Advancing our understanding and capacity to engineer nature's CO2-sequestering enzyme, Rubisco

Engineering photorespiration: current state and future possibilities

Reduction of flux through photorespiration has been viewed as a major way to improve crop carbon fixation and yield since the energy-consuming reactions associated with this pathway were discovered. This view has been supported by the biomasses increases observed in model species that expressed artificial bypass reactions to photorespiration. Here, we present an overview about the major current attempts to reduce photorespiratory losses in crop species and provide suggestions for future research priorities.

Assembly chaperones: a perspective

The historical origins and current interpretation of the molecular chaperone concept are presented, with the emphasis on the distinction between folding chaperones and assembly chaperones. Definitions of some basic terms in this field are offered and misconceptions pointed out. Two examples of assembly chaperone are discussed in more detail: the role of numerous histone chaperones in fundamental nuclear processes and the co-operation of assembly chaperones with folding chaperones in the production of the world's most important enzyme.

Design and development of synthetic microbial platform cells for bioenergy

The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO₂ fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy.

Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding

Conventional plant breeding exploits existing genetic variability and introduces new variability by mutagenesis. This has proven highly successful in securing food supplies for an ever-growing human population. The use of genetically modified plants is a complementary approach but all plant breeding techniques have limitations. Here, we discuss how the recent evolution of targeted mutagenesis and DNA insertion techniques based on tailor-made site-directed nucleases (SDNs) provides opportunities to overcome such limitations. Plant breeding companies are exploiting SDNs to develop a new generation of crops with new and improved traits. Nevertheless, some technical limitations as well as significant uncertainties on the regulatory status of SDNs may challenge their use for commercial plant breeding.

Temperature response of carbon isotope discrimination and mesophyll conductance in tobacco

The partial pressure of CO2 at the sites of carboxylation within chloroplasts depends on the conductance to CO2 diffusion from intercellular airspace to the sites of carboxylation, termed mesophyll conductance (gm ). We investigated the temperature response of gm in tobacco (Nicotiana tabacum) by combining gas exchange in high light, ambient CO2 in either 2 or 21% O2 with carbon isotope measurements using tuneable diode laser spectroscopy. The gm increased linearly with temperature in 2 or 21% O2 . In 21% O2 , isotope discrimination associated with gm decreased from 5.0 ± 0.2 to 1.8 ± 0.2‰ as temperature increased from 15 to 40 °C, but the photorespiratory contribution to the isotopic signal is significant. While the fractionation factor for photorespiration (f = 16.2 ± 0.7‰) was independent of temperature between 20 and 35 °C, discrimination associated with photorespiration increased from 1.1 ± 0.01 to 2.7 ± 0.02‰ from 15 to 40 °C. Other mitochondrial respiration contributed around 0.2 ± 0.03‰. The drawdown in CO2 partial pressure from ambient air to intercellular airspaces was nearly independent of leaf temperature. By contrast, the increase in gm with increasing leaf temperature resulted in the drawdown in CO2 partial pressure between intercellular airspaces and the sites of carboxylation decreasing substantially at high temperature.

Strategies for engineering C(4) photosynthesis

C(3) photosynthesis is an inefficient process, because the enzyme that lies at the heart of the Benson-Calvin cycle, ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco) is itself a very inefficient enzyme. The oxygenase activity of Rubisco is an unavoidable side reaction that is a consequence of its reaction mechanism. The product of oxygenation, glycollate 2-P, has to be retrieved by photorespiration, a process which results in the loss of a quarter of the carbon that was originally present in glycollate 2-P. Photorespiration therefore reduces carbon gain. Purely in terms of carbon economy, there is, therefore, a strong selection pressure on plants to reduce the rate of photorespiration so as to increase carbon gain, but it also improves water- and nitrogen-use efficiency. Possibilities for the manipulation of plants to decrease the amount of photorespiration include the introduction of improved Rubisco from other species, reconfiguring photorespiration, or introducing carbon-concentrating mechanisms, such as inorganic carbon transporters, carboxysomes or pyrenoids, or engineering a full C(4) Kranz pathway using the existing evolutionary progression in C(3)-C(4) intermediates as a blueprint. Possible routes and progress to suppressing photorespiration by introducing C(4) photosynthesis in C(3) crop plants will be discussed, including whether single cell C(4) photosynthesis is feasible, how the evolution of C(3)-C(4) intermediates can be used as a blueprint for engineering C(4) photosynthesis, which pathway for the C(4) cycle might be introduced and the extent to which processes and structures in C(3) plant might require optimisation.

Metabolic engineering of sugars and simple sugar derivatives in plants

Carbon captured through photosynthesis is transported, and sometimes stored in plants, as sugar. All organic compounds in plants trace to carbon from sugars, so sugar metabolism is highly regulated and integrated with development. Sugars stored by plants are important to humans as foods and as renewable feedstocks for industrial conversion to biofuels and biomaterials. For some purposes, sugars have advantages over polymers including starches, cellulose or storage lipids. This review considers progress and prospects in plant metabolic engineering for increased yield of endogenous sugars and for direct production of higher-value sugars and simple sugar derivatives. Opportunities are examined for enhancing export of sugars from leaves. Focus then turns to manipulation of sugar metabolism in sugar-storing sink organs such as fruits, sugarcane culms and sugarbeet tubers. Results from manipulation of suspected 'limiting' enzymes indicate a need for clearer understanding of flux control mechanisms, to achieve enhanced levels of endogenous sugars in crops that are highly selected for this trait. Outcomes from in planta conversion to novel sugars and derivatives range from severe interference with plant development to field demonstration of crops accumulating higher-value sugars at high yields. The differences depend on underlying biological factors including the effects of the novel products on endogenous metabolism, and on biotechnological fine-tuning including developmental expression and compartmentation patterns. Ultimately, osmotic activity may limit the accumulation of sugars to yields below those achievable using polymers; but results indicate the potential for increases above current commercial sugar yields, through metabolic engineering underpinned by improved understanding of plant sugar metabolism.

The mesophyll anatomy enhancing CO2 diffusion is a key trait for improving rice photosynthesis

Increases in rates of individual leaf photosynthesis (P(n)) are critical for future increases in yields of rice plants. Although many efforts have been made to improve rice P(n) with transgenic technology, the desired increases in P(n) have not yet been achieved. Two rice lines with extremely high values of P(n) were identified among the backcrossed inbred lines derived from the indica variety Takanari, one of the most productive varieties in Japan, and the elite japonica variety Koshihikari (Koshihikari/Takanari//Takanari). The P(n) values of the two lines at an ambient CO(2) concentration of 370μmol mol(-1) as well as at a saturating concentration of CO(2) were 20-50% higher than those of the parental varieties. Compared with Takanari, these lines had neither a higher content nor a higher activity of ribulose 1,5-bisphosphate carboxylase/oxygenase when the leaf nitrogen contents were similar, but they did have high mesophyll conductance with respect to CO(2) flux due to their higher density and more highly developed lobes of mesophyll cells. These lines also had higher electron transport rates. The plant growth rates of these lines were higher than that of Takanari. The findings show that it is possible to increase P(n) significantly, both at the current atmospheric concentration of CO(2) and at the increased concentration of CO(2) expected in the future, using appropriate combinations of genetic resources that are available at present.

The cyanobacterial CCM as a source of genes for improving photosynthetic CO2 fixation in crop species

Crop yields need to nearly double over the next 35 years to keep pace with projected population growth. Improving photosynthesis, via a range of genetic engineering strategies, has been identified as a promising target for crop improvement with regard to increased photosynthetic yield and better water-use efficiency (WUE). One approach is based on integrating components of the highly efficient CO(2)-concentrating mechanism (CCM) present in cyanobacteria (blue-green algae) into the chloroplasts of key C(3) crop plants, particularly wheat and rice. Four progressive phases towards engineering components of the cyanobacterial CCM into C(3) species can be envisaged. The first phase (1a), and simplest, is to consider the transplantation of cyanobacterial bicarbonate transporters to C(3) chloroplasts, by host genomic expression and chloroplast targeting, to raise CO(2) levels in the chloroplast and provide a significant improvement in photosynthetic performance. Mathematical modelling indicates that improvements in photosynthesis as high as 28% could be achieved by introducing both of the single-gene, cyanobacterial bicarbonate transporters, known as BicA and SbtA, into C(3) plant chloroplasts. Part of the first phase (1b) includes the more challenging integration of a functional cyanobacterial carboxysome into the chloroplast by chloroplast genome transformation. The later three phases would be progressively more elaborate, taking longer to engineer other functional components of the cyanobacterial CCM into the chloroplast, and targeting photosynthetic and WUE efficiencies typical of C(4) photosynthesis. These later stages would include the addition of NDH-1-type CO(2) pumps and suppression of carbonic anhydrase and C(3) Rubisco in the chloroplast stroma. We include a score card for assessing the success of physiological modifications gained in phase 1a.

Rubisco activity and regulation as targets for crop improvement

Rubisco (ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase) enables net carbon fixation through the carboxylation of RuBP. However, some characteristics of Rubisco make it surprisingly inefficient and compromise photosynthetic productivity. For example, Rubisco catalyses a wasteful reaction with oxygen that leads to the release of previously fixed CO(2) and NH(3) and the consumption of energy during photorespiration. Furthermore, Rubisco is slow and large amounts are needed to support adequate photosynthetic rates. Consequently, Rubisco has been studied intensively as a prime target for manipulations to 'supercharge' photosynthesis and improve both productivity and resource use efficiency. The catalytic properties of Rubiscos from diverse sources vary considerably, suggesting that changes in turnover rate, affinity, or specificity for CO(2) can be introduced to improve Rubisco performance in specific crops and environments. While attempts to manipulate plant Rubisco by nuclear transformation have had limited success, modifying its catalysis by targeted changes to its catalytic large subunit via chloroplast transformation have been much more successful. However, this technique is still in need of development for most major food crops including maize, wheat, and rice. Other bioengineering approaches for improving Rubisco performance include improving the activity of its ancillary protein, Rubisco activase, in addition to modulating the synthesis and degradation of Rubisco's inhibitory sugar phosphate ligands. As the rate-limiting step in carbon assimilation, even modest improvements in the overall performance of Rubisco pose a viable pathway for obtaining significant gains in plant yield, particularly under stressful environmental conditions.

Chloroplast transformation for engineering of photosynthesis

Many efforts are underway to engineer improvements in photosynthesis to meet the challenges of increasing demands for food and fuel in rapidly changing environmental conditions. Various transgenes have been introduced into either the nuclear or plastid genomes in attempts to increase photosynthetic efficiency. We examine the current knowledge of the critical features that affect levels of expression of plastid transgenes and protein accumulation in transplastomic plants, such as promoters, 5' and 3' untranslated regions, RNA-processing sites, translation signals and amino acid sequences that affect protein turnover. We review the prior attempts to manipulate the properties of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) through plastid transformation. We illustrate how plastid operons could be created for expression of the multiple genes needed to introduce new pathways or enzymes to enhance photosynthetic rates or reduce photorespiration. We describe here the past accomplishments and future prospects for manipulating plant enzymes and pathways to enhance carbon assimilation through plastid transformation.

Engineering photosynthesis in plants and synthetic microorganisms

Photosynthetic organisms, such as cyanobacteria, algae, and plants, sustain life on earth by converting light energy, water, and CO(2) into chemical energy. However, due to global change and a growing human population, arable land is becoming scarce and resources, including water and fertilizers, are becoming exhausted. It will therefore be crucial to design innovative strategies for sustainable plant production to maintain the food and energy bases of human civilization. Several different strategies for engineering improved photosynthesis in crop plants and introducing novel photosynthetic capacity into microorganisms have been reviewed.

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.

Growth of transplastomic cells expressing D-amino acid oxidase in chloroplasts is tolerant to D-alanine and inhibited by D-valine

Dual-conditional positive/negative selection markers are versatile genetic tools for manipulating genomes. Plastid genomes are relatively small and conserved DNA molecules that can be manipulated precisely by homologous recombination. High-yield expression of recombinant products and maternal inheritance of plastid-encoded traits make plastids attractive sites for modification. Here, we describe the cloning and expression of a dao gene encoding D-amino acid oxidase from Schizosaccharomyces pombe in tobacco (Nicotiana tabacum) plastids. The results provide genetic evidence for the uptake of D-amino acids into plastids, which contain a target that is inhibited by D-alanine. Importantly, this nonantibiotic-based selection system allows the use of cheap and widely available D-amino acids, which are relatively nontoxic to animals and microbes, to either select against (D-valine) or for (D-alanine) cells containing transgenic plastids. Positive/negative selection with d-amino acids was effective in vitro and against transplastomic seedlings grown in soil. The dual functionality of dao is highly suited to the polyploid plastid compartment, where it can be used to provide tolerance against potential D-alanine-based herbicides, control the timing of recombination events such as marker excision, influence the segregation of transgenic plastid genomes, identify loci affecting dao function in mutant screens, and develop D-valine-based methods to manage the spread of transgenic plastids tagged with dao.

Effects of exogenous auxin and ethylene on the Arabidopsis root proteome

The phytohormones, auxin and ethylene, together control a wide range of physiological and developmental processes in plants. The lack of knowledge regarding how the underlying signaling processes are reflected at the protein level represents a major gap in understanding phytohormone signaling, including that mediated by crosstalk between auxin and ethylene. Herein is a parallel comparison of the effects of these two hormones on the Arabidopsis root proteome. Arabidopsis seedlings were exposed to 1 μm indole-3-acetic acid (IAA, auxin) or 1 μm 1-amino-cyclopropane carboxylic acid (ACC) for 24h. Root protein extracts were fractionated using two-dimensional gel electrophoresis and the proteins that changed the most were analyzed by MALDI TOF/TOF mass spectrometry. Of the 500 total spots that were matched across all gels, 24 were significantly different after IAA exposure, while seven others were different after ACC exposure. Using rigorous criteria, identities of eight proteins regulated by IAA and five regulated by ACC were assigned. Interestingly, although both hormones affected proteins associated with fundamental cellular processes, no overlap was observed among the proteins affected by auxin or ethylene treatment. This report provides a comparison of the effects of these two hormones relative to a control utilizing equivalent treatment regimes and suggests that, while these hormones communicate to control similar physiological and transcriptional processes, they have different effects on the most abundant proteins in Arabidopsis roots.

Opinion: prospects for improving photosynthesis by altering leaf anatomy

Engineering higher photosynthetic efficiency for greater crop yields has gained significant attention among plant biologists and breeders. To achieve this goal, manipulation of metabolic targets and canopy architectural features has been heavily emphasized. Given the substantial variations in leaf anatomical features among and within plant species, there is large potential to engineer leaf anatomy for improved photosynthetic efficiency. Here we review how different leaf anatomical features influence internal light distribution, delivery of CO(2) to Rubisco and water relations, and accordingly recommend features to engineer for increased leaf photosynthesis under different environments. More research is needed on (a) elucidating the genetic mechanisms controlling leaf anatomy, and (b) the development of a three dimensional biochemical and biophysical model of leaf photosynthesis, which can help pinpoint anatomical features required to gain a higher photosynthesis.

Hornwort pyrenoids, carbon-concentrating structures, evolved and were lost at least five times during the last 100 million years

Ribulose-1,5-biphosphate-carboxylase-oxygenase (RuBisCO) has a crucial role in carbon fixation but a slow catalytic rate, a problem overcome in some plant lineages by physiological and anatomical traits that elevate carbon concentrations around the enzyme. Such carbon-concentrating mechanisms are hypothesized to have evolved during periods of low atmospheric CO(2). Hornworts, the sister to vascular plants, have a carbon-concentrating mechanism that relies on pyrenoids, proteinaceous bodies mostly consisting of RuBisCO. We generated a phylogeny based on mitochondrial and plastid sequences for 36% of the approximately 200 hornwort species to infer the history of gains and losses of pyrenoids in this clade; we also used fossils and multiple dating approaches to generate a chronogram for the hornworts. The results imply five to six origins and an equal number of subsequent losses of pyrenoids in hornworts, with the oldest pyrenoid gained ca. 100 Mya, and most others at <35 Mya. The nonsynchronous appearance of pyrenoid-containing clades, the successful diversification of pyrenoid-lacking clades during periods with low [CO(2)], and the maintenance of pyrenoids during episodes of high [CO(2)] all argue against the previously proposed relationship between pyrenoid origin and low [CO(2)]. The selective advantages, and costs, of hornwort pyrenoids thus must relate to additional factors besides atmospheric CO(2).

Rubisco small-subunit α-helices control pyrenoid formation in Chlamydomonas

The pyrenoid is a subcellular microcompartment in which algae sequester the primary carboxylase, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The pyrenoid is associated with a CO(2)-concentrating mechanism (CCM), which improves the operating efficiency of carbon assimilation and overcomes diffusive limitations in aquatic photosynthesis. Using the model alga Chlamydomonas reinhardtii, we show that pyrenoid formation, Rubisco aggregation, and CCM activity relate to discrete regions of the Rubisco small subunit (SSU). Specifically, pyrenoid occurrence was shown to be conditioned by the amino acid composition of two surface-exposed α-helices of the SSU: higher plant-like helices knock out the pyrenoid, whereas native algal helices establish a pyrenoid. We have also established that pyrenoid integrity was essential for the operation of an active CCM. With the algal CCM being functionally analogous to the terrestrial C(4) pathway in higher plants, such insights may offer a route toward transforming algal and higher plant productivity for the future.

Plastid genetic engineering in Solanaceae

Plastid genetic engineering has come of age, becoming today an attractive alternative approach for the expression of foreign genes, as it offers several advantages over nuclear transformants. Significant progress has been made in plastid genetic engineering in tobacco and other Solanaceae plants, through the use of improved regeneration procedures and transformation vectors with efficient promoters and untranslated regions. Many genes encoding for industrially important proteins and vaccines, as well as genes conferring important agronomic traits, have been stably integrated and expressed in the plastid genome. Despite these advances, it remains a challenge to achieve marked levels of plastid transgene expression in non-green tissues. In this review, we summarize the basic requirements of plastid genetic engineering and discuss the current status, limitations, and the potential of plastid transformation for expanding future studies relating to Solanaceae plants.

Achieving diversity in the face of constraints: lessons from metabolism

Metabolic engineering of plants can reduce the cost and environmental impact of agriculture while providing for the needs of a growing population. Although our understanding of plant metabolism continues to increase at a rapid pace, relatively few plant metabolic engineering projects with commercial potential have emerged, in part because of a lack of principles for the rational manipulation of plant phenotype. One underexplored approach to identifying such design principles derives from analysis of the dominant constraints on plant fitness, and the evolutionary innovations in response to those constraints, that gave rise to the enormous diversity of natural plant metabolic pathways.

Proteomic study participating the enhancement of growth and salt tolerance of bottle gourd rootstock-grafted watermelon seedlings

An insertion grafting technique to do research on salt tolerance was applied using watermelon (Citrullus lanatus [Thunb.] Mansf. cv. Xiuli) as a scion and bottle gourd (Lagenaria siceraria Standl. cv. Chaofeng Kangshengwang) as a rootstock. Rootstock-grafting significantly relieved the inhibition of growth and photosynthesis induced by salt stress in watermelon plants. Proteomic analysis revealed 40 different expressed proteins in response to rootstock-grafting and/or salt stress. These proteins were involved in Calvin cycle, amino acids biosynthesis, carbohydrate and energy metabolism, ROS defense, hormonal biosynthesis and signal transduction. Most of these proteins were up-regulated by rootstock-grafting and/or susceptible to salt stress. The enhancement of the metabolic activities of Calvin cycle, biosynthesis of amino acids, carotenoids and peroxisomes, glycolytic pathway and tricarboxylic acid cycle will probably contribute to intensify the biomass and photosynthetic capacity in rootstock-grafted seedlings under condition without salt. The accumulation of key enzymes included in these biological processes described above seems to play an important role in the enhancement of salt tolerance of rootstock-grafted seedlings. Furthermore, leucine-rich repeat transmembrane protein kinase and phospholipase may be involved in transmitting the internal and external stimuli induced by grafting and/or salt stress.

Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants

Development of sustainable energy is a pivotal step towards solutions for today's global challenges, including mitigating the progression of climate change and reducing dependence on fossil fuels. Biofuels derived from agricultural crops have already been commercialized. However the impacts on environmental sustainability and food supply have raised ethical questions about the current practices. Cyanobacteria have attracted interest as an alternative means for sustainable energy productions. Being aquatic photoautotrophs they can be cultivated in non-arable lands and do not compete for land for food production. Their rich genetic resources offer means to engineer metabolic pathways for synthesis of valuable bio-based products. Currently the major obstacle in industrial-scale exploitation of cyanobacteria as the economically sustainable production hosts is low yields. Much effort has been made to improve the carbon fixation and manipulating the carbon allocation in cyanobacteria and their evolutionary photosynthetic relatives, algae and plants. This review aims at providing an overview of the recent progress in the bioengineering of carbon fixation and allocation in cyanobacteria; wherever relevant, the progress made in plants and algae is also discussed as an inspiration for future application in cyanobacteria.

Improving carbon fixation pathways

A recent resurgence in basic and applied research on photosynthesis has been driven in part by recognition that fulfilling future food and energy requirements will necessitate improvements in crop carbon-fixation efficiencies. Photosynthesis in traditional terrestrial crops is being reexamined in light of molecular strategies employed by photosynthetic microbes to enhance the activity of the Calvin cycle. Synthetic biology is well-situated to provide original approaches for compartmentalizing and enhancing photosynthetic reactions in a species independent manner. Furthermore, the elucidation of alternative carbon-fixation routes distinct from the Calvin cycle raises possibilities that novel pathways and organisms can be utilized to fix atmospheric carbon dioxide into useful materials.

Evolutionary context for understanding and manipulating plant responses to past, present and future atmospheric [CO2]

Variation in atmospheric [CO(2)] is a prominent feature of the environmental history over which vascular plants have evolved. Periods of falling and low [CO(2)] in the palaeo-record appear to have created selective pressure for important adaptations in modern plants. Today, rising [CO(2)] is a key component of anthropogenic global environmental change that will impact plants and the ecosystem goods and services they deliver. Currently, there is limited evidence that natural plant populations have evolved in response to contemporary increases in [CO(2)] in ways that increase plant productivity or fitness, and no evidence for incidental breeding of crop varieties to achieve greater yield enhancement from rising [CO(2)]. Evolutionary responses to elevated [CO(2)] have been studied by applying selection in controlled environments, quantitative genetics and trait-based approaches. Findings to date suggest that adaptive changes in plant traits in response to future [CO(2)] will not be consistently observed across species or environments and will not be large in magnitude compared with physiological and ecological responses to future [CO(2)]. This lack of evidence for strong evolutionary effects of elevated [CO(2)] is surprising, given the large effects of elevated [CO(2)] on plant phenotypes. New studies under more stressful, complex environmental conditions associated with climate change may revise this view. Efforts are underway to engineer plants to: (i) overcome the limitations to photosynthesis from today's [CO(2)] and (ii) benefit maximally from future, greater [CO(2)]. Targets range in scale from manipulating the function of a single enzyme (e.g. Rubisco) to adding metabolic pathways from bacteria as well as engineering the structural and functional components necessary for C(4) photosynthesis into C(3) leaves. Successfully improving plant performance will depend on combining the knowledge of the evolutionary context, cellular basis and physiological integration of plant responses to varying [CO(2)].

Accelerating yield potential in soybean: potential targets for biotechnological improvement

Soybean (Glycine max Merr.) is the world's most widely grown legume and provides an important source of protein and oil. Global soybean production and yield per hectare increased steadily over the past century with improved agronomy and development of cultivars suited to a wide range of latitudes. In order to meet the needs of a growing world population without unsustainable expansion of the land area devoted to this crop, yield must increase at a faster rate than at present. Here, the historical basis for the yield gains realized in the past 90 years are examined together with potential metabolic targets for achieving further improvements in yield potential. These targets include improving photosynthetic efficiency, optimizing delivery and utilization of carbon, more efficient nitrogen fixation and altering flower initiation and abortion. Optimization of investment in photosynthetic enzymes, bypassing photorespiratory metabolism, engineering the electron transport chain and engineering a faster recovery from the photoprotected state are different strategies to improve photosynthesis in soybean. These potential improvements in photosynthetic carbon gain will need to be matched by increased carbon and nitrogen transport to developing soybean pods and seeds in order to maximize the benefit. Better understanding of control of carbon and nitrogen transport along with improved knowledge of the regulation of flower initiation and abortion will be needed to optimize sink capacity in soybean. Although few single targets are likely to deliver a quantum leap in yields, biotechnological advances in molecular breeding techniques that allow for alteration of the soybean genome and transcriptome promise significant yield gains.

Non-invasive approaches for phenotyping of enhanced performance traits in bean

Plant phenotyping is an emerging discipline in plant biology. Quantitative measurements of functional and structural traits help to better understand gene-environment interactions and support breeding for improved resource use efficiency of important crops such as bean (Phaseolus vulgaris L.). Here we provide an overview of state-of-the-art phenotyping approaches addressing three aspects of resource use efficiency in plants: belowground roots, aboveground shoots and transport/allocation processes. We demonstrate the capacity of high-precision methods to measure plant function or structural traits non-invasively, stating examples wherever possible. Ideally, high-precision methods are complemented by fast and high-throughput technologies. High-throughput phenotyping can be applied in the laboratory using automated data acquisition, as well as in the field, where imaging spectroscopy opens a new path to understand plant function non-invasively. For example, we demonstrate how magnetic resonance imaging (MRI) can resolve root structure and separate root systems under resource competition, how automated fluorescence imaging (PAM fluorometry) in combination with automated shape detection allows for high-throughput screening of photosynthetic traits and how imaging spectrometers can be used to quantify pigment concentration, sun-induced fluorescence and potentially photosynthetic quantum yield. We propose that these phenotyping techniques, combined with mechanistic knowledge on plant structure-function relationships, will open new research directions in whole-plant ecophysiology and may assist breeding for varieties with enhanced resource use efficiency varieties.

Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco

BACKGROUND

One of the key forces shaping proteins is coevolution of amino acid residues. Knowing which residues coevolve in a particular protein may facilitate our understanding of protein evolution, structure and function, and help to identify substitutions that may lead to desired changes in enzyme kinetics. Rubisco, the most abundant enzyme in biosphere, plays an essential role in the process of carbon fixation through photosynthesis, thus facilitating life on Earth. This makes Rubisco an important model system for studying the dynamics of protein fitness optimization on the evolutionary landscape. In this study we investigated the selective and coevolutionary forces acting on large subunit of land plants Rubisco using Markov models of codon substitution and clustering approaches applied to amino acid substitution histories.

RESULTS

We found that both selection and coevolution shape Rubisco, and that positively selected and coevolving residues have their specifically favored amino acid composition and pairing preference. The mapping of these residues on the known Rubisco tertiary structures showed that the coevolving residues tend to be in closer proximity with each other compared to the background, while positively selected residues tend to be further away from each other. This study also reveals that the residues under positive selection or coevolutionary force are located within functionally important regions and that some residues are targets of both positive selection and coevolution at the same time.

CONCLUSION

Our results demonstrate that coevolution of residues is common in Rubisco of land plants and that there is an overlap between coevolving and positively selected residues. Knowledge of which Rubisco residues are coevolving and positively selected could be used for further work on structural modeling and identification of substitutions that may be changed in order to improve efficiency of this important enzyme in crops.

NanoESI mass spectrometry of Rubisco and Rubisco activase structures and their interactions with nucleotides and sugar phosphates

Ribulose bisphosphate carboxylase/oxygenase (Rubisco) is the protein that is responsible for the fixation of carbon dioxide in photosynthesis. Inhibitory sugar phosphate molecules, which can include its substrate ribulose-1,5-bisphosphate (RuBP), can bind to Rubisco catalytic sites and inhibit catalysis. These are removed by interaction with Rubisco activase (RA) via an ATP hydrolytic reaction. Here we show the first nanoESI mass spectra of the hexadecameric Rubisco and of RA from a higher plant (tobacco). The spectra of recombinant, purified RA revealed polydispersity in its oligomeric forms (up to hexamer) and that ADP was bound. ADP was removed by dialysis against a high ionic strength solution and nucleotide binding experiments showed that ADP bound more tightly to RA than AMP-PNP (a non-hydrolysable ATP analog). There was evidence that there may be two nucleotide binding sites per RA monomer. The oligomerization capacity of mutant and wild-type tobacco RA up to hexamers is analogous to the subunit stoichiometry for other AAA+ enzymes. This suggests assembly of RA into hexamers is likely the most active conformation for removing inhibitory sugar phosphate molecules from Rubisco to enable its catalytic competency. Stoichiometric binding of RuBP or carboxyarabinitol bisphosphate (CABP) to each of the eight catalytic sites of Rubisco was observed.

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.

Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco

The form I Rubisco of autotrophic bacteria, algae and plants is a complex of eight large (RbcL) and eight small (RbcS) subunits. It fixes atmospheric CO(2) in the dark reaction of photosynthesis. As shown for the cyanobacterial enzyme, folding of the RbcL subunits is mediated by the GroEL-GroES chaperonin system, and assembly requires the specialized chaperone RbcX, a homodimer of ~15-kDa subunits. Here we present the 3.2-Å crystal structure of a Rubisco assembly intermediate, consisting of the RbcL(8) core with eight RbcX(2) molecules bound. The structure reveals the molecular mechanism by which RbcX(2) mediates oligomeric assembly. Specifically, RbcX(2) provides positional information for proper formation of antiparallel RbcL dimers, thereby preventing RbcL-RbcL misalignment and off-pathway aggregation. The RbcL(8)(RbcX(2))(8) structure also suggests that RbcS functions by stabilizing the '60s loop' of RbcL in the catalytically active conformation.

Functional incorporation of sorghum small subunit increases the catalytic turnover rate of Rubisco in transgenic rice

Rubisco limits photosynthetic CO(2) fixation because of its low catalytic turnover rate (k(cat)) and competing oxygenase reaction. Previous attempts to improve the catalytic efficiency of Rubisco by genetic engineering have gained little progress. Here we demonstrate that the introduction of the small subunit (RbcS) of high k(cat) Rubisco from the C(4) plant sorghum (Sorghum bicolor) significantly enhances k(cat) of Rubisco in transgenic rice (Oryza sativa). Three independent transgenic lines expressed sorghum RbcS at a high level, accounting for 30%, 44%, and 79% of the total RbcS. Rubisco was likely present as a chimera of sorghum and rice RbcS, and showed 1.32- to 1.50-fold higher k(cat) than in nontransgenic rice. Rubisco from transgenic lines showed a higher K(m) for CO(2) and slightly lower specificity for CO(2) than nontransgenic controls. These results suggest that Rubisco in rice transformed with sorghum RbcS partially acquires the catalytic properties of sorghum Rubisco. Rubisco content in transgenic lines was significantly increased over wild-type levels but Rubisco activation was slightly decreased. The expression of sorghum RbcS did not affect CO(2) assimilation rates under a range of CO(2) partial pressures. The J(max)/V(cmax) ratio was significantly lower in transgenic line compared to the nontransgenic plants. These observations suggest that the capacity of electron transport is not sufficient to support the increased Rubisco capacity in transgenic rice. Although the photosynthetic rate was not enhanced, the strategy presented here opens the way to engineering Rubisco for improvement of photosynthesis and productivity in the future.