SummaryThe plant genome is a highly redundant and dynamic genome. Here, we show that double antisense plants lacking the two major hydrogen peroxide-detoxifying enzymes, ascorbate peroxidase (APX) and catalase (CAT), activate an alternative/redundant defense mechanism that compensates for the lack of APX and CAT. A similar mechanism was not activated in single antisense plants that lacked APX or CAT, paradoxically rendering these plants more sensitive to oxidative stress compared to double antisense plants. The reduced susceptibility of double antisense plants to oxidative stress correlated with suppressed photosynthetic activity, the induction of metabolic genes belonging to the pentose phosphate pathway, the induction of monodehydroascorbate reductase, and the induction of IMMUTANS, a chloroplastic homologue of mitochondrial alternative oxidase. Our results suggest that a co-ordinated induction of metabolic and defense genes, coupled with the suppression of photosynthetic activity, can compensate for the lack of APX and CAT. In addition, our findings demonstrate that the plant genome has a high degree of plasticity and will respond differently to different stressful conditions, namely, lack of APX, lack of CAT, or lack of both APX and CAT.

Photorespiration, a process that diminishes net photosynthesis by Ϸ25% in most plants, has been viewed as the unfavorable consequence of plants having evolved when the atmosphere contained much higher levels of carbon dioxide than it does today. Here we used two independent methods to show that exposure of Arabidopsis and wheat shoots to conditions that inhibited photorespiration also strongly inhibited nitrate assimilation. Thus, nitrate assimilation in both dicotyledonous and monocotyledonous species depends on photorespiration. This previously undescribed role for photorespiration (i) explains several responses of plants to rising carbon dioxide concentrations, including the inability of many plants to sustain rapid growth under elevated levels of carbon dioxide; and (ii) raises concerns about genetic manipulations to diminish photorespiration in crops.global climate change ͉ CO2 acclimation ͉ Arabidopsis ͉ wheat R ubisco, the most prevalent protein in plants, indeed in the biosphere, catalyzes the reaction of ribulose-1,5-bisphosphate with either CO 2 or O 2 and thereby initiates, respectively, the CO 2 assimilatory (C 3 reductive) or photorespiratory (C 2 oxidative) pathways. The balance between the two reactions depends on the relative concentrations of CO 2 and O 2 at the site of catalysis. At current atmospheric levels of CO 2 (Ϸ360 mol⅐mol Ϫ1 ) and O 2 (Ϸ209,700 mol⅐mol Ϫ1 ), photorespiration in C 3 plants dissipates Ͼ25% of the carbon fixed during CO 2 assimilation (1). Thus, photorespiration has been viewed as a wasteful process, a vestige of the high CO 2 atmospheres under which plants evolved (2). At best, according to current thought, photorespiration may mitigate photoinhibition under high light and drought stress (2, 3) or may generate amino acids such as glycine for other metabolic pathways (4). Genetic modification of Rubisco to minimize photorespiration in crop plants has been the goal of many investigations (5).Atmospheric CO 2 concentrations will rise to somewhere between 600 and 1,000 mol⅐mol Ϫ1 by the end of the 21st century (6). Transferring C 3 plants from ambient (Ϸ360 mol⅐mol Ϫ1 ) to elevated (Ϸ720 mol⅐mol Ϫ1 ) CO 2 concentrations decreases photorespiration and initially stimulates net CO 2 assimilation and growth by Ϸ30% (7). With longer exposures to elevated CO 2 concentrations (days to weeks), however, net CO 2 assimilation and plant growth slow down until they stabilize at rates that average 12% (8) and 8% (9), respectively, above those of plants kept at ambient CO 2 concentrations. This phenomenon, known as CO 2 acclimation, is often associated with diminished activities of Rubisco and other enzymes in the C 3 reductive photosynthetic carbon cycle (10, 11), but the influence of elevated CO 2 may not be specific to these enzymes (12). Rather, CO 2 acclimation follows a 14% decline in overall shoot nitrogen concentrations (13), a change nearly double what would be expected if a given amount of nitrogen were diluted by the additional biomass that accumulates under elevated CO 2 conce...

[1] The triple isotopic composition of atmospheric O 2 is a new tracer used to estimate changes in global productivity. To estimate such changes, knowledge of the relationship between the discrimination against 17 O and the discrimination against 18O is needed. This relationship is presented as q = ln( 17 a)/ln( 18 a). Here, the value of theta was evaluated for the most important processes that affect the isotopic composition of oxygen. Similar values were found for dark respiration through the cytochrome pathway (0.516 ± 0.001) and the alternative pathway (0.514 ± 0.001), and slightly higher value was found for diffusion in air (0.521 ± 0.001). The combined effect of diffusion and respiration on the atmosphere was shown to be close to that of dark respiration. The value we found for photorespiration (0.506 ± 0.005) is considerably lower than that of dark respiration. Our results clearly show that the triple isotopic composition of the atmosphere is affected by the relative rates of photorespiration and dark respiration. Also, we show that closing the current global isotopic balance will enable the estimation of the current global rate of photorespiration. Using the Last Glacial Maximum as a case study, we show that variations in global rate of photorespiration affected the triple isotopic composition in the past. Strong fractionations measured in illuminated plants indicated that the alternative pathway is activated in the same conditions that favor high rate of photorespiration. This activation suggests that the global rate of the alternative pathway is higher than believed thus far, and may help to close the gap between the calculated and measured Dole Effect.

BackgroundGrapevine metabolism in response to water deficit was studied in two cultivars, Shiraz and Cabernet Sauvignon, which were shown to have different hydraulic behaviors (Hochberg et al. Physiol. Plant. 147:443–453, 2012).ResultsProgressive water deficit was found to effect changes in leaf water potentials accompanied by metabolic changes. In both cultivars, but more intensively in Shiraz than Cabernet Sauvignon, water deficit caused a shift to higher osmolality and lower C/N ratios, the latter of which was also reflected in marked increases in amino acids, e.g., Pro, Val, Leu, Thr and Trp, reductions of most organic acids, and changes in the phenylpropanoid pathway. PCA analysis showed that changes in primary metabolism were mostly associated with water stress, while diversification of specialized metabolism was mostly linked to the cultivars. In the phloem sap, drought was characterized by higher ABA concentration and major changes in benzoate levels coinciding with lower stomatal conductance and suberinization of vascular bundles. Enhanced suberin biosynthesis in Shiraz was reflected by the higher abundance of sap hydroxybenzoate derivatives. Correlation-based network analysis revealed that compared to Cabernet Sauvignon, Shiraz had considerably larger and highly coordinated stress-related changes, reflected in its increased metabolic network connectivity under stress. Network analysis also highlighted the structural role of major stress related metabolites, e.g., Pro, quercetin and ascorbate, which drastically altered their connectedness in the Shiraz network under water deficit.ConclusionsTaken together, the results showed that Vitis vinifera cultivars possess a common metabolic response to water deficit. Central metabolism, and specifically N metabolism, plays a significant role in stress response in vine. At the cultivar level, Cabernet Sauvignon was characterized by milder metabolic perturbations, likely due to a tighter regulation of stomata upon stress induction. Network analysis was successfully implemented to characterize plant stress molecular response and to identify metabolites with a significant structural and biological role in vine stress response.

BackgroundGrapevine berries undergo complex biochemical changes during fruit maturation, many of which are dependent upon the variety and its environment. In order to elucidate the varietal dependent developmental regulation of primary and specialized metabolism, berry skins of Cabernet Sauvignon and Shiraz were subjected to gas chromatography–mass spectrometry (GC-MS) and liquid chromatography–mass spectrometry (LC-MS) based metabolite profiling from pre-veraison to harvest. The generated dataset was augmented with transcript profiling using RNAseq.ResultsThe analysis of the metabolite data revealed similar developmental patterns of change in primary metabolites between the two cultivars. Nevertheless, towards maturity the extent of change in the major organic acid and sugars (i.e. sucrose, trehalose, malate) and precursors of aromatic and phenolic compounds such as quinate and shikimate was greater in Shiraz compared to Cabernet Sauvignon. In contrast, distinct directional projections on the PCA plot of the two cultivars samples towards maturation when using the specialized metabolite profiles were apparent, suggesting a cultivar-dependent regulation of the specialized metabolism. Generally, Shiraz displayed greater upregulation of the entire polyphenol pathway and specifically higher accumulation of piceid and coumaroyl anthocyanin forms than Cabernet Sauvignon from veraison onwards. Transcript profiling revealed coordinated increased transcript abundance for genes encoding enzymes of committing steps in the phenylpropanoid pathway. The anthocyanin metabolite profile showed F3′5′H-mediated delphinidin-type anthocyanin enrichment in both varieties towards maturation, consistent with the transcript data, indicating that the F3′5′H-governed branching step dominates the anthocyanin profile at late berry development. Correlation analysis confirmed the tightly coordinated metabolic changes during development, and suggested a source-sink relation between the central and specialized metabolism, stronger in Shiraz than Cabernet Sauvignon. RNAseq analysis also revealed that the two cultivars exhibited distinct pattern of changes in genes related to abscisic acid (ABA) biosynthesis enzymes.ConclusionsCompared with CS, Shiraz showed higher number of significant correlations between metabolites, which together with the relatively higher expression of flavonoid genes supports the evidence of increased accumulation of coumaroyl anthocyanins in that cultivar. Enhanced stress related metabolism, e.g. trehalose, stilbene and ABA in Shiraz berry-skin are consistent with its relatively higher susceptibility to environmental cues.