesis into C3 crops. A fundamental understanding of the C4 network is thus needed. New experimental and informatics methods can facilitate the accumulation and analysis of high-throughput data to define components of the C4 system. The use of new model plants, closely related to C4 crops, will also contribute to our understanding of the mechanisms that regulate this complex and important pathway.

Photorespiration and the evolution of C4 photosynthesis

C(4) photosynthesis is one of the most convergent evolutionary phenomena in the biological world, with at least 66 independent origins. Evidence from these lineages consistently indicates that the C(4) pathway is the end result of a series of evolutionary modifications to recover photorespired CO(2) in environments where RuBisCO oxygenation is high. Phylogenetically informed research indicates that the repositioning of mitochondria in the bundle sheath is one of the earliest steps in C(4) evolution, as it may establish a single-celled mechanism to scavenge photorespired CO(2) produced in the bundle sheath cells. Elaboration of this mechanism leads to the two-celled photorespiratory concentration mechanism known as C(2) photosynthesis (commonly observed in C(3)-C(4) intermediate species) and then to C(4) photosynthesis following the upregulation of a C(4) metabolic cycle.

Multiple Arabidopsis genes primed for recruitment into C₄ photosynthesis

C(4) photosynthesis occurs in the most productive crops and vegetation on the planet, and has become widespread because it allows increased rates of photosynthesis compared with the ancestral C(3) pathway. Leaves of C(4) plants typically possess complicated alterations to photosynthesis, such that its reactions are compartmented between mesophyll and bundle sheath cells. Despite its complexity, the C(4) pathway has arisen independently in 62 separate lineages of land plants, and so represents one of the most striking examples of convergent evolution known. We demonstrate that elements in untranslated regions (UTRs) of multiple genes important for C(4) photosynthesis contribute to the metabolic compartmentalization characteristic of a C(4) leaf. Either the 5' or the 3' UTR is sufficient for cell specificity, indicating that functional redundancy underlies this key aspect of C(4) gene expression. Furthermore, we show that orthologous PPDK and CA genes from the C(3) plant Arabidopsis thaliana are primed for recruitment into the C(4) pathway. Elements sufficient for M-cell specificity in C(4) leaves are also present in both the 5' and 3' UTRs of these C(3) A. thaliana genes. These data indicate functional latency within the UTRs of genes from C(3) species that have been recruited into the C(4) pathway. The repeated recruitment of pre-existing cis-elements in C(3) genes may have facilitated the evolution of C(4) photosynthesis. These data also highlight the importance of alterations in trans in producing a functional C(4) leaf, and so provide insight into both the evolution and molecular basis of this important type of photosynthesis.

Carbonic anhydrase and the molecular evolution of C4 photosynthesis

C(4) photosynthesis, a biochemical CO(2)-concentrating mechanism (CCM), evolved more than 60 times within the angiosperms from C(3) ancestors. The genus Flaveria, which contains species demonstrating C(3), C(3)-C(4), C(4)-like or C(4) photosynthesis, is a model for examining the molecular evolution of the C(4) pathway. Work with carbonic anhydrase (CA), and C(3) and C(4) Flaveria congeners has added significantly to the understanding of this process. The C(4) form of CA3, a β-CA, which catalyses the first reaction in the C(4) pathway by hydrating atmospheric CO(2) to bicarbonate in the cytosol of mesophyll cells (mcs), evolved from a chloroplastic C(3) ancestor. The molecular modifications to the ancestral CA3 gene included the loss of the sequence encoding the chloroplast transit peptide, and mutations in regulatory regions that resulted in high levels of expression in the C(4) mesophyll. Analyses of the CA3 proteins and regulatory elements from Flaveria photosynthetic intermediates indicated C(4) biochemistry very likely evolved in a specific, stepwise manner in this genus. The details of the mechanisms involved in the molecular evolution of other C(4) plant β-CAs are unknown; however, comparative genetics indicate gene duplication and neofunctionalization played significant roles as they did in Flaveria.

Regulation of the photorespiratory GLDPA gene in C(4) flaveria: an intricate interplay of transcriptional and posttranscriptional processes

The mitochondrial Gly decarboxylase complex (GDC) is a key component of the photorespiratory pathway that occurs in all photosynthetically active tissues of C(3) plants but is restricted to bundle sheath cells in C(4) species. GDC is also required for general cellular C(1) metabolism. In the Asteracean C(4) species Flaveria trinervia, a single functional GLDP gene, GLDPA, encodes the P-subunit of GDC, a decarboxylating Gly dehydrogenase. GLDPA promoter reporter gene fusion studies revealed that this promoter is active in bundle sheath cells and the vasculature of transgenic Flaveria bidentis (C(4)) and the Brassicacean C(3) species Arabidopsis thaliana, suggesting the existence of an evolutionarily conserved gene regulatory system in the bundle sheath. Here, we demonstrate that GLDPA gene regulation is achieved by an intricate interplay of transcriptional and posttranscriptional mechanisms. The GLDPA promoter is composed of two tandem promoters, P(R2) and P(R7), that together ensure a strong bundle sheath expression. While the proximal promoter (P(R7)) is active in the bundle sheath and vasculature, the distal promoter (P(R2)) drives uniform expression in all leaf chlorenchyma cells and the vasculature. An intron in the 5' untranslated leader of P(R2)-derived transcripts is inefficiently spliced and apparently suppresses the output of P(R2) by eliciting RNA decay.

Phylogenetic relationships of Aristida and relatives (Poaceae, Aristidoideae) based on noncoding chloroplast (trnL-F, rpl16) and nuclear (ITS) DNA sequences

PREMISE

The cosmopolitan and ecologically important grass subfamily Aristidoideae comprises the widely distributed genus Aristida (250-290 species), Stipagrostis (50 species, with an African-Asian distribution), and Sartidia (five species, Africa and Madagascar). The subfamily includes species with C(3) (Sartidia and a single species of Aristida) and C(4) photosynthetic pathways. Rigorous phylogenetic reconstructions of species relationships are required to explain the biogeographic, physiological, and ecological diversity within this subfamily.

METHODS

Chloroplast (trnL-F, rpl16) and nuclear (ITS) DNA sequences were obtained from 198 accessions, and the combined data set was subjected to parsimony, maximum likelihood, and Bayesian inference analyses. Dating analyses calibrated using previously published node ages were conducted to determine the ages of major radiations.

RESULTS

The C(3) Sartidia is sister to a monophyletic Stipagrostis, and the (Sartidia, Stipagrostis) clade is sister to Aristida. Within Aristida, the only known C(3) species, A. longifolia, is sister to the remainder of the genus. Infrageneric sections of Aristida were not supported, and there are no synapomorphic morphological characters for the clades retrieved. Within Aristida, monophyletic Australian, African, North American, and South American clades are retrieved.

CONCLUSIONS

The subfamily dates back to the late Miocene, with the major lineages present by the Pliocene. With one exception, regional clades of Aristida evolved in the Pliocene. The C(3) photosynthetic pathway is hypothesized to be the pleisomorphic condition for the subfamily, wherein two independent C(4) pathways (each with unique anatomical and genetic features) evolved, one within Aristida and one in Stipagrostis.

Characterization of C₃--C₄ intermediate species in the genus Heliotropium L. (Boraginaceae): anatomy, ultrastructure and enzyme activity

Photosynthetic pathway characteristics were studied in nine species of Heliotropium (sensu lato, including Euploca), using assessments of leaf anatomy and ultrastructure, activities of PEP carboxylase and C₄ acid decarboxylases, and immunolocalization of ribulose 1·5-bisphosphate carboxylase/oxygenase (Rubisco) and the P-subunit of glycine decarboxylase (GDC). Heliotropium europaeum, Heliotropium calcicola and Heliotropium tenellum are C₃ plants, while Heliotropium texanum and Heliotropium polyphyllum are C₄ species. Heliotropium procumbens and Heliotropium karwinskyi are functionally C₃, but exhibit 'proto-Kranz' anatomy where bundle sheath (BS) cells are enlarged and mitochondria primarily occur along the centripetal (inner) wall of the BS cells; GDC is present throughout the leaf. Heliotropium convolvulaceum and Heliotropium greggii are C₃--C₄ intermediates, with Kranz-like enlargement of the BS cells, localization of mitochondria along the inner BS wall and a loss of GDC in the mesophyll (M) tissue. These C₃--C₄ species of Heliotropium probably shuttle photorespiratory glycine from the M to the BS tissue for decarboxylation. Heliotropium represents an important new model for studying C₄ evolution. Where existing models such as Flaveria emphasize diversification of C₃--C₄ intermediates, Heliotropium has numerous C₃ species expressing proto-Kranz traits that could represent a critical initial phase in the evolutionary origin of C₄ photosynthesis.

Phylogenetics of the Chamaesyce clade (Euphorbia, Euphorbiaceae): reticulate evolution and long-distance dispersal in a prominent C4 lineage

PREMISE OF THE STUDY

The Chamaesyce clade of Euphorbia is the largest lineage of C(4) plants among the eudicots, with 350 species including both narrow endemics and cosmopolitan weeds. We sampled this group worldwide to address questions about subclade relationships, the origin of C(4) photosynthesis, the evolution of weeds, and the role of hybridization and long-distance dispersal in the diversification of the group. •

METHODS

Two nuclear (ITS and exon 9 of EMB2765) and three chloroplast markers (matK, rpl16, and trnL-F) were sequenced for 138 ingroup and six outgroup species. Exon 9 of EMB2765 was cloned in accessions with >1% superimposed peaks. •

KEY RESULTS

The Chamaesyce clade is monophyletic and consists of three major subclades [1(2,3)]: (1) the Acuta clade, containing three North American species with C(3) photosynthesis and C(3)-C(4) intermediates; (2) the Peplis clade, mostly North American and entirely C(4); and (3) the Hypericifolia clade, all C(4), with both New World and Old World groups. Incongruence between chloroplast and ITS phylogenies and divergent cloned copies of EMB2765 exon 9 suggest extensive hybridization, especially in the Hawaiian Islands radiation. •

CONCLUSIONS

The Chamaesyce clade originated in warm, arid areas of North America, where it evolved C(4) photosynthesis. From there, it diversified globally with extensive reticulate evolution and frequent long-distance dispersals. Although many species are weedy, there are numerous local adaptations to specific substrates and regional or island radiations, which have contributed to the great diversity of this group.

Isoleucine 309 acts as a C4 catalytic switch that increases ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) carboxylation rate in Flaveria

Improving global yields of important agricultural crops is a complex challenge. Enhancing yield and resource use by engineering improvements to photosynthetic carbon assimilation is one potential solution. During the last 40 million years C(4) photosynthesis has evolved multiple times, enabling plants to evade the catalytic inadequacies of the CO(2)-fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco). Compared with their C(3) ancestors, C(4) plants combine a faster rubisco with a biochemical CO(2)-concentrating mechanism, enabling more efficient use of water and nitrogen and enhanced yield. Here we show the versatility of plastome manipulation in tobacco for identifying sequences in C(4)-rubisco that can be transplanted into C(3)-rubisco to improve carboxylation rate (V(C)). Using transplastomic tobacco lines expressing native and mutated rubisco large subunits (L-subunits) from Flaveria pringlei (C(3)), Flaveria floridana (C(3)-C(4)), and Flaveria bidentis (C(4)), we reveal that Met-309-Ile substitutions in the L-subunit act as a catalytic switch between C(4) ((309)Ile; faster V(C), lower CO(2) affinity) and C(3) ((309)Met; slower V(C), higher CO(2) affinity) catalysis. Application of this transplastomic system permits further identification of other structural solutions selected by nature that can increase rubisco V(C) in C(3) crops. Coengineering a catalytically faster C(3) rubisco and a CO(2)-concentrating mechanism within C(3) crop species could enhance their efficiency in resource use and yield.

Exploiting the engine of C(4) photosynthesis

Ever since the discovery of C(4) photosynthesis in the mid-1960s, plant biologists have envisaged the introduction of the C(4) photosynthetic pathway into C(3) crops such as rice and soybeans. Recent advances in genomics capabilities, and new evolutionary and developmental studies indicate that C(4) engineering will be feasible in the next few decades. Furthermore, better understanding of the function of C(4) photosynthesis provides new ways to improve existing C(4) crops and bioenergy species, for example by creating varieties with ultra-high water and nitrogen use efficiencies. In the case of C(4) engineering, the main enzymes of the C(4) metabolic cycle have already been engineered into various C(3) plants. In contrast, knowledge of the genes controlling Kranz anatomy lags far behind. Combining traditional genetics, high-throughput sequencing technologies, systems biology, bioinformatics, and the use of the new C(4) model species Setaria viridis, the discovery of the key genes controlling the expression of C(4) photosynthesis can be dramatically accelerated. Sustained investment in the research areas directly related to C(4) engineering has the potential for substantial return in the decades to come, primarily by increasing crop production at a time when global food supplies are predicted to fall below world demand.

The occurrence of C(2) photosynthesis in Euphorbia subgenus Chamaesyce (Euphorbiaceae)

This study investigated whether Euphorbia subgenus Chamaesyce subsection Acutae contains C(3)-C(4) intermediate species utilizing C(2) photosynthesis, the process where photorespired CO(2) is concentrated into bundle sheath cells. Euphorbia species in subgenus Chamaesyce are generally C(4), but three species in subsection Acutae (E. acuta, E. angusta, and E. johnstonii) have C(3) isotopic ratios. Phylogenetically, subsection Acutae branches between basal C(3) clades within Euphorbia and the C(4) clade in subgenus Chamaesyce. Euphorbia angusta is C(3), as indicated by a photosynthetic CO(2) compensation point (Г) of 69 μmol mol(-1) at 30 °C, a lack of Kranz anatomy, and the occurrence of glycine decarboxylase in mesophyll tissues. Euphorbia acuta utilizes C(2) photosynthesis, as indicated by a Г of 33 μmol mol(-1) at 30 °C, Kranz-like anatomy with mitochondria restricted to the centripetal (inner) wall of the bundle sheath cells, and localization of glycine decarboxlyase to bundle sheath mitochondria. Low activities of PEP carboxylase, NADP malic enzyme, and NAD malic enzyme demonstrated no C(4) cycle activity occurs in E. acuta thereby classifying it as a Type I C(3)-C(4) intermediate. Kranz-like anatomy in E. johnstonii indicates it also utilizes C(2) photosynthesis. Given the phylogenetically intermediate position of E. acuta and E. johnstonii, these results support the hypothesis that C(2) photosynthesis is an evolutionary intermediate condition between C(3) and C(4) photosynthesis.

C(4) eudicots are not younger than C(4) monocots

C(4) photosynthesis is a plant adaptation to high levels of photorespiration. Physiological models predict that atmospheric CO(2) concentration selected for C(4) grasses only after it dropped below a critical threshold during the Oligocene (∼30 Ma), a hypothesis supported by phylogenetic and molecular dating analyses. However the same models predict that CO(2) should have reached much lower levels before selecting for C(4) eudicots, making C(4) eudicots younger than C(4) grasses. In this study, different phylogenetic datasets were combined in order to conduct the first comparative analysis of the age of C(4) origins in eudicots. Our results suggested that all lineages of C(4) eudicots arose during the last 30 million years, with the earliest before 22 Ma in Chenopodiaceae and Aizoaceae, and the latest probably after 2 Ma in Flaveria. C(4) eudicots are thus not globally younger than C(4) monocots. All lineages of C(4) plants evolved in a similar low CO(2) atmosphere that predominated during the last 30 million years. Independent C(4) origins were probably driven by different combinations of specific factors, including local ecological characteristics such as habitat openness, aridity, and salinity, as well as the speciation and dispersal history of each clade. Neither the lower number of C(4) species nor the frequency of C(3)-C(4) intermediates in eudicots can be attributed to a more recent origin, but probably result from variation in diversification and evolutionary rates among the different groups that evolved the C(4) pathway.

The role of proteins in C(3) plants prior to their recruitment into the C(4) pathway

Our most productive crops and native vegetation use a modified version of photosynthesis known as the C(4) pathway. Leaves of C(4) crops have increased nitrogen and water use efficiencies compared with C(3) species. Although the modifications to leaves of C(4) plants are complex, their faster growth led to the proposal that C(4) photosynthesis should be installed in C(3) crops in order to increase yield potential. Typically, a limited set of proteins become restricted to mesophyll or bundle sheath cells, and this allows CO(2) to be concentrated around the primary carboxylase RuBisCO. The role that these proteins play in C(3) species prior to their recruitment into the C(4) pathway is addressed here. Understanding the role of these proteins in C(3) plants is likely to be of use in predicting how the metabolism of a C(3) leaf will alter as components of the C(4) pathway are introduced as part of efforts to install characteristics of C(4) photosynthesis in leaves of C(3) crops.