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Photosynthetic induction describes the transient increase in leaf CO2 uptake with an increase in light. During induction, efficiency is lower than at steady state. Under field conditions of fluctuating light, this lower efficiency during induction may cost > 20% of potential crop assimilation. Accelerating induction would boost photosynthetic and resource-use efficiencies. Variation between rice accessions and potential for accelerating induction was analysed by gas exchange. Induction during shade to sun transitions of 14 accessions representing five subpopulations from the 3000 Rice Genome Project Panel (3K RGP) was analysed. Differences of 109% occurred in the CO2 fixed during the first 300 s of induction, 117% in the half-time to completion of induction, and 65% in intrinsic water-use efficiency during induction, between the highest and lowest performing accessions. Induction in three accessions with contrasting responses (AUS 278, NCS 771 A and IR64-21) was compared for a range of [CO2] to analyse limitations. This showed in vivo capacity for carboxylation at Rubisco (Vc,max), and not stomata, as the primary limitation to induction, with significant differences between accessions. Variation in nonsteady-state efficiency greatly exceeded that at steady state, suggesting a new and more promising opportunity for selection of greater crop photosynthetic efficiency in this key food crop. © 2020 The Authors. New Phytologist © 2020 New Phytologist Trust

Leaf development is crucial to establish the photosynthetic competency of plants. It is a process that requires coordinated changes in cell number and differentiation, transcriptomes, metabolomes and physiology. However, despite the importance of leaf formation for our major crops, early developmental processes for rice have not been comprehensively described. Here we detail the temporal developmental trajectory of early rice leaf development and connect morphological changes to metabolism. In particular, a developmental index based on the patterning of epidermal differentiation visualised by electron microscopy enabled high resolution staging of early growth for single primordium metabolite profiling. These data demonstrate that a switch in the constellation of tricarboxylic acid (TCA) cycle metabolites defines a narrow window towards the end of the P3 stage of leaf development. Taken in the context of other data in the literature, our results substantiate that this phase of rice leaf growth, equivalent to a change of primordium length from around 5 to 7.5 mm, defines a major shift in rice leaf determination towards a photosynthetically defined structure. We speculate that efforts to engineer rice leaf structure should focus on the developmental window prior to these determining events.HighlightRice leaves undergo a shift in fundamental metabolism during a very early and narrow developmental window which co-incides with them acquiring the ability to capture light for photosynthesis

Improvement of photosynthetic traits in crops to increase yield potential and crop resilience has recently become a major breeding target. Synthetic biology and genetic technologies offer unparalleled opportunities to create new genetics for photosynthetic traits driven by existing fundamental knowledge. However, large ‘gene bank’ collections of germplasm comprising historical collections of crop species and their relatives offer a wealth of opportunities to find novel allelic variation in the key steps of photosynthesis, to identify new mechanisms and to accelerate genetic progress in crop breeding programmes. Here we explore the available genetic resources in food and fibre crops, strategies to selectively target allelic variation in genes underpinning key photosynthetic processes, and deployment of this variation via gene editing in modern elite material.

C4 photosynthetic plants have evolved from C3 ancestors and are characterized by differential expression of several hundred genes. Strict compartmentalization of key C4 enzymes either to mesophyll (M) or bundle sheath cells is considered a crucial step towards the evolution of C4 photosynthesis. In this study, we demonstrate that the 5'-flanking sequences of the C4 type phosphoenolpyruvate carboxylase (Ppc) gene from three C4 grass species could drive M-cell-specific expression of a reporter gene in rice. In addition to that, we identified about 450 bp (upstream of their transcription start site) of the analyzed C4 Ppc promoters contain all the essential regulatory elements for driving M-cell-specific expression in rice leaves. Importantly, four motifs of conserved nucleotide sequences (CNSs) were also determined, which are essential for the activity of the promoter. A putative interaction between the CNSs and an unknown upstream element(s) is required for driving M-cell-specific expression. This work identifies the evolutionary conservation of C4 Ppc regulatory mechanisms of multiple closely related C4 grass species.

The engineering process of C4 photosynthesis into C3 plants requires an increased activity of phosphoenolpyruvate carboxylase (PEPC) in the cytosol of leaf mesophyll cells. The literature varies on the physiological effect of transgenic maize (Zea mays) PEPC (ZmPEPC) leaf expression in Oryza sativa (rice). Therefore, to address this issue, leaf–atmosphere CO2 and 13CO2 exchanges were measured, both in the light (at atmospheric O2 partial pressure of 1.84 kPa and at different CO2 levels) and in the dark, in transgenic rice expressing ZmPEPC and wild-type (WT) plants. The in vitro PEPC activity was 25 times higher in the PEPC overexpressing (PEPC-OE) plants (~20% of maize) compared to the negligible activity in WT. In the PEPC-OE plants, the estimated fraction of carboxylation by PEPC (β) was ~6% and leaf net biochemical discrimination against 13CO2$$\left( {\Delta_{\text{bio}} } \right)$$ was ~ 2‰ lower than in WT. However, there were no differences in leaf net CO2 assimilation rates (A) between genotypes, while the leaf dark respiration rates (Rd) over three hours after light–dark transition were enhanced (~ 30%) and with a higher 13C composition $$\left( {\delta^{ 1 3} {\text{C}}_{\text{Rd}} } \right)$$ in the PEPC-OE plants compared to WT. These data indicate that ZmPEPC in the PEPC-OE rice plants contributes to leaf carbon metabolism in both the light and in the dark. However, there are some factors, potentially posttranslational regulation and PEP availability, which reduce ZmPEPC activity in vivo.

The disruption of photorespiration in GDC knockdown rice plants alters leaf photorespiratory 13CO2 fractionation and carbon isotope exchange., The influence of reduced glycine decarboxylase complex (GDC) activity on leaf atmosphere CO2 and 13CO2 exchange was tested in transgenic Oryza sativa with the GDC H-subunit knocked down in leaf mesophyll cells. Leaf measurements on transgenic gdch knockdown and wild-type plants were carried out in the light under photorespiratory and low photorespiratory conditions (i.e. 18.4 kPa and 1.84 kPa atmospheric O2 partial pressure, respectively), and in the dark. Under approximately current ambient O2 partial pressure (18.4 kPa pO2), the gdch knockdown plants showed an expected photorespiratory-deficient phenotype, with lower leaf net CO2 assimilation rates (A) than the wild-type. Additionally, under these conditions, the gdch knockdown plants had greater leaf net discrimination against 13CO2 (Δo) than the wild-type. This difference in Δo was in part due to lower 13C photorespiratory fractionation (f) ascribed to alternative decarboxylation of photorespiratory intermediates. Furthermore, the leaf dark respiration rate (Rd) was enhanced and the 13CO2 composition of respired CO2 (δ13CRd) showed a tendency to be more depleted in the gdch knockdown plants. These changes in Rd and δ13CRd were due to the amount and carbon isotopic composition of substrates available for dark respiration. These results demonstrate that impairment of the photorespiratory pathway affects leaf 13CO2 exchange, particularly the 13C decarboxylation fractionation associated with photorespiration.

Significant natural variation was found in rice flag leaves for photosynthetic traits measured in steady- and non-steady-state conditions, with implications for improving water use efficiency and photosynthesis in this key crop., Several breeding initiatives have sought to improve flag leaf performance as its health and physiology are closely correlated to rice yield. Previous studies have described natural variation of photosynthesis for flag leaves; however, none has examined their performance under the non-steady-state conditions that prevail in crop fields. Photosynthetic induction is the transient response of photosynthesis to a change from low to high light. Rice flag leaf photosynthesis was measured in both steady- and non-steady-state conditions to characterize natural variation. Between the lowest and highest performing accession, there was a 152% difference for average CO2 assimilation during induction (Ā300), a 77% difference for average intrinsic water use efficiency during induction (iWUEavg), and a 185% difference for the speed of induction (IT50), indicating plentiful variation. No significant correlation was found between steady- and non-steady-state photosynthetic traits. Additionally, measures of neither steady-state nor non-steady-state photosynthesis of flag leaves correlated with the same measures of leaves in the vegetative growth stage, with the exception of iWUEavg. Photosynthetic induction was measured at six [CO2], to determine biochemical and diffusive limitations to photosynthesis in vivo. Photosynthetic induction in rice flag leaves was limited primarily by biochemistry.

Introduction of a C4photosynthetic pathway into C3rice (Oryza sativa) requires installation of a biochemical pump that concentrates CO2at the site of carboxylation in modified bundle sheath cells. To investigate the feasibility of this, we generated a quadruple line that simultaneously expresses four of the core C4photosynthetic enzymes from the NADP-malic enzyme subtype, phosphoenolpyruvate carboxylase (ZmPEPC), NADP-malate dehydrogenase (ZmNADP-MDH), NADP-malic enzyme (ZmNADP-ME) and pyruvate phosphate dikinase (ZmPPDK), in a cell-specific manner. This led to enhanced enzyme activity but was largely neutral in its effects on photosynthetic rate and growth. Measurements of the flux of13CO2through photosynthetic metabolism revealed a significant increase in the incorporation of13C into malate, consistent with increased fixation of13CO2via PEP carboxylase in lines expressing the maize PEPC enzyme. We also showed13C labelling of aspartate indicating additional13CO2fixation into oxaloacetate by PEPC and conversion to aspartate by the endogenous aspartate aminotransferase activity. However, there were no significant differences in labelling of 3-phosphoglycerate (3PGA) or phosphoenolpyruvate (PEP) indicating limited carbon flux through C4enzymes into the Calvin-Benson cycle. Crossing the quadruple line with a line with reduced glycine decarboxylase H-protein (OsGDCH) abundance led to a photosynthetic phenotype characteristic of the reducedOsGDCH line and higher labelling of malate, aspartate and citrate. While Kranz anatomy or other anatomical modifications have not yet been installed in these plants to enable a fully functional C4cycle, these results demonstrate for the first-time flux through the carboxylation phase of C4metabolism in transgenic rice containing the key metabolic steps in the C4pathway.

Solute transport across the chloroplast envelope is controlled by metabolite concentration gradients and transporter abundance. Overexpression of an envelope dicarboxylate transporter causes a pronounced metabolic phenotype, indicating that transporter abundance directly affects metabolism., The chloroplastic 2-oxaloacetate (OAA)/malate transporter (OMT1 or DiT1) takes part in the malate valve that protects chloroplasts from excessive redox poise through export of malate and import of OAA. Together with the glutamate/malate transporter (DCT1 or DiT2), it connects carbon with nitrogen assimilation, by providing 2-oxoglutarate for the GS/GOGAT (glutamine synthetase/glutamate synthase) reaction and exporting glutamate to the cytoplasm. OMT1 further plays a prominent role in C4 photosynthesis: OAA resulting from phosphoenolpyruvate carboxylation is imported into the chloroplast, reduced to malate by plastidic NADP-malate dehydrogenase, and then exported for transport to bundle sheath cells. Both transport steps are catalyzed by OMT1, at the rate of net carbon assimilation. To engineer C4 photosynthesis into C3 crops, OMT1 must be expressed in high amounts on top of core C4 metabolic enzymes. We report here high-level expression of ZmOMT1 from maize in rice (Oryza sativa ssp. indica IR64). Increased activity of the transporter in transgenic rice was confirmed by reconstitution of transporter activity into proteoliposomes. Unexpectedly, overexpression of ZmOMT1 in rice negatively affected growth, CO2 assimilation rate, total free amino acid content, tricarboxylic acid cycle metabolites, as well as sucrose and starch contents. Accumulation of high amounts of aspartate and the impaired growth phenotype of OMT1 rice lines could be suppressed by simultaneous overexpression of ZmDiT2. Implications for engineering C4 rice are discussed.

Summary Much of humanity relies on rice (Oryza sativa) as a food source, but cultivation is water intensive and the crop is vulnerable to drought and high temperatures. Under climate change, periods of reduced water availability and high temperature are expected to become more frequent, leading to detrimental effects on rice yields.We engineered the high‐yielding rice cultivar ‘IR64’ to produce fewer stomata by manipulating the level of a developmental signal. We overexpressed the rice epidermal patterning factor OsEPF1, creating plants with substantially reduced stomatal density and correspondingly low stomatal conductance.Low stomatal density rice lines were more able to conserve water, using c. 60% of the normal amount between weeks 4 and 5 post germination. When grown at elevated atmospheric CO 2, rice plants with low stomatal density were able to maintain their stomatal conductance and survive drought and high temperature (40°C) for longer than control plants. Low stomatal density rice gave equivalent or even improved yields, despite a reduced rate of photosynthesis in some conditions.Rice plants with fewer stomata are drought tolerant and more conservative in their water use, and they should perform better in the future when climate change is expected to threaten food security.

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

Rice is the most important crop in the world. It is a staple food for more than half of the human population and a primary food source for the world’s poorest people. Asia currently accounts for 90% of global rice production but it will need to increase this by 50% within the next 30 years. By this time the region will be home to nearly 90% of the global population increase and will likely be experiencing extreme climatic conditions. Agriculture will be challenged by diminishing water resources, reduced nutrient inputs and an increase in abiotic stresses. Rice yield increases have already stagnated and so a new paradigm is needed to meet these future challenges. Most crop plants, like rice and wheat, have a simple and less efficient photosynthetic mechanism (C3 photosynthesis) that as a consequence results in considerable loss of water through stomatal pores on their leaves that open widely to let in more carbon dioxide. They also make a large amount of photosynthetic protein to maximise their photosynthetic rate that requires a large investment of nitrogen and hence fertiliser application. However, a few plants have evolved a more efficient C4 photosynthetic pathway that greatly alleviates these problems. The installation of a C4 photosynthetic pathway into major crops like rice could potentially increase yields by 50%, double the water-use efficiency and reduce fertiliser use by 40%. This is because plants with a C4 photosynthetic pathway concentrate CO2 within the leaf prior to photosynthetic fixation leading to increased photosynthetic efficiency and large reductions in the requirement for scarce resources like water and nitrogen (fertiliser). These modifications would be particularly advantageous in future climate scenarios where water scarcity and global temperature are predicted to increase.

Genetic improvement of photosynthetic performance of cereal crops and increasing the efficiency with which solar radiation is converted into biomass has recently become a major focus for crop physiologists and breeders. The pulse amplitude modulated chlorophyll fluorescence technique (PAM) allows quantitative leaf level monitoring of the utilization of energy for photochemical light conversion and photoprotection in natural environments, potentially over the entire crop lifecycle. Here, the diurnal relationship between electron transport rate (ETR) and irradiance was measured in five cultivars of rice (Oryza sativa) in canopy conditions with PAM fluorescence under natural solar radiation. This relationship differed substantially from that observed for conventional short term light response curves measured under controlled actinic light with the same leaves. This difference was characterized by a reduced curvature factor when curve fitting was used to model this diurnal response. The engagement of photoprotective processes in chloroplast electron transport in leaves under canopy solar radiation was shown to be a major contributor to this difference. Genotypic variation in the irradiance at which energy flux into photoprotective dissipation became greater than ETR was observed. Cultivars capable of higher ETR at midrange light intensities were shown to produce greater leaf area over time, estimated by noninvasive imaging.

Rice is an important crop for a large portion of the population of the world, being the main source of food and the agriculture of which is the main source of income. Genome editing being the focal point of research in recent times is now rightly being targeted towards improving the quality of rice. Research using the CRISPR genome editing tools has increased the ability to target and modify rice genes for the development of improved varieties. However, current research is focused on improving even further the efficiency of the CRISPR genome editing tools to successfully edit endogenous rice genes. These studies indicate that genome editing is a successful and feasible venture in rice. Newer developments and improvements of CRIPSR tools have further enabled researchers to modify more genes in rice with increased efficiency. The ability of the CRISPR system to generate transgene free genome edited plants is further reason for continued research as it helps to step past genome modification regulatory issues. The successful application and development of CRISPR tools for genome editing in rice will not only help in making site-specific integration events, but will also help in regulating gene expression, gene discovery, rice functional genomics and creating new improved traits in rice.

The engineering process of C4 photosynthesis into C3 plants requires an increased activity of phosphoenolpyruvate carboxylase (PEPC) in the cytosol of leaf mesophyll cells. The literature varies on the physiological effect of transgenic maize (Zea mays) PEPC (ZmPEPC) leaf expression in Oryza sativa (rice). Therefore, to address this issue, leaf–atmosphere CO2 and 13CO2 exchanges were measured, both in the light (at atmospheric O2 partial pressure of 1.84 kPa and at different CO2 levels) and in the dark, in transgenic rice expressing ZmPEPC and wild-type (WT) plants. The in vitro PEPC activity was 25 times higher in the PEPC overexpressing (PEPC-OE) plants (~20% of maize) compared to the negligible activity in WT. In the PEPC-OE plants, the estimated fraction of carboxylation by PEPC (β) was ~6% and leaf net biochemical discrimination against 13CO2\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\left( {\Delta_{\text{bio}} } \right)$$\end{document}Δbio was ~ 2‰ lower than in WT. However, there were no differences in leaf net CO2 assimilation rates (A) between genotypes, while the leaf dark respiration rates (Rd) over three hours after light–dark transition were enhanced (~ 30%) and with a higher 13C composition \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\left( {\delta^{ 1 3} {\text{C}}_{\text{Rd}} } \right)$$\end{document}δ13CRd in the PEPC-OE plants compared to WT. These data indicate that ZmPEPC in the PEPC-OE rice plants contributes to leaf carbon metabolism in both the light and in the dark. However, there are some factors, potentially posttranslational regulation and PEP availability, which reduce ZmPEPC activity in vivo. Electronic supplementary material The online version of this article (10.1007/s11120-019-00655-4) contains supplementary material, which is available to authorized users.

Since the ground breaking work of Norman Borlaug in the 1960s produced large increases in yields of our major cereal crops, we have seen a gradual decline in annual yield progress. The genetic potential of the yield components harvest index and grain number, which were targeted in the “green revolution” and subsequently by cereal breeders have largely been optimised in our two largest global cereal crops, rice and wheat. Physiologists and breeders are turning to the biomass portion of the yield equation and in particular radiation use efficiency, as a means to push the yield potential barrier. Consequently, in the last decade a large effort has been initiated to identify targets to improve photosynthetic performance both using non-transgenic Phenomics approaches and transgenic technologies. Efficiency of light interception, harvesting and energy utilisation have been targeted but most efforts have so far focussed on improving photosynthetic capacity and efficiency in photosynthetic carbon metabolism in rice, wheat and model plants. Here the targets for improving light harvesting and carbon fixation are reviewed, the progress thus far evaluated and the likelihood of success of these activities in improving crop yields discussed in the context of modelling and scaling from the leaf to the canopy.

To assist with efforts to engineer a C4 photosynthetic pathway into rice, forward-genetic approaches are being used to identify the genes modulating key C4 traits. Currently, a major challenge is how to screen for a variety of different traits in a high-throughput manner. Here we describe a method for identifying C4 mutant plants with increased CO2 compensation points. This is used as a signature for decreased photosynthetic efficiency associated with a loss of C4 function. By exposing plants to a CO2 concentration close to the CO2 compensation point of a wild-type plant, individuals can be identified from measurements of chlorophyll a fluorescence. We use this method to screen a mutant population of the C4 monocot Setaria viridis (L.)P.Beauv. generated using N-nitroso-N-methylurea (NMU). Mutants were identified at a frequency of 1 per 157 lines screened. Forty-six candidate lines were identified and one line with a heritable homozygous phenotype selected for further characterisation. The CO2 compensation point of this mutant was increased to a value similar to that of C3 rice. Photosynthesis and growth was significantly reduced under ambient conditions. These data indicate that the screen was capable of identifying mutants with decreased photosynthetic efficiency. Characterisation and next-generation sequencing of all the mutants identified in this screen may lead to the discovery of novel genes underpinning C4 photosynthesis. These can be used to engineer a C4 photosynthetic pathway into rice.

Campylobacter jejuni is the most frequent cause of human food-borne bacterial gastroenteritis but its physiology and biochemistry are poorly understood. Only a few amino-acids can be catabolised and these are known to be important for host colonization. Here we have established methods for rapid high throughput analyses of global metabolism in C. jejuni using direct injection mass spectrometry (DIMS) to compare metabolite fingerprints of wild-type and mutant strains. Principal component analyses show that the metabolic fingerprint of mutants that have a genomic deletion in genes for key amino-acid catabolic enzymes (either sdaA, serine dehydratase; aspA, aspartase or aspB, aspartate:glutamate transaminase) can easily be distinguished from the isogenic parental strain. Assignment of putative metabolites showed predictable changes directly associated with the particular metabolic lesion in these mutants as well as more extensive changes in the aspA mutant compared to the sdaA or aspB strains. Further analyses of a cj0150c mutant strain, which has no obvious phenotype, suggested a role for Cj0150 in the conversion of cystathionine to homocysteine. Our results show that DIMS is a useful technique for probing the metabolism of this important pathogen and may help in assigning function to genes encoding novel enzymes with currently unknown metabolic roles.

Whilst genotype–environment interaction is increasingly receiving attention by ecologists and evolutionary biologists, such studies need genetically homogeneous replicates—a challenging hurdle in outcrossing plants. This could potentially be overcome by using tissue culture techniques. However, plants regenerated from tissue culture may show aberrant phenotypes and “somaclonal” variation. Here we examined the effects of tissue culturing by clonal growth on the response to cold treatment in the photosynthetic efficiency (chlorophyll fluorescence measurements for Fv/Fm, Fv′/Fm′ and ФPSII, representing maximum efficiency of photosynthesis for dark- and light-adapted leaves, and the actual electron transport operating efficiency, respectively), compared to half-sibling seedlings from three different families ofArabidopsis lyratassp.petraea. Somaclonal variation was limited and we could successfully detect within-family variation in change in chlorophyll fluorescence by cold shock with the help of tissue-culture derived replicates. Icelandic and Norwegian families exhibited higher chlorophyll fluorescence, suggesting higher cold tolerance, than a Swedish family. Although the main effect of tissue culture on Fv/Fm, Fv′/Fm′ and ФPSII was small, there were significant interactions between tissue culture and family, suggesting that the effect of tissue culture is genotype-specific. Tissue-cultured plantlets were less affected by cold treatment than seedlings, but to a different extent in each family. These interactive effects, however, were comparable to, or much smaller than the single effect of family. These results suggest that tissue culture is a useful method for obtaining genetically homogenous replicates for studying genotype‐environment interaction related to adaptively relevant phenotypes, such as cold tolerance, in non-model outcrossing 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 C4 plant maize, compartmentalized function of the two GLK genes in bundle sheath and mesophyll cells regulates dimorphic chloroplast differentiation, whereas in the C3 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 C4 monocot Sorghum bicolor and C4 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 C3 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 C3 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 C4 plants with dimorphic chloroplasts. In this scenario, GLK gene duplication preconditioned the evolution of C4 physiology that is associated with chloroplast dimorphism. Electronic supplementary material The online version of this article (doi:10.1007/s00425-012-1754-3) contains supplementary material, which is available to authorized users.

In the present study, Na+ manipulating genes could contribute not only to ion homeostasis but also to growth stimulation with exposing the halophyte Atriplex halimus L. to moderate NaCl concentration. The stimulation of growth was attributed to Na+ accumulation inside the vacuole leading to increase leaf cell size as well as accelerate leaf cell division. Increasing the assimilatory surface could result in enhancing the photosynthetic rate. The reduction of A. halimus growth compared to optimum growth at 50 and 200 mM NaCl could be attributed to osmotic effect rather than the ionic one of salt stress. The inhibition of photosynthesis seemed to be resulted from limitation of CO2 due to the osmotic effect on stomatal conductance rather than the activity loss of photosynthetic machinery. The depletion of starch content along with the increase in sucrose content could imply that photosynthesis may be a limiting for A. halimus growth. The fast coordinate induction of Na+ manipulating genes could reveal that the tolerance of A. halimus to high concentrations evolved from its ability to regulate and control Na+ influx and efflux. V-H+-PPase may play a vital role in A. halimus tolerance to osmotic and/or ionic stress due to its kinetics of induction. It seemed that H+-ATPase plays a pivotal role in A. halimus tolerance to stress due to the increase in its protein level was detected with all NaCl concentrations as well as with PEG treatments. Both of these genes might be useful in improving stress tolerance in transgenic crops.

Studying the regulation of stress inducible genes can lead to understanding of the mechanisms by which halophytes maintain growth and thrive under abiotic stress. Verifying whether ionic or osmotic components of salt stress control the regulation of Dehydration Responsive Element- binding transcription factor (DREB) was investigated in the present study. DREB belongs to AP2/EREB group that is induced under abiotic stress and regulates many stress inducible genes that contain DRE binding sites in their promoters. DREB in Atriplex halimus was regulated by the osmotic component but not by the ionic one of salt stress. It seemed that DREB was not involved in the regulation of sodium manipulating genes like NHX1, SOS1 or H +-PPase. Moreover, DREB could be involved directly of indirectly in CMO regulation because of timing of induction. Also, DREB was the most upregulated gene under salt (fivefold) and drought (twofold) conditions, which reinforced the importance of this gene in A. halimus tolerance to stress. Moreover, its constitutive expression under normal conditions also indicated its involvement in other growth and developmental programs. The tolerance of A. halimus and of halophytes, in general, could be attributed to the constitutive expression of its genes and differences in protein structures between halophytes and glycophytes.

To assist with efforts to engineer a C4 photosynthetic pathway into rice, forward-genetic approaches are being used to identify the genes modulating key C4 traits. Currently, a major challenge is how to screen for a variety of different traits in a high-throughput manner. Here we describe a method for identifying C4 mutant plants with increased CO2 compensation points. This is used as a signature for decreased photosynthetic efficiency associated with a loss of C4 function. By exposing plants to a CO2 concentration close to the CO2 compensation point of a wild-type plant, individuals can be identified from measurements of chlorophyll a fluorescence. We use this method to screen a mutant population of the C4 monocot Setaria viridis (L.)P.Beauv. generated using N-nitroso-N-methylurea (NMU). Mutants were identified at a frequency of 1 per 157 lines screened. Forty-six candidate lines were identified and one line with a heritable homozygous phenotype selected for further characterisation. The CO2 compensation point of this mutant was increased to a value similar to that of C3 rice. Photosynthesis and growth was significantly reduced under ambient conditions. These data indicate that the screen was capable of identifying mutants with decreased photosynthetic efficiency. Characterisation and next-generation sequencing of all the mutants identified in this screen may lead to the discovery of novel genes underpinning C4 photosynthesis. These can be used to engineer a C4 photosynthetic pathway into rice.

Summary Cells associated with veins of petioles of C3 tobacco possess high activities of the decarboxylase enzymes required in C4 photosynthesis. It is not clear whether this is the case in other C3 species, nor whether these enzymes provide precursors for specific biosynthetic pathways. Here, we investigate the activity of C4 acid decarboxylases in the mid-vein of Arabidopsis, identify regulatory regions sufficient for this activity, and determine the impact of removing individual isoforms of each protein on mid-vein metabolite profiles. This showed that radiolabelled malate and bicarbonate fed to the xylem stream were incorporated into soluble and insoluble material in the mid-vein of Arabidopsis leaves. Compared with the leaf lamina, mid-veins possessed high activities of NADP-dependent malic enzyme (NADP-ME), NAD-dependent malic enzyme (NAD-ME) and phosphoenolpyruvate carboxykinase (PEPCK). Transcripts derived from both NAD-ME, one PCK and two of the four NADP-ME genes were detectable in these veinal cells. The promoters of each decarboxylase gene were sufficient for expression in mid-veins. Analysis of insertional mutants revealed that cytosolic NADP-ME2 is responsible for 80% of NADP-ME activity in mid-veins. Removing individual decarboxylases affected the abundance of amino acids derived from pyruvate and phosphoenolpyruvate. Reducing cytosolic NADP-ME activity preferentially affected the sugar content, whereas abolishing NAD-ME affected both the amino acid and the glucosamine content of mid-veins.

In this study we describe the selection and characterization of barnyard grass (Echinochloa crusgalli L.) mutants (fows B) with vegetative salt tolerance as compared to a previously described mutant with salt tolerant germination (fows A3). Salt tolerance of both types of mutants was characterized in two distinctive stages of plant development, germination and vegetative growth. About 46% of fows A3 seeds germinated in 300 mM NaCl but none of the seeds of the wild type or fows B mutants were able to germinate in this salt concentration. However, fows B mutants showed significantly higher fresh weights compared to the wild type and the fows A3 mutant when grown in the presence of 200 mM NaCl for 25 days. This indicated that fows B mutants are more salt tolerant than fows A3 mutant as well the wild type. The vegetative salt tolerance of the fows B mutants depended mainly on maintaining more efficient photosynthetic machinery, by keeping significantly higher chlorophyll and Rubisco contents and accumulating soluble sugars particularly sucrose. In addition, fows B mutants had significantly lower malondialdehyde (MDA) contents than did fows A3 and the wild type. This was apparently the result of higher activities of catalase (CAT) and peroxidase (POD) in fows B mutants compared to the wild type and fows A3, indicating that more efficient control of reactive oxygen species correlates with salt tolerance. However, proline accumulation and K+/Na+ ratio did seem to be essential to vegetative salt tolerance. The vegetative salt tolerance mechanisms in fows B mutants were weakly expressed in the wild type and fows A3 mutant. The results provide evidence that salt tolerance during germination and vegetative growth could involve different mechanisms.

Trifolium alexandrinum L. (Egyptian clover) is one of the most important forage crops in the world. Its regeneration in tissue culture has been described in a few reports but the efficiency, accurate time scales and applicability to various genotypes of the described procedures are uncertain. Therefore their suitability for genetic transformation is unclear. In this study, were report new fast procedures for regeneration of Egyptian clover that are applicable to the regeneration of various genotypes (Mescawi-ahaly, Sakha3 and Sakha4). Shoots were regenerated from intact and wounded cotyledons as well as hypocotyls of Mescawi-ahaly on naphthaleneacetic acid/benzyladenine (NAA/BA) and naphthaleneacetic acid/thidiazuron (NAA/TDZ) media. The highest shoot regeneration frequencies were obtained from intact cotyledons on NAA/BA (0.05 mg l−1 NAA combined with 2.0 mg l−1 BA) and NAA/TDZ (0.05 mg l−1 NAA combined with 1.0 mg l−1 TDZ) media (66.2 and 43.1% respectively) compared to 18.4 and 10.1% for wounded cotyledons on NAA/BA and NAA/TDZ respectively. 21.0% shoot regeneration frequency was observed for hypocotyls on NAA/BA (2.0 mg l−1 NAA combined with 0.5 mg l−1 BA) medium but no regeneration was obtained on NAA/TDZ medium. Rooting of the regenerated shoots was induced on indole butyric acid (IBA: 0.24 mg l−1) or NAA (2.0 mg l−1) media where IBA medium supported significantly higher frequencies of rooting as well as survival of the whole plantlets after transfer to soil. However, the rooting and survival frequencies also depended on the type of explant and the medium used for shoot regeneration. The two cultivars Sakha3 and Sakha4 were regenerated using the culture conditions optimized for Mescawi-ahaly with comparable efficiencies, indicating that the described procedure is not genotype dependent. The time scale of whole plantlet regeneration ranged from 7.5 weeks for intact and wounded cotyledons to 10 weeks for hypocotyl explants.

Improving salt tolerance of economically important plants is imperative to cope with the increasing soil salinity in many parts of the world. Mutation breeding has been widely used to improve plant performance under salinity stress. In this study, we have mutagenized Echinochloa crusgalli L. with sodium azide and three selected mutants (designated fows A) with salt tolerant germination. Their vegetative growth was compared to that of the wild type after short-term and long-term salt stress. The germination of the three fows A mutants in the presence of inhibitory concentrations of NaCl, KCL, and mannitol was better than that of the wild type. Early growth of the mutants in the presence of 200 mM NaCl was also better than that of the wild type perhaps due to improved K+ uptake and enhanced accumulation of sugars particularly sucrose at least in two mutants. But the three mutants and the wild type responded similarly to long-term salt stress. The tolerance mechanisms during short-term and long-term salt stress are discussed.

Atmospheric temperature is a key factor in determining the distribution of a plant species. Alongside this, plant populations growing at the margin of their range may exhibit traits that indicate genetic differentiation and adaptation to their local abiotic environment. We investigated whether geographically separated marginal populations of Arabidopsis lyrata ssp. petraea have distinct metabolic phenotypes associated with exposure to cold temperatures. Seeds of A. petraea were obtained from populations along a latitudinal gradient, namely Wales, Sweden and Iceland and grown in a controlled cabinet environment. Mannose, glucose, fructose, sucrose and raffinose concentrations were different between cold treatments and populations, especially in the Welsh population, but polyhydric alcohol concentrations were not. The free amino acid compositions were population specific, with fold differences in most amino acids, especially in the Icelandic populations, with gross changes in amino acids, particularly those associated with glutamine metabolism. Metabolic fingerprints and profiles were obtained. Principal component analysis (PCA) of metabolite fingerprints revealed metabolic characteristic phenotypes for each population and temperature. It is suggested that amino acids and carbohydrates were responsible for discriminating populations within the PCA. Metabolite fingerprinting and profiling has proved to be sufficiently sensitive to identify metabolic differences between plant populations at different atmospheric temperatures. These findings show that there is significant natural variation in cold metabolism among populations of A. l. petraea which may signify plant adaptation to local climates.

[EN] Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering., Programme Grants ‘Understanding and exploiting plant and microbial metabolism’ and ‘Biotic interactions for crop productivity’, the John Innes Foundation and the Gatsby Foundation. Supported by the Engineering Nitrogen Symbiosis for Africa (ENSA) project, through a grant to the John Innes Centre from The Bill & Melinda Gates Foundation, the DOE Early Career Award and the DOE Joint BioEnergy Institute supported by the US Department of Energy, Office of Biological and Environmental through contract DE-AC02-05CH1123. The authors also acknowledge the support of COST Action FA1006, PlantEngine.

The glycine decarboxylase complex (GDC) plays a critical role in the photorespiratory C2 cycle of C3 species by recovering carbon following the oxygenation reaction of ribulose-1,5-bisphosphate carboxylase/oxygenase. Loss of GDC from mesophyll cells (MCs) is considered a key early step in the evolution of C4 photosynthesis. To assess the impact of preferentially reducing GDC in rice MCs, we decreased the abundance of OsGDCH (Os10g37180) using an artificial microRNA (amiRNA) driven by a promoter that preferentially drives expression in MCs. GDC H- and P-proteins were undetectable in leaves of gdch lines. Plants exhibited a photorespiratory-deficient phenotype with stunted growth, accelerated leaf senescence, reduced chlorophyll, soluble protein and sugars, and increased glycine accumulation in leaves. Gas exchange measurements indicated an impaired ability to regenerate ribulose 1,5-bisphosphate in photorespiratory conditions. In addition, MCs of gdch lines exhibited a significant reduction in chloroplast area and coverage of the cell wall when grown in air, traits that occur during the later stages of C4 evolution. The presence of these two traits important for C4 photosynthesis and the non-lethal, down-regulation of the photorespiratory C2 cycle positively contribute to efforts to produce a C4 rice prototype.

Evidence from laboratory experiments indicates that fractionation against the heavy stable isotope of carbon (Δ 13 C) by bryophytes (liverworts and mosses) is strongly dependent on atmospheric CO 2 . This physiological response may therefore provide the basis for developing a new terrestrial CO 2 proxy [Fletcher, B.J., Beerling, D.J., Brentnall, S.J., Royer, D.L., 2005. Fossil bryophytes as recorders of ancient CO 2 levels: experimental evidence and a Cretaceous case study. Global Biogeochem. Cycles 19 , GB3012]. Here, we establish a theoretical basis for the proxy by developing an extended model of bryophyte carbon isotope fractionation (BRYOCARB) that integrates the biochemical theory of photosynthetic CO 2 assimilation with controls on CO 2 supply by diffusion from the atmosphere. The BRYOCARB model is evaluated against measurements of the response of liverwort photosynthesis and Δ 13 C to variations in atmospheric O 2 , temperature and irradiance at different CO 2 concentrations. We show that the bryophyte proxy is at least as sensitive to variations in atmosphere CO 2 as the two other leading carbon isotope-based approaches to estimating palaeo-CO 2 levels ( δ 13 C of phytoplankton and of paleosols). Mathematical inversion of BRYOCARB provides a mechanistic means of estimating atmospheric CO 2 levels from fossil bryophyte carbon that can explicitly account for the effects of past differences in O 2 and climate.

The oxidative pentose phosphate pathway (OPPP) provides plants with important substrates for both primary and secondary metabolism via the oxidation of glucose-6-phosphate. The OPPP is also thought to generate large amounts of reducing power to drive various anabolic processes. In animals this major pathway is located within the cytoplasm of cells, but in plants its subcellular compartmentation is far from clear. Although several enzymes of the OPPP were demonstrated to have both cytosolic and plastidic counterparts, there is yet no evidence for a full set of functional enzymes in each compartment. We report here the isolation of two coding sequences from tomato (Lycopersicon esculentum L.) which encode phylogenetically distant sequences (ToTal1 and ToTal2) that putatively encode distinct plastidic TA isoforms. The kinetic characterization of ToTal1 revealed that, unlike other enzymes of the non-oxidative branch of the OPPP, ToTal1 does not follow a Michaelis-Menten mode of catalysis which has implications for its role in regulating carbon flux between primary and secondary metabolism. TA genes appear to be differentially regulated at the level of gene expression in plant tissues and in response to environmental factors which suggests that TA isoforms have a non-overlapping role for plant metabolism.

Total soluble solids content is a key determinant of tomato fruit quality for processing. Several tomato lines carrying defined introgressions from S. pennellii in a S. lycopersicum background produce fruit with elevated Brix, a refractive index measure of soluble solids. The genetic basis for this trait can be determined by fine-mapping each QTL to a single gene, but this is time-consuming and technically demanding. As an alternative, high-throughput analytical technologies can be used to provide useful information that helps characterize molecular changes in the introgression lines. This paper presents a study of transcriptomic changes in six introgression lines with increased fruit Brix. Each line also showed altered patterns of fruit carbohydrate accumulation. Transcriptomic changes in fruit at 20 d after anthesis (DAA) were assessed using a 12 000-element EST microarray and significant changes analysed by SAM (significance analysis of microarrays). Each non-overlapping introgression resulted in a unique set of transcriptomic changes with 78% of significant changes being unique to a single line. Principal components analysis allowed a clear separation of the six lines, but also revealed evidence of common changes; lines with quantitatively similar increases in Brix clustered together. A detailed examination of genes encoding enzymes of primary carbon metabolism demonstrated that few of the known introgressed alleles were altered in expression at the 20 DAA time point. However, the expression of other metabolic genes did change. Particularly striking was the co-ordinated up-regulation of enzymes of sucrose mobilization and respiration that occurred only in the two lines with the highest Brix increase. These common downstream changes suggest a similar mechanism is responsible for large Brix increases.

Summary • We report the influence of a systemic irradiance signal, from mature leaves, on the anatomical characteristics of developing leaves. • A systemic signal of reduced irradiance was induced by growing tobacco (Nicotiana tabaccum) plants at high irradiance and then measuring the effect of shading mature leaves on the development of new leaves. The reverse, a systemic signal of increased irradiance was induced by growing plants at low irradiance and then measuring the effect of increasing the irradiance of mature leaves. • Stomatal pore length, stomatal density and index, epidermal cell shape, epidermal cell size and developing leaf size were all influenced by the irradiance signal. These responses were reversible with changing irradiance, except for stomatal pore length.

Constitutive over-expression of a maize sucrose-phosphate synthase (SPS) gene in tobacco (Nicotiana tabacum) had major effects on leaf carbohydrate budgets with consequences for whole plant development. Transgenic tobacco plants flowered earlier and had greater flower numbers than wild-type plants. These changes were not linked to modified source leaf carbon assimilation or carbon export, although sucrose to starch ratios were significantly higher in leaves expressing the transgene. The youngest and oldest leaves of plants over-expressing SPS had up to 10-fold wild-type maximal extractable SPS activity, but source leaf SPS activities were only 2-3 times greater in these lines than in the wild type. In the oldest leaves, where the expression of the transgene led to the most marked enhancement in SPS activity, photosynthesis was also increased. It was concluded that these increases in the capacity for sucrose synthesis and carbon assimilation, particularly in older leaves, accelerate the whole plant development and increase the abundance of flowers without substantial changes in the overall shoot biomass.

Recently, it has been reported that tubers of transgenic potato ( Solanum tuberosum L.) plants with decreased activity of the plastidic ATP/ADP transporter (AATP1) contain less starch, despite having an increased glucose level [P. Geigenberger et al. (2001) Plant Physiol 125:1667-1678]. The metabolic alterations correlated with enhanced resistance to the bacterium Erwinia carotovora. Here it is shown that transgenic potato tubers, possessing less starch yet increased glucose levels due to the expression of a cytoplasm-localized yeast invertase, exhibit drastic susceptibility to E. carotovora. In addition, it is demonstrated that AATP1 anti-sense tubers show an increased capacity to ward off the pathogenic fungus Alternaria solani. In contrast to AATP1 anti-sense tubers, the corresponding leaf tissue does not show changes in carbohydrate accumulation. However, upon elicitor treatment, AATP1 anti-sense leaves possess an increased capacity to release H(2)O(2) and activate various defence-related genes, reactions that are associated with substantially delayed appearance of disease symptoms caused by Phytophthora infestans. Grafting experiments between AATP1 anti-sense plants and wild-type plants indicate the presence of a signal that is generated in AATP1 rootstocks and primes wild-type scions for potentiated activation of cellular defence responses in leaves. Together, the results suggest that (i) the enhanced pathogen tolerance of AATP1 anti-sense tubers is not due to "high sugar resistance", (ii) the increased disease resistance of AATP1 anti-sense tubers is effective against different types of pathogen and (iii) a systemic signal induced by antisensing the plastidic ATP/ADP transporter in potato tubers confers increased resistance to pathogens.

Stomatal numbers are tightly controlled by environmental signals including light intensity and atmospheric CO(2) partial pressure. This requires control of epidermal cell development during the early phase of leaf growth and involves changes in both the density of cells on the leaf surface and the proportion of cells that adopt a stomatal fate. This paper reviews the current understanding of how stomata develop and describes recent advances that have given insights into the regulatory mechanisms involved using mutant Arabidopsis plants that implicates a role for long-chain fatty acids in cell-to-cell communication. Evidence is presented which indicates that long-distance signalling from mature to newly developing leaves forms part of the mechanism by which stomatal development responds to environmental cues. Analysis of mutant plants suggests that the plant hormones abscisic acid, ethylene and jasmonates are implicated in the long-distance signalling pathway and that the action may be mediated by reactive oxygen species.

Most plants are known as C3 plants because the first product of photosynthetic CO2 fixation is a three-carbon compound1. C4 plants, which use an alternative pathway in which the first product is a four-carbon compound, have evolved independently many times and are found in at least 18 families2,3. In addition to differences in their biochemistry, photosynthetic organs of C4 plants show alterations in their anatomy and ultrastructure4. Little is known about whether the biochemical or anatomical characteristics of C4 photosynthesis evolved first. Here we report that tobacco, a typical C3 plant, shows characteristics of C4 photosynthesis in cells of stems and petioles that surround the xylem and phloem, and that these cells are supplied with carbon for photosynthesis from the vascular system and not from stomata. These photosynthetic cells possess high activities of enzymes characteristic of C4 photosynthesis, which allow the decarboxylation of four-carbon organic acids from the xylem and phloem, thus releasing CO2 for photosynthesis. These biochemical characteristics of C4 photosynthesis in cells around the vascular bundles of stems of C3 plants might explain why C4 photosynthesis has evolved independently many times.

Tobacco plants, transformed with a maize sucrose phosphate synthase (SPS) cDNA clone, had threefold increased SPS activity compared to wild-type tobacco. Measurement of SPS maximal activity and protein abundance using specific antibodies to the maize protein showed that the specific activity of the maize SPS protein was maintained when expressed in tobacco. Comparison of the kinetic properties of SPS in the transgenic lines compared to either wild-type maize or tobacco revealed that the heterologously expressed protein had reduced affinity for both substrates (fructose-6-phosphate and UDP-glucose) and reduced sensitivity to allosteric inhibition by inorganic phosphate. Moreover, the extent of light-induced activation was reduced in the transgenic lines, with smaller changes observed in the K m for both F6P compared to maize and tobacco wild-type plants. Increased sucrose concentrations were observed in the transgenic lines at the end of the photoperiod and this was linearly related to SPS activity and associated with a parallel decrease in starch content. This suggests that SPS is a major control point for carbohydrate partitioning between starch and sucrose during photosynthesis.

The gradients in photosynthetic and carbohydrate metabolism which persist within the fully expanded second leaf of barley (Hordeum vulgare) were examined. Although all regions of the leaf blade were green and photosynthetically active, the basal 5 cm, representing approximately 20% of the leaf area, retained some characteristics of sink tissue. The leaf blade distal from the leaf sheath exhibited characteristics typical of source tissue; the activities of sucrolytic enzymes (invertase and sucrose synthase) were relatively low, whilst that of sucrose phosphate synthase was high. These regions of the leaf accumulated sucrose throughout the photoperiod and starch only in the second half of the photoperiod whilst hexose sugars remained low. By contrast the leaf blade proximal to the leaf sheath retained relatively high activities of sucrolytic enzymes (especially soluble, acid invertase) whilst sucrose phosphate synthase activity was low. Glucose, as well as sucrose, accumulated throughout the photoperiod. Although starch accumulated in the second half of the photoperiod, a basal level of starch was present throughout the photoperiod, by contrast with the rest of the leaf. The 14CO2 feeding experiments indicated that a constant amount of photosynthate was partitioned towards starch in this region of the leaf irrespective of irradiance. These findings are interpreted as the base of the leaf blade acting as a localized sink for carbohydrate as a result of sucrose hydrolysis by acid invertase.

Because recalcitrant seeds are not desiccation-tolerant they must be stored moist. Their limited storage potential presents significant practical problems, but the cause of viability loss is not known. It has been suggested that a stress-induced metabolic imbalance can develop during storage that results in free-radical generation and consequent damage. To investigate this hypothesis, the presence of a stable free radical, lipid peroxidation and representative enzymatic and nonenzymatic protection mechanisms against oxidative attack were monitored in nondormant recalcitrant seeds during moist storage. A comparison was made between seeds of a short-lived sub-tropical species (Avicennia marina) and two longer-lived temperate species (Quercus robur and Castanea sativa). As a test of the hypothesis, seeds of both temperate species were held under conditions of elevated temperature and oxygen concentration to develop different rates of respiration during storage. The number of normal seedlings produced from seeds of the two temperate species declined during storage, but viability remained high, so effects of ageing were not confounded with an increasing proportion of dead seeds in the population. Under these conditions, lipid peroxidation changed little over the storage period, although there was evidence of accumulation of a stable free radical in Q. robur axes. However, this response was not affected by storage conditions that elevated respiration rates. In the shorter-lived A. marina seeds viability declined soon after the start of storage, but the significant increase in free radicals shown by EPR measurement was only evident when an increasing percentage of the seed population was no longer viable. Changes in the activity of scavenging enzymes and the concentration of antioxidants were time-dependent and not related to respiration rates. Therefore, in the present work, no consistent evidence was found to show that metabolism-induced free-radical activity was a significant contributing factor to pre-mortem deterioration in moist-stored recalcitrant seeds.

The aim of this study was to investigate the interactions between cytokinin, sugar repression, and light in the senescence-related decline in photosynthetic enzymes of leaves. In transgenic tobacco (Nicotiana tabacum) plants that induce the production of cytokinin in senescing tissue, the age-dependent decline in NADH-dependent hydroxypyruvate reductase (HPR), ribulose-1,5-bisphosphate carboxylase/oxygenase, and other enzymes involved in photosynthetic metabolism was delayed but not prevented. Glucose (Glc) and fructose contents increased with leaf age in wild-type tobacco and, to a greater extent, in transgenic tobacco. To study whether sugar accumulation in senescing leaves can counteract the effect of cytokinin on senescence, discs of wild-type leaves were incubated with Glc and cytokinin solutions. The photorespiratory enzyme HPR declined rapidly in the presence of 20 mm Glc, especially at very low photon flux density. Although HPR protein was increased in the presence of cytokinin, cytokinin did not prevent the Glc-dependent decline. Illumination at moderate photon flux density resulted in the rapid synthesis of HPR and partially prevented the negative effect of Glc. Similar results were obtained for the photosynthetic enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase. It is concluded that sugars, cytokinin, and light interact during senescence by influencing the decline in proteins involved in photosynthetic metabolism.

Campylobacter jejuni is the most frequent cause of human food-borne bacterial gastroenteritis but its physiology and biochemistry are poorly understood. Only a few amino-acids can be catabolised and these are known to be important for host colonization. Here we have established methods for rapid high throughput analyses of global metabolism in C. jejuni using direct injection mass spectrometry (DIMS) to compare metabolite fingerprints of wild-type and mutant strains. Principal component analyses show that the metabolic fingerprint of mutants that have a genomic deletion in genes for key amino-acid catabolic enzymes (either sdaA, serine dehydratase; aspA, aspartase or aspB, aspartate:glutamate transaminase) can easily be distinguished from the isogenic parental strain. Assignment of putative metabolites showed predictable changes directly associated with the particular metabolic lesion in these mutants as well as more extensive changes in the aspA mutant compared to the sdaA or aspB strains. Further analyses of a cj0150c mutant strain, which has no obvious phenotype, suggested a role for Cj0150 in the conversion of cystathionine to homocysteine. Our results show that DIMS is a useful technique for probing the metabolism of this important pathogen and may help in assigning function to genes encoding novel enzymes with currently unknown metabolic roles. Electronic supplementary material The online version of this article (doi:10.1007/s11306-014-0644-z) contains supplementary material, which is available to authorized users.