Spatiotemporal metabolic responses to water deficit stress in distinct leaf cell-types of poplar.

The impact of water-deficit (WD) stress on plant metabolism has been predominantly studied at the whole tissue level. However, plant tissues are made of several distinct cell types with unique and differentiated functions, which limits whole tissue 'omics'-based studies to determine only an averaged molecular signature arising from multiple cell types. Advancements in spatial omics technologies provide an opportunity to understand the molecular mechanisms underlying plant responses to WD stress at distinct cell-type levels. Here, we studied the spatiotemporal metabolic responses of two poplar (Populus tremula× P. alba) leaf cell types -palisade and vascular cells- to WD stress using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). We identified unique WD stress-mediated metabolic shifts in each leaf cell type when exposed to early and prolonged WD stresses and recovery from stress. During water-limited conditions, flavonoids and phenolic metabolites were exclusively accumulated in leaf palisade cells. However, vascular cells mainly accumulated sugars and fatty acids during stress and recovery conditions, respectively, highlighting the functional divergence of leaf cell types in response to WD stress. By comparing our MALDI-MSI metabolic data with whole leaf tissue gas chromatography-mass spectrometry (GC-MS)-based metabolic profile, we identified only a few metabolites including monosaccharides, hexose phosphates, and palmitic acid that showed a similar accumulation trend at both cell-type and whole leaf tissue levels. Overall, this work highlights the potential of the MSI approach to complement the whole tissue-based metabolomics techniques and provides a novel spatiotemporal understanding of plant metabolic responses to WD stress. This will help engineer specific metabolic pathways at a cellular level in strategic perennial trees like poplars to help withstand future aberrations in environmental conditions and to increase bioenergy sustainability.

The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum.

Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.

A zinc finger protein SlSZP1 protects SlSTOP1 from SlRAE1-mediated degradation to modulate aluminum resistance.

In acidic soils, aluminum (Al) toxicity is the main factor inhibiting plant root development and reducing crops yield. STOP1 (SENSITIVE TO PROTON RHIZOTOXICITY 1) was a critical factor in detoxifying Al stress. Under Al stress, STOP1 expression was not induced, although STOP1 protein accumulated, even in the presence of RAE1 (STOP1 DEGRADATION E3-LIGASE). How the Al stress triggers and stabilises the accumulation of STOP1 is still unknown. Here, we characterised SlSTOP1-interacting zinc finger protein (SlSZP1) using a yeast-two-hybrid screening, and generated slstop1, slszp1 and slstop1/slszp1 knockout mutants using clustered regularly interspaced short palindromic repeats (CRISPR) in tomato. SlSZP1 is induced by Al stress but it is not regulated by SlSTOP1. The slstop1, slszp1 and slstop1/slszp1 knockout mutants exhibited hypersensitivity to Al stress. The expression of SlSTOP1-targeted genes, such as SlRAE1 and SlASR2 (ALUMINUM SENSITIVE), was inhibited in both slstop1 and slszp1 mutants, but not directly regulated by SlSZP1. Furthermore, the degradation of SlSTOP1 by SlRAE1 was prevented by SlSZP1. Al stress increased the accumulation of SlSTOP1 in wild-type (WT) but not in slszp1 mutants. The overexpression of either SlSTOP1 or SlSZP1 did not enhance plant Al resistance. Altogether, our results show that SlSZP1 is an important factor for protecting SlSTOP1 from SlRAE1-mediated degradation.

A Cytoplasmic Receptor-like Kinase Contributes to Salinity Tolerance.

Receptor-like cytoplasmic kinases (RLCKs) are receptor kinases that lack extracellular ligand-binding domains and have emerged as a major class of signaling proteins that regulate plant cellular activities in response to biotic/abiotic stresses and endogenous extracellular signaling molecules. We have identified a rice RLCK (OsRLCK311) that was significantly higher in transgenic pSARK-IPT rice (Oryza sativa) that exhibited enhanced growth under saline conditions. Overexpression of OsRLCK311 full-length protein (RLCK311FL) and the C-terminus of OsRLCK311 (ΔN) in Arabidopsis confirmed its role in salinity tolerance, both in seedlings and mature plants. Protein interaction assays indicated that OsRLCK311 and ΔN interacted in-vivo with the plasma membrane AQP AtPIP2;1. The RLCK311-PIP2;1 binding led to alterations in the stomata response to ABA, which was characterized by more open stomata of transgenic plants. Moreover, OsRLCK311-ΔN effect in mediating enhanced plant growth under saline conditions was also observed in the perennial grass Brachypodium sylvaticum, confirming its role in both dicots and monocots species. Lastly, OsRLCK311 interacted with the rice OsPIP2;1. We suggest that the rice OsRLCK311 play a role in regulating the plant growth response under saline conditions via the regulation of the stomata response to stress. This role seems to be independent of the RLCK311 kinase activity, since the overexpression of the RLCK311 C-terminus (ΔN), which lacks the kinase full domain, has a similar phenotype to RLCK311FL.

Correlation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing tolerance.

Perennial grasses will account for approximately 16 billion gallons of renewable fuels by the year 2022, contributing significantly to carbon and nitrogen sequestration. However, perennial grasses productivity can be limited by severe freezing conditions in some geographical areas, although these risks could decrease with the advance of climate warming, the possibility of unpredictable early cold events cannot be discarded. We conducted a study on the model perennial grass Brachypodium sylvaticum to investigate the molecular mechanisms that contribute to cold and freezing adaption. The study was performed on two different B. sylvaticum accessions, Ain1 and Osl1, typical to warm and cold climates, respectively. Both accessions were grown under controlled conditions with subsequent cold acclimation followed by freezing stress. For each treatment a set of morphological parameters, transcription, metabolite, and lipid profiles were measured. State-of-the-art algorithms were employed to analyze cross-component relationships. Phenotypic analysis revealed higher adaption of Osl1 to freezing stress. Our analysis highlighted the differential regulation of the TCA cycle and the GABA shunt between Ain1 and Osl1. Osl1 adapted to freezing stress by repressing the GABA shunt activity, avoiding the detrimental reduction in fatty acid biosynthesis and the concomitant detrimental effects on membrane integrity.

Silencing of OsCV (chloroplast vesiculation) maintained photorespiration and N assimilation in rice plants grown under elevated CO2.

High CO2 concentrations stimulate net photosynthesis by increasing CO2 substrate availability for Rubisco, simultaneously suppressing photorespiration. Previously, we reported that silencing the chloroplast vesiculation (cv) gene in rice increased source fitness, through the maintenance of chloroplast stability and the expression of photorespiration-associated genes. Because high atmospheric CO2 conditions diminished photorespiration, we tested whether CV silencing might be a viable strategy to improve the effects of high CO2 on grain yield and N assimilation in rice. Under elevated CO2 , OsCV expression was induced, and OsCV was targeted to peroxisomes where it facilitated the removal of OsPEX11-1 from the peroxisome and delivered it to the vacuole for degradation. This process correlated well with the reduction in the number of peroxisomes, the decreased catalase activity and the increased H2 O2 content in wild-type plants under elevated CO2 . At elevated CO2 , CV-silenced rice plants maintained peroxisome proliferation and photorespiration and displayed higher N assimilation than wild-type plants. This was supported by higher activity of enzymes involved in NO3- and NH4+ assimilation and higher total and seed protein contents. Co-immunoprecipitation of OsCV-interacting proteins suggested that, similar to its role in chloroplast protein turnover, OsCV acted as a scaffold, binding peroxisomal proteins.

Delaying chloroplast turnover increases water-deficit stress tolerance through the enhancement of nitrogen assimilation in rice.

Abiotic stress-induced senescence in crops is a process particularly affecting the photosynthetic apparatus, decreasing photosynthetic activity and inducing chloroplast degradation. A pathway for stress-induced chloroplast degradation that involves the CHLOROPLAST VESICULATION (CV) gene was characterized in rice (Oryza sativa) plants. OsCV expression was up-regulated with the age of the plants and when plants were exposed to water-deficit conditions. The down-regulation of OsCV expression contributed to the maintenance of the chloroplast integrity under stress. OsCV-silenced plants displayed enhanced source fitness (i.e. carbon and nitrogen assimilation) and photorespiration, leading to water-deficit stress tolerance. Co-immunoprecipitation, intracellular co-localization, and bimolecular fluorescence demonstrated the in vivo interaction between OsCV and chloroplastic glutamine synthetase (OsGS2), affecting source-sink relationships of the plants under stress. Our results would indicate that the OsCV-mediated chloroplast degradation pathway is involved in the regulation of nitrogen assimilation during stress-induced plant senescence.

Effects of abiotic stress on physiological plasticity and water use of Setaria viridis (L.).

The emerging model Setaria viridis with its C4 photosynthesis and adaptation to hot and dry locations is a promising system to investigate water use and abiotic stress tolerance. We investigated the physiological plasticity of six S. viridis natural accessions that originated from different regions of the world under normal conditions and conditions of water-deficit stress and high temperatures. Accessions Zha-1, A10.1 and Ula-1 showed significantly higher leaf water potential (Ψleaf), photosynthesis (A), transpiration (E), and stomatal conductance (gs) rates compared to Ast-1, Aba-1 and Sha-1 when grown under stress conditions. Expression analysis of genes associated with C4 photosynthesis, aquaporins, ABA biosynthesis and signaling including genes involved in stress revealed an increased sensitivity of Ast-1, Aba-1 and Sha-1 to stresses. Correlation analysis of gene expression data with physiological and biochemical changes characterized A10.1 and Ast-1 as two extreme tolerant and sensitive accessions originated from United States and Azerbaijan under water-deficit and heat stress, respectively. Although preliminary, our study demonstrated the plasticity of S. viridis accessions under stress, and allows the identification of tolerant and sensitive accessions that could be use to study the mechanisms associated with stress tolerance and to characterize of the regulatory networks involved in C4 grasses.

Response of carbon and nitrogen-rich metabolites to nitrogen deficiency in PSARK::IPT tobacco plants.

Wild type (WT) and transgenic tobacco plants expressing isopentenyltransferase (IPT), a gene coding the rate-limiting step in cytokinin (CKs) synthesis, were grown under limited nitrogen (N) conditions. Here, we analyse the possible effect of N deficiency on C-rich compounds such as phenolic compounds, as well as on N-rich compounds such as polyamines (PAs) and proline (Pro), examining the pathways involved in their synthesis and degradation. N deficiency was found to stimulate phenolic metabolism and increase these compounds both in P(SARK):IPT as well as in WT tobacco plants. This suggests that nitrate (NO(3)(-)) tissue concentration may act as a signal triggering phenolic compound accumulation in N deficiency plants. In addition, we found the maintenance of PAs in the WT plants would be correlated with the higher stress response to N deficiency. On the contrary, the reduction of free PAs and Pro found in the P(SARK)::IPT plants subjected to N deficiency would indicate the operation of an N-recycling mechanism that could stimulate a more efficient N utilization in P(SARK)::IPT plants.

Antioxidant response resides in the shoot in reciprocal grafts of drought-tolerant and drought-sensitive cultivars in tomato under water stress.

Recently grafted plants have been used to induce resistance to different abiotic stresses. In our work, grafted plants of tomato cultivars differing in water stress tolerance (Zarina and Josefina) were grown under moderate stress, to test the roles of roots and shoots in production of foliar biomass and antioxidant response. Stress indicators and activities of selected enzymes related to antioxidant response were determined. Our results showed that when shoots are of the drought tolerant genotype Zarina, the changes in antioxidant enzyme activities were large and consistent. However, when shoots are of the drought-sensitive genotype Josefina, the antioxidant enzyme activities were more limited and the oxidative stress was evident. These results reflect that the technique of grafting using Zarina as scion can be useful and effective for improving the antioxidant response in tomato under water stress.

Ammonium formation and assimilation in P(SARK)∷IPT tobacco transgenic plants under low N.

Wild Type (WT) and transgenic tobacco plants expressing isopentenyltransferase (IPT), a gene encoding the enzyme regulating the rate-limiting step in cytokinins (CKs) synthesis, were grown under limited nitrogen (N) conditions. We analyzed nitrogen forms, nitrogen metabolism related-enzymes, amino acids and photorespiration related-enzymes in WT and P(SARK)∷IPT tobacco plants. Our results indicate that the WT plants subjected to N deficiency displayed reduced nitrate (NO3⁻) assimilation. However, an increase in the production of ammonium (NH4⁺), by the degradation of proteins and photorespiration led to an increase in the glutamine synthetase/glutamate synthase (GS/GOGAT) cycle in WT plants. In these plants, the amounts of amino acids decreased with N deficiency, although the relative amounts of glutamate and glutamine increased with N deficiency. Although the transgenic plants expressing P(SARK)∷IPT and growing under suboptimal N conditions displayed a significant decline in the N forms in the leaf, they maintained the GS/GOGAT cycle at control levels. Our results suggest that, under N deficiency, CKs prevented the generation and assimilation of NH4⁺ by increasing such processes as photorespiration, protein degradation, the GS/GOGAT cycle, and the formation of glutamine.

Cytokinin-dependent improvement in transgenic P(SARK)::IPT tobacco under nitrogen deficiency.

Wild-type (WT) and transgenic tobacco plants overexpressing isopentenyltransferase (IPT), a gene coding the rate-limiting step in cytokinin (CKs) synthesis, were grown under limited nitrogen (N) conditions to evaluate the role of CKs in NUE (N-use efficiency) and in different parameters that determine the quality of tobacco leaves. The results indicate that WT tobacco plants submitted to N deficiency show a decline in the leaf/root ratio, associated with a decrease in the NUE and in tobacco-leaf quality, defined by an increase in the quantity of nicotine. On the contrary, the transgenic plants submitted to N deficiency maintained the leaf/root ratio, presenting a higher NUE and greater quality of tobacco leaves than the WT plants, as the latter showed reduced nicotine and an increase in reducing sugars under severe N-deficiency conditions. Therefore, the overexpression of CKs under N deficiency could be a useful tool to improve tobacco cultivation, given that it could reduce N-fertilizer application and thereby provide economic savings and environmental benefits, maintaining yield and improving tobacco leaf quality.

Differential responses of five cherry tomato varieties to water stress: changes on phenolic metabolites and related enzymes.

Different tomato cultivars (Solanum lycopersicum L.) with differences in tolerance to drought were subjected to moderate water stress to test the effects on flavonoids and caffeoyl derivatives and related enzymes. Our results indicate that water stress resulted in decreased shikimate pathway (DAHP synthase, shikimate dehydrogenase, phenylalanine ammonium lyase, cinnamate 4-hydroxylase, 4-coumarate CoA ligase) and phenolic compounds (caffeoylquinic acid derivatives, quercetin and kaempferol) in the cultivars more sensitive to water stress. However, cv. Zarina is more tolerant, and registered a rise in querc-3-rut-pent, kaempferol-3-api-rut, and kaempferol-3-rut under the treatment of water stress. Moreover, this cultivar show increased activities of flavonoid and phenylpropanoid synthesis and decreased in degradation-related enzymes. These results show that moderate water stress can induce shikimate pathway in tolerant cultivar.

Ammonia production and assimilation: its importance as a tolerance mechanism during moderate water deficit in tomato plants.

Nitrate assimilation diminishes under water stress. This can augment the photorespiratory rate as a protection mechanism, increasing the ammonium concentration, which must be rapidly assimilated. We therefore examined the effect of moderate water stress in photorespiration and N assimilation, as possible tolerance mechanisms in cherry tomato. Five cherry tomato cultivars with different degrees of water stress tolerance were submitted to two water treatments: well-watered (100% FC) and water stress (50% FC). In the susceptible cultivars, nitrate assimilation declined but without stimulating photorespiration. Zarina, a stress-tolerant cultivar, showed increased activity of the main enzymes involved in photorespiration, together with greater assimilation of nitrates and of the resulting ammonium. This translates as higher concentrations of N as well as amino acids and proteins. We characterize these mechanisms in the cv. Zarina (tolerant) as essential to water stress tolerance, acting on N metabolism as well as helping to maintain or augment biomass.

The effect of environmental conditions on nutritional quality of cherry tomato fruits: evaluation of two experimental Mediterranean greenhouses.

BACKGROUND: The aim of this study was to examine how different environmental factors (temperature, solar radiation, and vapour-pressure deficit [VPD]) influenced nutritional quality and flavour of cherry tomato fruits (Solanum lycopersicum L. cv. Naomi) grown in two types of experimental Mediterranean greenhouses: parral (low technology) and multispan (high technology). RESULTS: Fruits were sampled three times during 3 years (2004, 2005 and 2006): at the beginning, middle and end of the fruit production period. Values for temperature, solar radiation, and VPD peaked in the third sampling in both greenhouses; values were higher in the parral-type greenhouse, triggering abiotic stress. This stress reduced the accumulation of lycopene and essential elements, augmenting the phytonutrient content and the antioxidant capacity of tomatoes. During the third sampling, sugars were increased while organic acid content diminished, producing tomatoes with a sweeter-milder flavour. The parral greenhouse produced tomatoes with higher phenolic compounds and ascorbic acid contents, together with a greater antioxidant capacity, without showing differences in flavour parameters. CONCLUSION: The higher phytonutrients content and antioxidant activity during the environmental stress, more pronounced in parral than multispan greenhouse, together with the sweeter-milder flavour, conferred a notable nutritional benefit, which considerably improved the nutritional and organoleptic quality of these tomatoes.