Physiological aspects of raffinose family oligosaccharides in plants: protection against abiotic stress

Integrated Transcriptomics and Metabolomics Analysis Reveal Key Metabolism Pathways Contributing to Cold Tolerance in Peanut

Low temperature (non-freezing) is one of the major limiting factors in peanut (Arachis hypogaea L.) growth, yield, and geographic distribution. Due to the complexity of cold-resistance trait in peanut, the molecular mechanism of cold tolerance and related gene networks were largely unknown. In this study, metabolomic analysis of two peanut cultivars subjected to chilling stress obtained a set of cold-responsive metabolites, including several carbohydrates and polyamines. These substances showed a higher accumulation pattern in cold-tolerant variety SLH than cold-susceptible variety ZH12 under cold stress, indicating their importance in protecting peanut from chilling injuries. In addition, 3,620 cold tolerance genes (CTGs) were identified by transcriptome sequencing, and the CTGs were most significantly enriched in the "phenylpropanoid biosynthesis" pathway. Two vital modules and several novel hub genes were obtained by weighted gene co-expression network analysis (WGCNA). Several key genes involved in soluble sugar, polyamine, and G-lignin biosynthetic pathways were substantially higher and/or responded more quickly in SLH (cold tolerant) than ZH12 (cold susceptible) under low temperature, suggesting they might be crucial contributors during the adaptation of peanut to low temperature. These findings will not only provide valuable resources for study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.

Cold-Triggered Induction of ROS- and Raffinose Metabolism in Freezing-Sensitive Taproot Tissue of Sugar Beet

Sugar beet (Beta vulgaris subsp. vulgaris) is the exclusive source of sugar in the form of sucrose in temperate climate zones. Sugar beet is grown there as an annual crop from spring to autumn because of the damaging effect of freezing temperatures to taproot tissue. A collection of hybrid and non-hybrid sugar beet cultivars was tested for winter survival rates and freezing tolerance. Three genotypes with either low or high winter survival rates were selected for detailed study of their response to frost. These genotypes differed in the severity of frost injury in a defined inner region in the upper part of the taproot, the so-called pith. We aimed to elucidate genotype- and tissue-dependent molecular processes during freezing and combined analyses of sugar beet anatomy and physiology with transcriptomic and metabolite profiles of leaf and taproot tissues at low temperatures. Freezing temperatures induced strong downregulation of photosynthesis in leaves, generation of reactive oxygen species (ROS), and ROS-related gene expression in taproots. Simultaneously, expression of genes involved in raffinose metabolism, as well as concentrations of raffinose and its intermediates, increased markedly in both leaf and taproot tissue at low temperatures. The accumulation of raffinose in the pith tissue correlated with freezing tolerance of the three genotypes. We discuss a protective role for raffinose and its precursors against freezing damage of sugar beet taproot tissue.

Metabolomic Profiling of Drought-Tolerant and Susceptible Peanut (Arachis hypogaea L.) Genotypes in Response to Drought Stress

Peanut is frequently constrained by extreme environmental conditions such as drought. To reveal the involvement of metabolites, TAG 24 (drought-tolerant) and JL 24 (drought-sensitive) peanut genotypes were investigated under control and 20% PEG 6000-mediated water scarcity conditions at the seedling stage. Samples were analyzed by gas chromatography-mass spectrometry (GC-MS) to identify untargeted metabolites and targeted metabolites, i.e., polyamines and polyphenols by high-performance liquid chromatography (HPLC) and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), respectively. The principal component analysis (PCA), partial least-squares discriminant analysis (PLS-DA), heat map, and cluster analysis were applied to the metabolomics data obtained by the GC-MS technique to determine the important metabolites for drought tolerance. Among 46 resulting metabolites, pentitol, phytol, xylonic acid, d-xylopyranose, stearic acid, and d-ribose were important drought-responsive metabolites. Agmatine and cadaverine were present in TAG 24 leaves and roots, respectively, during water-deficit conditions and believed to be the potential polyamines for drought tolerance. Polyphenols such as syringic acid and vanillic acid were produced more in the leaves of TAG 24, while catechin production was high in JL 24 during stress conditions. Seven metabolic pathways, namely, galactose metabolism, starch and sucrose metabolism, fructose and mannose metabolism, pentose and glucuronate interconversion, propanoate metabolism, amino sugar and nucleotide sugar metabolism, and biosynthesis of unsaturated fatty acids were significantly affected by water-deficit conditions. This study provides valuable information about the metabolic response of peanut to drought stress and metabolites identified, which encourages further study by transcriptome and proteomics to improve drought tolerance in peanut.

Morpho-physiological and biochemical changes in finger millet [Eleusine coracana (L.) Gaertn.] under drought stress

Finger millet (Eleusine coracana L. Gaertn.) is a nutritious and climate-resilient crop with a C₄ type carbon fixation pathway. The present study was aimed to assess the drought tolerance capacities of four finger millet genotypes based on their physiological and biochemical characteristics at three different phenological stages. Finger millet genotypes RAU 8, GPU 67, GPU 28 and MS 9272 were subjected to two water regimes, regular irrigation (control) and suspended irrigation (drought stress). During water regimes, morpho-physiological [biomass accumulation, leaf relative water content, and photosynthetic pigments] and biochemical changes [proline content, water soluble carbohydrates, antioxidant enzymes, and malondialdehyde content] were studied during seedling (18th day), vegetative (49th day) and early flowering stages (73rd day). The maintenance of growth especially root growth, biomass accumulation, the differential response in the concentration and changes of pigments, accumulation of proline, water-soluble carbohydrates and increased levels of antioxidant enzymes under drought stress play a major role in differential tolerance in finger millet genotypes that is conferred by the biplot analysis. The genotype RAU 8 is the most drought-tolerant genotype at all the three different phenological stages. Whereas the genotype GPU 67 was identified as sensitive at the seedling stage and its tolerance level was improved at vegetative and early flowering stages. The genotypes GPU 28 and MS 9272 were considered as drought sensitive at all three different phenological stages. Our results provide inputs to the breeders to select genotypes as parents and to design effective strategies in crop improvement programs.

Developmentally controlled changes during Arabidopsis leaf development indicate causes for loss of stress tolerance with age

Leaf senescence is the final stage of leaf development and is induced by the gradual occurrence of age-related changes (ARCs). The process of leaf senescence has been well described, but the cellular events leading to this process are still poorly understood. By analysis of progressively ageing, but not yet senescing, Arabidopsis thaliana rosette leaves, we aimed to better understand processes occurring prior to the onset of senescence. Using gene expression analysis, we found that as leaves mature, genes responding to oxidative stress and genes involved in stress hormone biosynthesis and signalling were up-regulated. A decrease in primary metabolites that provide protection against oxidative stress was a possible explanation for the increased stress signature. The gene expression and metabolomics changes occurred concomitantly to a decrease in drought, salinity, and dark stress tolerance of individual leaves. Importantly, stress-related genes showed elevated expression in the early ageing mutant old5 and decreased expression in the delayed ageing mutant ore9. We propose that the decreased stress tolerance with age results from the occurrence of senescence-inducing ARCs that is integrated into the leaf developmental programme, and that this ensures a timely and certain death.

Multi-gene metabolic engineering of tomato plants results in increased fruit yield up to 23%

The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given that all of these processes have the potential to co-limit growth, multiple genetic interventions in source and sink tissues, plus transport processes may be necessary to reach the full yield potential of a crop. We used biolistic combinatorial co-transformation (up to 20 transgenes) for increasing C and N flows with the purpose of increasing tomato fruit yield. We observed an increased fruit yield of up to 23%. To better explore the reconfiguration of metabolic networks in these transformants, we generated a dataset encompassing physiological parameters, gene expression and metabolite profiling on plants grown under glasshouse or polytunnel conditions. A Sparse Partial Least Squares regression model was able to explain the combination of genes that contributed to increased fruit yield. This combinatorial study of multiple transgenes targeting primary metabolism thus offers opportunities to probe the genetic basis of metabolic and phenotypic variation, providing insight into the difficulties in choosing the correct combination of targets for engineering increased fruit yield.

Recent advances in the knowledge of wine oligosaccharides

Oligosaccharides are carbohydrates with a low polymerization degree containing between three and fifteen monosaccharide residues covalently linked through glycosidic bonds. Oligosaccharides are related to plant defense responses and possess beneficial attributes for human health. Research has focused in wine oligosaccharides only in the last decade. In this paper, a summary of these works is provided. They include: (i) wine oligosaccharides origins, (ii) techniques for isolating oligosaccharide fraction and determining their content, composition and structure, (iii) their dependence on the grape origin and cultivar and winemaking process, and (iv) the connection between oligosaccharides and wine sensorial attributes. Further research is required regarding the impact of agricultural aspects and winemaking techniques on wine oligosaccharides. The knowledge concerning their influence on sensorial and physicochemical properties of wines and on human health should also be improved. The implementation of laboratory methods will provide better understanding of these compounds and their performance within wine's matrix.

Biochemical characterization of recombinant UDP-sugar pyrophosphorylase and galactinol synthase from Brachypodium distachyon

Raffinose (Raf) protects plant cells during seed desiccation and under different abiotic stress conditions. The biosynthesis of Raf starts with the production of UDP-galactose by UDP-sugar pyrophosphorylase (USPPase) and continues with the synthesis of galactinol by galactinol synthase (GolSase). Galactinol is then used by Raf synthase to produce Raf. In this work, we report the biochemical characterization of USPPase (BdiUSPPase) and GolSase 1 (BdiGolSase1) from Brachypodium distachyon. The catalytic efficiency of BdiUSPPase was similar with galactose 1-phosphate and glucose 1-phosphate, but 5- to 17-fold lower with other sugar 1-phosphates. The catalytic efficiency of BdiGolSase1 with UDP-galactose was three orders of magnitude higher than with UDP-glucose. A structural model of BdiGolSase1 allowed us to determine the residues putatively involved in the binding of substrates. Among these, we found that Cys²⁶¹ lies within the putative catalytic pocket. BdiGolSase1 was inactivated by oxidation with diamide and H₂O₂. The activity of the diamide-oxidized enzyme was recovered by reduction with dithiothreitol or E. coli thioredoxin, suggesting that BdiGolSase1 is redox-regulated.

Characterization of raffinose metabolism genes uncovers a wild Arachis galactinol synthase conferring tolerance to abiotic stresses

Raffinose family oligosaccharides (RFOs) are implicated in plant regulatory mechanisms of abiotic stresses tolerance and, despite their antinutritional proprieties in grain legumes, little information is available about the enzymes involved in RFO metabolism in Fabaceae species. In the present study, the systematic survey of legume proteins belonging to five key enzymes involved in the metabolism of RFOs (galactinol synthase, raffinose synthase, stachyose synthase, alpha-galactosidase, and beta-fructofuranosidase) identified 28 coding-genes in Arachis duranensis and 31 in A. ipaënsis. Their phylogenetic relationships, gene structures, protein domains, and chromosome distribution patterns were also determined. Based on the expression profiling of these genes under water deficit treatments, a galactinol synthase candidate gene (AdGolS3) was identified in A. duranensis. Transgenic Arabidopsis plants overexpressing AdGolS3 exhibited increased levels of raffinose and reduced stress symptoms under drought, osmotic, and salt stresses. Metabolite and expression profiling suggested that AdGolS3 overexpression was associated with fewer metabolic perturbations under drought stress, together with better protection against oxidative damage. Overall, this study enabled the identification of a promising GolS candidate gene for metabolic engineering of sugars to improve abiotic stress tolerance in crops, whilst also contributing to the understanding of RFO metabolism in legume species.

The Level of Methionine Residues in Storage Proteins Is the Main Limiting Factor of Protein-Bound-Methionine Accumulation in Arabidopsis Seeds

The low level of methionine, an essential sulfur-containing amino acid, limits the nutritional quality of seeds. Two main factors can control the level of protein-bound methionine: the level of free methionine that limits protein accumulation and the methionine residues inside the storage proteins. To reveal the main limiting factor, we generated transgenic Arabidopsis thaliana seed-specific plants expressing the methionine-rich sunflower seed storage (SSA) protein (A1/A2). The contents of protein-bound methionine in the water-soluble protein fraction that includes the SSA in A1/A2 were 5.3- and 10.5-fold, respectively, compared to control, an empty vector (EV). This suggests that free methionine can support this accumulation. To elucidate if the level of free methionine could be increased further in the protein-bound methionine, these lines were crossed with previously characterized plants having higher levels of free methionine in seeds (called SSE). The progenies of the crosses (A1S, A2S) exhibited the highest level of protein-bound methionine, but this level did not differ significantly from A2, suggesting that all the methionine residues of A2 were filled with methionine. It also suggests that the content of methionine residues in the storage proteins is the main limiting factor. The results also proposed that the storage proteins can change their content in response to high levels of free methionine or SSA. This was assumed since the water-soluble protein fraction was highest in A1S/A2S as well as in SSE compared to EV and A1/A2. By using these seeds, we also aimed at gaining more knowledge about the link between high free methionine and the levels of metabolites that usually accumulate during abiotic stresses. This putative connection was derived from a previous analysis of SSE. The results of metabolic profiling showed that the levels of 29 and 20 out of the 56 metabolites were significantly higher in SSE and A1, respectively, that had higher level of free methionine, compared A1S/A2S, which had lower free methionine levels. This suggests a strong link between high free methionine and the accumulation of stress-associated metabolites.

Metabolic signatures provide novel insights to Picrorhiza kurroa adaptation along the altitude in Himalayan region

INTRODUCTION

Along the altitude, environmental conditions vary significantly that might influence plant performance and distribution. Adaptation to these changing conditions is a complex biological process that involves reprogramming of genes, proteins and metabolites. The metabolic response of medicinal plants along the altitude has been less explored yet.

OBJECTIVES

In the present study, we investigated the adaptation strategies of Picrorhiza kurroa Royle ex Benth. along the altitude in organ specific manner using metabolomic approach.

METHODS

Picrorhiza kurroa plants at flowering stage were randomly sampled from three altitudes viz. 3400, 3800 and 4100 masl in the Himalayan region. Leaf, root and rhizome were used for LC-MS based non-targeted metabolite profiling and targeted analysis of sugars, amino acids, picrosides and their corresponding phenolic acids.

RESULTS

A total of 220, primary and secondary metabolites (SMs) were identified (p < 0.05) representing an extensive inventory of metabolites and their spatial distribution in P. kurroa. Differential accumulation of metabolites suggests source-sink carbon partitioning, occurrence of partial TCA cycle, ascorbate metabolism, purine catabolism and salvage route, pyrimidine synthesis, lipid alteration besides gibberellins and cytokinin inhibition might be an adaptive strategy to alpine environmental stress along the altitude. Further, marked differences of organ and altitude specific SMs reflect alteration in secondary metabolic pathways. Significant accumulation of picrosides suggests their probable role in P. kurroa adaptation.

CONCLUSION

This study provides a platform that would be useful in deciphering the role of metabolites considered to be involved in plant adaptation.

Root Growth Adaptation to Climate Change in Crops

Climate change is threatening crop productivity worldwide and new solutions to adapt crops to these environmental changes are urgently needed. Elevated temperatures driven by climate change affect developmental and physiological plant processes that, ultimately, impact on crop yield and quality. Plant roots are responsible for water and nutrients uptake, but changes in soil temperatures alters this process limiting crop growth. With the predicted variable climatic forecast, the development of an efficient root system better adapted to changing soil and environmental conditions is crucial for enhancing crop productivity. Root traits associated with improved adaptation to rising temperatures are increasingly being analyzed to obtain more suitable crop varieties. In this review, we will summarize the current knowledge about the effect of increasing temperatures on root growth and their impact on crop yield. First, we will describe the main alterations in root architecture that different crops undergo in response to warmer soils. Then, we will outline the main coordinated physiological and metabolic changes taking place in roots and aerial parts that modulate the global response of the plant to increased temperatures. We will discuss on some of the main regulatory mechanisms controlling root adaptation to warmer soils, including the activation of heat and oxidative pathways to prevent damage of root cells and disruption of root growth; the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will also consider that in the field, increasing temperatures are usually associated with other abiotic and biotic stresses such as drought, salinity, nutrient deficiencies, and pathogen infections. We will present recent advances on how the root system is able to integrate and respond to complex and different stimuli in order to adapt to an increasingly changing environment. Finally, we will discuss the new prospects and challenges in this field as well as the more promising pathways for future research.

Comparative time-course transcriptome analysis in contrasting Carex rigescens genotypes in response to high environmental salinity

Soil salinization is one of most crucial environmental problems around the world and negatively affects plant growth and production. Carex rigescens is a turfgrass with favorable stress tolerance and great application prospect in salinity soil remediation and utilization; however, the molecular mechanisms behind its salt stress response are unknown. We performed a time-course transcriptome analysis between salt tolerant 'Huanghua' (HH) and salt sensitive 'Beijing' (BJ) genotypes. Physiological changes within 24 h were observed, with the HH genotype exhibiting increased salt tolerance compared to BJ. 5764 and 10752 differentially expressed genes were approved by transcriptome in BJ and HH genotype, respectively, and dynamic analysis showed a discrepant profile between two genotypes. In the BJ genotype, genes related to carbohydrate metabolism and stress response were more active and ABA signal transduction pathway might play a more important role in salt stress tolerance than in HH genotype. In the HH genotype, unique increases in the regulatory network of transcription factors, hormone signal transduction, and oxidation-reduction processes were observed. Moreover, trehalose and pectin biosynthesis and chitin catabolic related genes were specifically involved in the HH genotype, which may have contributed to salt tolerance. Moreover, some candidate genes like mannan endo-1,4-beta-mannosidase and EG45-like domain-containing protein are highlighted for future research about salt stress resistance in C. rigescens and other plant species. Our study revealed unique salt adaptation and resistance characteristics of two C. rigescens genotypes and these findings could help to enrich the currently available knowledge and clarify the detailed salt stress regulatory mechanisms in C. rigescens and other plants.

A matter of life and death: Molecular, physiological, and environmental regulation of seed longevity

Both seed germination and early seedling establishment are important biological processes in a plant's lifecycle. Seed longevity is a key trait in agriculture, which directly influences seed germination and ultimately determines crop productivity and hence food security. Numerous studies have demonstrated that seed deterioration is regulated by complex interactions between diverse endogenous genetically controlled factors and exogenous environmental cues, including temperature, relative humidity, and oxygen partial pressure during seed storage. The endogenous factors, including the chlorophyll concentration, the structure of the seed coat, the balance of phytohormones, the concentration of reactive oxygen species, the integrity of nucleic acids and proteins and their associated repair systems, are also involved in the control of seed longevity. A precise understanding of the regulatory mechanisms underlying seed longevity is becoming a hot topic in plant molecular biology. In this review, we describe recent research into the regulation of seed longevity and the interactions between the various environmental and genetic factors. Based on this, the current state-of-play regarding seed longevity regulatory networks will be presented, particularly with respect to agricultural seed storage, and the research challenges to be faced in the future will be discussed.

Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress

Drought is a major limiting factor of crop yields. In response to drought, plants reprogram their gene expression, which ultimately regulates a multitude of biochemical and physiological processes. The timing of this reprogramming and the nature of the drought-regulated genes in different genotypes are thought to confer differential tolerance to drought stress. Sorghum is a highly drought-tolerant crop and has been increasingly used as a model cereal to identify genes that confer tolerance. Also, there is considerable natural variation in resistance to drought in different sorghum genotypes. Here, we evaluated drought resistance in four genotypes to polyethylene glycol (PEG)-induced drought stress at the seedling stage and performed transcriptome analysis in seedlings of sorghum genotypes that are either drought-resistant or drought-sensitive to identify drought-regulated changes in gene expression that are unique to drought-resistant genotypes of sorghum. Our analysis revealed that about 180 genes are differentially regulated in response to drought stress only in drought-resistant genotypes and most of these (over 70%) are up-regulated in response to drought. Among these, about 70 genes are novel with no known function and the remaining are transcription factors, signaling and stress-related proteins implicated in drought tolerance in other crops. This study revealed a set of drought-regulated genes, including many genes encoding uncharacterized proteins that are associated with drought tolerance at the seedling stage.

Metabolite profiling of onion landraces and the cold storage effect

Today, commercial onion breeders focus almost entirely on conventional farming which reduces diversity in the market and leads to loss of desirable traits such as those that impact nutritional and sensory aspects of onions. A way to preserve phenotypic and genetic diversity is to re-evaluate traditional landraces to introduce their benefits to the broader public. Common onion genotypes vary greatly in their storability. In particular, temperature and relative humidity during storage have significant impact on the metabolites in onions after storage. The aim of this study was to assess changes in the metabolite profile of ten onion genotypes after five months of cold storage. In addition, a characterization of onion landraces in their fresh state was also conducted in order to compare their properties against a commercial genotype. Onion genotypes were grown under organic farming conditions. After harvest and curing, bulbs were stored for up to 22 weeks. Before and after storage, bulb samples were analyzed through targeted and untargeted methods. Out of 189 identified metabolites, 128 showed a storage effect. Mainly fructans decreased because of respiration and energy demand, while monosaccharides increased. Further, amino acids were altered in their concentration after storage with an effect on aroma precursors. Eight of the nine landraces had good storability without critical losses. In their fresh state, the onion genotypes clustered into three major groups. For instance, landraces of group III showed consistently and substantially higher levels of amino acids and certain sugars, indicating a high potential of aromatic properties in those onion landraces.

Poaceae Type II Galactinol Synthase 2 from Antarctic Flowering Plant Deschampsia antarctica and Rice Improves Cold and Drought Tolerance by Accumulation of Raffinose Family Oligosaccharides in Transgenic Rice Plants

Deschampsia antarctica is a Poaceae grass that has adapted to and colonized Antarctica. When D. antarctica plants were subjected to cold and dehydration stress both in the Antarctic field and in laboratory experiments, galactinol, a precursor of raffinose family oligosaccharides (RFOs) and raffinose were highly accumulated, which was accompanied by upregulation of galactinol synthase (GolS). The Poaceae monocots have a small family of GolS genes, which are divided into two distinct groups called types I and II. Type II GolSs are highly expanded in cold-adapted monocot plants. Transgenic rice plants, in which type II D. antarctica GolS2 (DaGolS2) and rice GolS2 (OsGolS2) were constitutively expressed, were markedly tolerant to cold and drought stress as compared to the wild-type rice plants. The RFO contents and GolS enzyme activities were higher in the DaGolS2- and OsGolS2-overexpressing progeny than in the wild-type plants under both normal and stress conditions. DaGolS2 and OsGolS2 overexpressors contained reduced levels of reactive oxygen species (ROS) relative to the wild-type plants after cold and drought treatments. Overall, these results suggest that Poaceae type II GolS2s play a conserved role in D. antarctica and rice in response to drought and cold stress by inducing the accumulation of RFO and decreasing ROS levels.

Phosphoglucomutase Is Not the Target for Galactose Toxicity in Plants

Plants synthesize a number of different oligomeric or polymeric sugars containing galactose. During growth and development some of these carbohydrates are metabolized or remodeled releasing galactose as a breakdown product. All plants have established recycling pathways for such sugars, for which they seem to have a limited capacity to cope with. Exceeding these limits results in sugar toxicity, which is observed already at concentrations as low as 1 mmol·l^-1 for galactose. The mechanism of galactose toxicity is poorly understood but it seems plausible that the enzymes involved in carbohydrate metabolism also might be the targets responsible for the adverse effects. Data from yeast and bacteria suggests that the enzyme phosphoglucomutase (PGM) is inhibited by galactose-1-phosphate. To test this hypothesis for plants we expressed recombinant cytosolic PGM3 from Arabidopsis in E. coli. Intriguingly, the enzyme was not inhibited by galactose-1-phosphate at physiological concentrations. Furthermore, PGM3 did not convert galactose-1-phosphate to galactose-6-phosphate, which was suggested as the inhibitory mode of action in yeast. In addition, metabolite levels in Arabidopsis roots were analyzed for their galactose-1-phosphate concentration by means of GC-MS. Seedlings grown on MS-media with sucrose contained less than 10 nmol·g FW^-1 of galactose-1-phosphate. However, seedlings from plates, in which the sucrose was replaced by galactose, showed a strong increase of Gal-1-P to levels of up to 200 nmol·g FW^-1.

Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.

Variation in seed longevity among diverse Indica rice varieties

BACKGROUND AND AIMS

Understanding variation in seed longevity, especially within closely related germplasm, will lead to better understanding of the molecular basis of this trait, which is particularly important for seed genebanks, but is also relevant to anyone handling seeds. We therefore set out to determine the relative seed longevity of diverse Indica rice accessions through storage experiments. Since antioxidants are purported to play a role in seed storability, the antioxidant activity and phenolic content of caryopses were determined.

METHODS

Seeds of 299 Indica rice accessions harvested at 31, 38 and 45 d after heading (DAH) between March and May 2015 and differing in harvest moisture content (MC) were subsequently stored at 10.9 % MC and 45 °C. Samples were taken at regular intervals and sown for germination. Germination data were subjected to probit analysis and the resulting parameters that describe the loss of viability during storage were used for genome-wide association (GWA) analysis.

KEY RESULTS

The seed longevity parameters, Ki [initial viability in normal equivalent deviates (NED)], -σ-1 (σ is the time for viability to fall by 1 NED in experimental storage) and p50 [time for viability to fall to 50 % (0 NED)], varied considerably across the 299 Indica accessions. Seed longevity tended to increase as harvest MC decreased and to decrease as harvest MC increased. Eight major loci associated with seed longevity parameters were identified through GWA analysis. The favourable haplotypes on chromosomes 1, 3, 4, 9 and 11 enhanced p50 by ratios of 0.22-1.86.

CONCLUSIONS

This is the first study to describe the extent of variation in σ within a species' variety group. A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.

Maize HSFA2 and HSBP2 antagonistically modulate raffinose biosynthesis and heat tolerance in Arabidopsis

Raffinose is thought to play an important role in plant tolerance of abiotic stress. We report here that maize HEAT SHOCK FACTOR A2 (ZmHSFA2) and HEAT SHOCK BINDING PROTEIN 2 (ZmHSBP2) physically interact with each other and antagonistically modulate expression of GALACTINOL SYNTHASE2 (ZmGOLS2) and raffinose biosynthesis in transformed maize protoplasts and Arabidopsis plants. Overexpression of ZmHSFA2 in Arabidopsis increased the expression of Arabidopsis AtGOLS1, AtGOLS2 and AtRS5 (RAFFINOSE SYNTHASE), increased the raffinose content in leaves and enhanced plant heat stress tolerance. Contrary to ZmHSFA2, overexpression of ZmHSBP2 in Arabidopsis decreased expression of AtGOLS1, AtGOLS2 and AtRS5, decreased the raffinose content in leaves and reduced plant heat stress tolerance. ZmHSFA2 and ZmHSBP2 also interact with their Arabidopsis counterparts AtHSBP and AtHSFA2 as determined using bimolecular fluorescence complementation assays. Furthermore, endogenous ZmHSBP2 and Rluc, controlled by the ZmHSBP2 promoter, are transcriptionally activated by ZmHSFA2 and inhibited by ZmHSBP2 in maize protoplasts. These findings provide insights into the transcriptional regulation of raffinose biosynthetic genes, and the tolerance their product confers to plant heat stress.

UV-C pretreatment of fresh-cut faba beans (Vicia faba) for shelf life extension: Effects of domestic microwaving for consumption

Faba beans have a short shelf life which is even reduced after fresh-cut processing mainly due to browning and dehydration. In that sense, the effects of a UV-C treatment (3 kJ m^-2), compared with non-exposed beans (CTRL), were studied on the sensory and microbial quality, and bioactive and anti-nutritional content of fresh-cut faba beans (cv. Muchamiel) during storage at 5 ℃. The effect of a domestic microwaving (3 min, 900 W) on bioactive and anti-nutritional compounds of fresh seeds prior to consumption at each sampling time was also studied. UV-C treatment extended the fresh-cut faba bean shelf life from 7 to 10 days with browning score (the main sensory parameter adversely affected) of 8 and 1 log unit lower than CTRL at day 10. UV-C did not negatively affect the total antioxidant capacity of samples during storage. The phytic acid and raffinose contents decreased by 30/40%, respectively, after 10 days, without influence of the UV-C treatment. Microwaving reduced the phytic acid and condensed tannins contents by 30% in those samples stored for up to six days, with low microwaving effect in the last storage days. Nevertheless, UV-C improved the condensed tannins reductions through storage (≈30%) compared with non-irradiated samples.

Transcript and metabolic adjustments triggered by drought in Ilex paraguariensis leaves

Abscisic acid is involved in the drought response of Ilex paraguariensis. Acclimation includes root growth stimulation, stomatal closure, osmotic adjustment, photoprotection, and regulation of nonstructural carbohydrates and amino acid metabolisms. Ilex paraguariensis (yerba mate) is cultivated in the subtropical region of South America, where the occurrence of drought episodes limit yield. To explore the mechanisms that allow I. paraguariensis to overcome dehydration, we investigated (1) how gene expression varied between water-stressed and non-stressed plants and (2) in what way the modulation of gene expression was linked to physiological status and metabolite composition. A total of 4920 differentially expressed transcripts were obtained through RNA-Seq after water deprivation. Drought induced the expression of several transcripts involved in the ABA-signalling pathway. Stomatal closure and leaf osmotic adjustments were promoted to minimize water loss, and these responses were accompanied by a high transcriptional remodeling of stress perception, signalling and transcriptional regulation, the photoprotective and antioxidant systems, and other stress-responsive genes. Simultaneously, significant changes in metabolite contents were detected. Glutamine, phenylalanine, isomaltose, fucose, and malate levels were shown to be positively correlated with dehydration. Principal component analysis showed differences in the metabolic profiles of control and stressed leaves. These results provide a comprehensive overview of how I. paraguariensis responds to dehydration at transcriptional and metabolomic levels and provide further characterization of the molecular mechanisms associated with drought response in perennial subtropical species.

Identification of Factors Linked to Higher Water-Deficit Stress Tolerance in Amaranthus hypochondriacus Compared to Other Grain Amaranths and A. hybridus, Their Shared Ancestor

Water deficit stress (WDS)-tolerance in grain amaranths (Amaranthus hypochondriacus, A. cruentus and A. caudatus), and A. hybridus, their presumed shared ancestor, was examined. A. hypochondriacus was the most WDS-tolerant species, a trait that correlated with an enhanced osmotic adjustment (OA), a stronger expression of abscisic acid (ABA) marker genes and a more robust sugar starvation response (SSR). Superior OA was supported by higher basal hexose (Hex) levels and high Hex/sucrose (Suc) ratios in A. hypochondriacus roots, which were further increased during WDS. This coincided with increased invertase, amylase and sucrose synthase activities and a strong depletion of the starch reserves in leaves and roots. The OA was complemented by the higher accumulation of proline, raffinose, and other probable raffinose-family oligosaccharides of unknown structure in leaves and/or roots. The latter coincided with a stronger expression of Galactinol synthase 1 and Raffinose synthase in leaves. Increased SnRK1 activity and expression levels of the class II AhTPS9 and AhTPS11 trehalose phosphate synthase genes, recognized as part of the SSR network in Arabidopsis, were induced in roots of stressed A. hypochondriacus. It is concluded that these physiological modifications improved WDS in A. hypochondriacus by raising its water use efficiency.

How fall dormancy benefits alfalfa winter-survival? Physiologic and transcriptomic analyses of dormancy process

BACKGROUND

Fall dormancy and freezing tolerance characterized as two important phenotypic traits, have great effects on productivity and persistence of alfalfa (Medicago sativa L.). Despite the fact that one of the most limiting traits for alfalfa freezing tolerance in winter is fall dormancy, the interplay between fall dormancy and cold acclimation processes of alfalfa remains largely unknown. We compared the plant regrowth, winter survival, raffinose and amino acids accumulation, and genome-wide differentially expressed genes of fall-dormant cultivar with non-dormant cultivar under cold acclimation.

RESULTS

Averaged over both years, the non-dormant alfalfa exhibited largely rapid regrowth compared with fall dormant alfalfa after last cutting in autumn, but the winter survival rate of fall dormant alfalfa was about 34-fold higher than that of non-dormant alfalfa. The accumulation of raffinose and amino acids were significantly increased in fall dormant alfalfa, whereas were decreased in non-dormant alfalfa under cold acclimation. Expressions of candidate genes encoding raffinose biosynthesis genes were highly up-regulated in fall dormant alfalfa, but down-regulated in non-dormant alfalfa under cold acclimation. In fall dormant alfalfa, there was a significantly down-regulated expression of candidate genes encoding the glutamine synthase, which is indirectly involved in the proline metabolism. A total of eight significantly differentially expressed transcription factors (TFs) related to CBF and ABRE-BFs were identified. The most up-regulated TFs in fall dormant alfalfa cultivar were ABF4 and DREB1C.

CONCLUSIONS

Fall dormant alfalfa drastically increased raffinose and amino acids accumulation under cold acclimation. Raffinose-associated and amino acid-associated genes involved in metabolic pathways were more highly expressed in fall dormant alfalfa than non-dormant alfalfa under cold acclimation. This global survey of transcriptome profiles provides new insights into the interplay between fall dormancy and cold acclimation in alfalfa.

Lignocellulose derived functional oligosaccharides: production, properties, and health benefits

Lignocellulosic biomass (LB) is the renewable feedstock for the production of fuel/energy, feed/food, chemicals, and materials. LB could also be the versatile source of the functional oligosaccharides, which are non-digestible food ingredients having numerous applications in food, cosmetics, pharmaceutical industries, and others. The burgeoning functional food demand is expected to be more than US$440 billion in 2022. Because of higher stability at low pH and high temperature, oligosaccharides stimulate the growth of prebiotic bifidobacteria and lactic acid bacteria. Xylooligosaccharides (XOS) are major constituents of oligosaccharides consisting of 2-7 xylose monomeric units linked via β-(1,4)-linkages. XOS can be obtained from various agro-residues by thermochemical pretreatment, enzymatic or chemoenzymatic methods. While thermochemical methods are fast, reproducible, enzymatic methods are substrate specific, costly, and produce minimum side products. Enzymatic methods are preferred for the production of food grade and pharmaceutically important oligosaccharides. XOS are potent prebiotics having antioxidant properties and enhance the bio-adsorption of calcium and improving bowel functions, etc. LB can cater to the increasing demand of oligosaccharides because of their foreseeable amount and the advancements in technology to recover oligosaccharides. This paper summarizes the methods for oligosaccharides production from LB, classification, and benefits of oligosaccharides on human health.

Metabolite and transcript profiling of Guinea grass (Panicum maximum Jacq) response to elevated [CO2] and temperature

INTRODUCTION

By mid-century, global atmospheric carbon dioxide concentration ([CO₂]) is predicted to reach 600 μmol mol^-1 with global temperatures rising by 2 °C. Rising [CO₂] and temperature will alter the growth and productivity of major food and forage crops across the globe. Although the impact is expected to be greatest in tropical regions, the impact of climate-change has been poorly studied in those regions.

OBJECTIVES

This experiment aimed to understand the effects of elevated [CO₂] (600 μmol mol^-1) and warming (+ 2 °C), singly and in combination, on Panicum maximum Jacq. (Guinea grass) metabolite and transcript profiles.

METHODS

We created a de novo assembly of the Panicum maximum transcriptome. Leaf samples were taken at two time points in the Guinea grass growing season to analyze transcriptional and metabolite profiles in plants grown at ambient and elevated [CO₂] and temperature, and statistical analyses were used to integrate the data.

RESULTS

Elevated temperature altered the content of amino acids and secondary metabolites. The transcriptome of Guinea grass shows a clear time point separations, with the changes in the elevated temperature and [CO₂] combination plots.

CONCLUSION

Field transcriptomics and metabolomics revealed that elevated temperature and [CO₂] result in alterations in transcript and metabolite profiles associated with environmental response, secondary metabolism and stomatal function. These metabolic responses are consistent with greater growth and leaf area production under elevated temperature and [CO₂]. These results show that tropical C₄ grasslands may have unpredicted responses to global climate change, and that warming during a cool growing season enhances growth and alleviates stress.

The metabolic response to drought

Metabolic regulation is one of the main mechanisms involved in the maintenance of cell osmotic potential under abiotic stress. To date, metabolite profiling approaches have been extensively used to characterize the molecular responses to abiotic stress in many plant species. However, studies revealing the specific metabolic responses of plants exposed to water-deficit stress remain limited. Here, we review the most recent developments that advance our understanding of the metabolic response to drought stress in Arabidopsis and rice. We provide an updated schematic overview of the specific metabolic signature of wild-type plants in response to drought.

Transcriptome and metabolome analyses of two contrasting sesame genotypes reveal the crucial biological pathways involved in rapid adaptive response to salt stress

BACKGROUND

Soil salinity is one of the major serious factors that affect agricultural productivity of almost all crops worldwide, including the important oilseed crop sesame. In order to improve salinity resistance in sesame, it is crucial to understand the molecular mechanisms underlying the adaptive response to salinity stress.

RESULTS

In the present study, two contrasting sesame genotypes differing in salt tolerance were used to decipher the adaptive responses to salt stress based on morphological, transcriptome and metabolome characterizations. Morphological results indicated that under salt stress, the salt-tolerant (ST) genotype has enhanced capacity to withstand salinity stress, higher seed germination rate and plant survival rate, as well as better growth rate than the salt-sensitive genotype. Transcriptome analysis revealed strongly induced salt-responsive genes in sesame mainly related to amino acid metabolism, carbohydrate metabolism, biosynthesis of secondary metabolites, plant hormone signal transduction, and oxidation-reduction process. Especially, several pathways were preferably enriched with differentially expressed genes in ST genotype, including alanine, aspartate and glutamate metabolism, carotenoid biosynthesis, galactose metabolism, glycolysis/gluconeogenesis, glyoxylate and dicarboxylate metabolism, porphyrin and chlorophyll metabolism. Metabolome profiling under salt stress showed a higher accumulation degree of metabolites involved in stress tolerance in ST, and further highlighted that the amino acid metabolism, and sucrose and raffinose family oligosaccharides metabolism were enhanced in ST.

CONCLUSIONS

These findings suggest that the candidate genes and metabolites involved in crucial biological pathways may regulate salt tolerance of sesame, and increase our understanding of the molecular mechanisms underlying the adaptation of sesame to salt stress.

Diversity among Pomegranate Varieties in Chilling Tolerance and Transcriptome Responses to Cold Storage

We found great variability in chilling tolerance among 84 pomegranate varieties from the Newe Ya'ar collection; among them, 'Ganesh' was chilling-sensitive, whereas 'Wonderful' was relatively chilling-tolerant. To evaluate the different molecular responses of these varieties to cold storage, we analyzed the transcriptomic changes in the inner membrane tissues of 'Ganesh' and 'Wonderful' fruit after 2 weeks of cold storage at 1 °C. By functional categorization of the differentially expressed transcripts using MapMan, we found that many transcripts related to various pathways, such as jasmonic acid biosynthesis and signaling, galactinol, raffinose, phenol, and phenylpropanoid biosynthesis, calcium and mitogen-activated protein kinase signaling, lipid metabolism, and various transcription factors and heat-shock proteins, have been massively upregulated in 'Wonderful' but not in 'Ganesh' fruit. Thus, it is suggested that these pathways most likely participate in imparting chilling tolerance in pomegranate fruit.

Comparative metabolic profiling of Vitis amurensis and Vitis vinifera during cold acclimation

Vitis amurensis is a wild Vitis plant that can withstand extreme cold temperatures. However, the accumulation of metabolites during cold acclimation (CA) in V. amurensis remains largely unknown. In this study, plantlets of V. amurensis and V. vinifera cv. Muscat of Hamburg were treated at 4 °C for 24 and 72 h, and changes of metabolites in leaves were detected by gas chromatography coupled with time-of-flight mass spectrometry. Most of the identified metabolites, including carbohydrates, amino acids, and organic acids, accumulated in the two types of grape after CA. Galactinol, raffinose, fructose, mannose, glycine, and ascorbate were continuously induced by cold in V. amurensis, but not in Muscat of Hamburg. Twelve metabolites, including isoleucine, valine, proline, 2-oxoglutarate, and putrescine, increased in V. amurensis during CA. More galactinol, ascorbate, 2-oxoglutarate, and putrescine, accumulated in V. amurensis, but not in Muscat of Hamburg, during CA, which may be responsible for the excellent cold tolerance in V. amurensis. The expression levels of the genes encoding β-amylase (BAMY), galactinol synthase (GolS), and raffinose synthase (RafS) were evaluated by quantitative reverse transcription-PCR. The expression BAMY (VIT_02s0012 g00170) and RafS (VIT_05s0077 g00840) were primarily responsible for the accumulation of maltose and raffinose, respectively. The accumulation of galactinol was attributed to different members of GolS in the two grapes. In conclusion, these results show the inherent differences in metabolites between V. amurensis and V. vinifera under CA.

An alternative to mineral phosphorus fertilizers: The combined effects of Trichoderma harzianum and compost on Zea mays, as revealed by 1H NMR and GC-MS metabolomics

The ability of Trichoderma harzianum (strain OMG-08) as plant growth promoting fungus (PGPF), was tested on Zea mays plants grown in soil pots added with different inorganic (triple superphosphate and rock phosphate) and organic (cow and horse manure composts) P fertilizers. The effect of treatments was evaluated by following the variations of plants dry biomass and nutrient content, as well as the metabolic changes in plant leaves by both GC-MS and NMR spectroscopy. A synergic effect was observed in treatments with both composts and fungus inoculation, in which not only plant growth and P uptake were enhanced, but also the expression of different metabolites related to an improved photosynthetic activity. Conversely, the combination of Trichoderma with inorganic fertilizers was less effective and even showed a reduction of plants shoot biomass and N content. The corresponding plant metabolome revealed metabolic compounds typical of biotic or abiotic stresses, which may be attributed to a reduced capacity of inorganic fertilizers to provide a sufficient P availability during plant growth. Our findings also indicate that the molecular composition of compost differentiated the Trichoderma activity in sustaining plant growth. The positive effects of the combined Trichoderma and compost treatment suggest that it may become an alternative to the phosphorus mineral fertilization.

Exogenous myo-inositol alleviates salinity-induced stress in Malus hupehensis Rehd

Myo-inositol mediates various physiological processes and stress responses. Here, we investigated its role in Malus hupehensis Rehd. plants when grown hydroponically under saline conditions. Salt-stressed plants showed reduced growth and marked declines in photosynthetic activity and chlorophyll concentrations. However, pretreatment with 50 μM myo-inositol significantly alleviated those inhibitions and enabled plants to maintain their photosynthetic capacity. In addition to changing stomatal behavior, exogenous myo-inositol inhibited ROS accumulation and Na⁺ uptake. In contrast, activities of antioxidant systems were enhanced, and expression was elevated for genes involved in Na⁺ uptake (e.g., HKT1, NHX1, SOS1, and SOS2). This exogenous application also provoked the accumulation of sugars or sugar alcohols, which partially contributed to the maintenance of osmotic balance, and the scavenging of ROS, either directly or indirectly. In summary, myo-inositol appears to alleviate the salt-induced inhibition of physiological processes for M. hupehensis, not only by supporting the plant's antioxidant defense system but also by mediating Na⁺ and K⁺ homeostasis and the osmotic balance.

Copper stress induces antioxidant responses and accumulation of sugars and phytochelatins in Antarctic Colobanthus quitensis (Kunth) Bartl

BACKGROUND

In field, C. quitensis is subjected to many abiotic extreme environmental conditions, such as low temperatures, high UV-B, salinity and reduced water potentials, but not metal or metalloid high concentrations in soil, however, other members of Caryophyllaceae family have tolerance to high concentrations of metals, this is the case of Silene genre. In this work, we hypothesize that C. quitensis have the same mechanisms of Silene to tolerate metals, involving accumulation and induction of antioxidant systems, sugar accumulation and the induction of thiols such as phytochelatins to tolerate.

RESULTS

The results showing an effective antioxidant defensive machinery involving non-enzymatic antioxidants such as phenolics, GSH and ascorbic acid, in another hand, GSH-related oligomers (phytochelatins) and sugars was induced as a defensive mechanism.

CONCLUSIONS

Colobanthus quitensis exhibits certain mechanisms to tolerate copper in vitro demonstrating its plasticity to tolerate several abiotic stress conditions.

FITNESS, a CCT domain-containing protein, deregulates reactive oxygen species levels and leads to fine-tuning trade-offs between reproductive success and defence responses in Arabidopsis

Environmental stresses are the major factors that limit productivity in plants. Here, we report on the function of an uncharacterized gene At1g07050, encoding a CCT domain-containing protein, from Arabidopsis thaliana. At1g07050 expression is highly repressed by oxidative stress. We used metabolomics, biochemical, and genomic approaches to analyse performance of transgenic lines with altered expression of At1g07050 under normal and oxidative stress conditions. At1g07050 overexpressing lines showed increased levels of reactive oxygen species (ROS), whereas knock-out mutants exhibited decreased levels of ROS and higher tolerance to oxidative stress generated in the chloroplast. Our results uncover a role for At1g07050 in cellular redox homeostasis controlling H₂ O₂ levels, due to changes in enzymes, metabolites, and transcripts related to ROS detoxification. Therefore, we call this gene FITNESS. Additionally, several genes such as ACD6, PCC1, and ICS1 related to salicylic acid signalling and defence were found differentially expressed among the lines. Notably, FITNESS absence significantly improved seed yield suggesting an effective fine-tuning trade-off between reproductive success and defence responses.

Metabolic process of raffinose family oligosaccharides during cold stress and recovery in cucumber leaves

Raffinose family oligosaccharides (RFOs) accumulate under stress conditions in many plants and have been suggested to act as stress protectants. To elucidate the metabolic process of RFOs under cold stress, levels of RFOs, and related carbohydrates, the expression and activities of main metabolic enzymes and their subcellular compartments were investigated during low-temperature treatment and during the recovery period in cucumber leaves. Cold stress induced the accumulation of stachyose in vacuoles, galactinol in vacuoles and cytosol, and sucrose and raffinose in vacuoles, cytosol, and chloroplasts. After cold stress removal, levels of these sugars decreased gradually in the respective compartments. Among four galactinol synthase genes (CsGS), CsGS1 was not affected by cold stress, while the other three CsGSs were up-regulated by low temperature. RNA levels of acid-α-galactosidase (GAL) 3 and alkaline-α-galactosidase (AGA) 2 and 3, and the activities of GAL and AGA, were up-regulated after cold stress removal. GAL3 protein and GAL activity were exclusively located in vacuoles, whereas AGA2 and AGA 3 proteins were found in cytosol and chloroplasts, respectively. The results indicate that RFOs, which accumulated during cold stress in different subcellular compartments in cucumber leaves, could be catabolized in situ by different galactosidases after stress removal.

The GARP/MYB-related grape transcription factor AQUILO improves cold tolerance and promotes the accumulation of raffinose family oligosaccharides

Grapevine (Vitis vinifera L.) is a widely cultivated fruit crop whose growth and productivity are greatly affected by low temperatures. On the other hand, wild Vitis species represent valuable genetic resources of natural stress tolerance. We have isolated and characterized a MYB-like gene encoding a putative GARP-type transcription factor from Amur grape (V. amurensis) designated as VaAQUILO. AQUILO (AQ) is induced by cold in both V. amurensis and V. vinifera, and its overexpression results in significantly improved tolerance to cold both in transgenic Arabidopsis and in Amur grape calli. In Arabidopsis, the ectopic expression of VaAQ increased antioxidant enzyme activities and up-regulated reactive oxygen species- (ROS) scavenging-related genes. Comparative mRNA sequencing profiling of 35S:VaAQ Arabidopsis plants suggests that this transcription factor is related to phosphate homeostasis like their Arabidopsis closest homologues: AtHRS1 and AtHHO2. However, when a cold stress is imposed, AQ is tightly associated with the cold-responsive pathway and with the raffinose family oligosaccharides (RFOs), as observed by the up-regulation of galactinol synthase (GoLS) and raffinose synthase genes. Gene co-expression network (GCN) and cis-regulatory element (CRE) analyses in grapevine indicated AQ as potentially regulating VvGoLS genes. Increased RFO content was confirmed in both transgenic Arabidopsis and Amur grape calli overexpressing VaAQ. Taken together, our results imply that AQ improves cold tolerance through promoting the accumulation of osmoprotectants.

Genome-wide identification and expression analyses of genes involved in raffinose accumulation in sesame

Sesame (Sesamum indicum L.) is an important oilseed crop. However, multiple abiotic stresses severely affect sesame growth and production. Raffinose family oligosaccharides (RFOs), such as raffinose and stachyose, play an important role in desiccation tolerance of plants and developing seeds. In the present study, three types of key enzymes, galactinol synthase (GolS), raffinose synthase (RafS) and stachyose synthase (StaS), responsible for the biosynthesis of RFOs were identified at the genome-wide scale in sesame. A total of 7 SiGolS and 15 SiRS genes were identified in the sesame genome. Transcriptome analyses showed that SiGolS and SiRS genes exhibited distinct expression profiles in different tissues and seed developmental stages. Comparative expression analyses under various abiotic stresses indicated that most of SiGolS and SiRS genes were significantly regulated by drought, osmotic, salt, and waterlogging stresses, but slightly affected by cold stress. The up-regulation of several SiGolS and SiRS genes by multiple abiotic stresses suggested their active implication in sesame abiotic stress responses. Taken together, these results shed light on the RFOs-mediated abiotic stress resistance in sesame and provide a useful framework for improving abiotic stress resistance of sesame through genetic engineering.

Genetic Architecture of Dietary Fiber and Oligosaccharide Content in a Middle American Panel of Edible Dry Bean

Common bean ( L.) is the most consumed edible grain legume worldwide and contains a wide range of nutrients for human health including dietary fiber. Diets high in beans are associated with lower rates of chronic diseases such as obesity and type 2 diabetes, and the content of dietary fibers varies among different market classes of dry bean. In this study, we evaluated the dietary fiber content in a Middle American diversity panel (MDP) of common bean and evaluated the genetic architecture of the various dietary fiber components. The dietary fiber components included insoluble and soluble dietary fibers as well as the antinutritional raffinose family of oligosaccharides (RFOs; raffinose, stachyose, and verbascose). All variables measured differed among market classes and entries. Colored bean seeds had higher levels of insoluble dietary fibers with the black market class showing also the highest raffinose and stachyose content. Cultivars and lines released since 1997 had higher insoluble dietary fibers and RFO content in race Durango. Higher levels of RFOs were also observed in cultivars with type II growth habit that was a recent breeding target in Durango race germplasm. Candidate genes for dietary fiber traits, especially homologs to two main genes in the RFO biosynthesis pathway, were identified. The knowledge of diversity of dietary fibers in the MDP accompanied with the identification of candidate genes could effectively improve dietary fiber components in common bean.

Evolutionary diversification of galactinol synthases in Rosaceae: adaptive roles of galactinol and raffinose during apple bud dormancy

Galactinol synthase (GolS) is a key enzyme in the biosynthetic pathway of raffinose family oligosaccharides (RFOs), which play roles in carbon storage, signal transduction, and osmoprotection. The present work assessed the evolutionary history of GolS genes across the Rosaceae using several bioinformatic tools. Apple (Malus × domestica) GolS genes were transcriptionally characterized during bud dormancy, in parallel with galactinol and raffinose measurements. Additionally, MdGolS2, a candidate to regulate seasonal galactinol and RFO content during apple bud dormancy, was functionally characterized in Arabidopsis. Evolutionary analyses revealed that whole genome duplications have driven GolS gene evolution and diversification in Rosaceae speciation. The strong purifying selection identified in duplicated GolS genes suggests that differential gene expression might define gene function better than protein structure. Interestingly, MdGolS2 was differentially expressed during bud dormancy, concomitantly with the highest galactinol and raffinose levels. One of the intrinsic adaptive features of bud dormancy is limited availability of free water; therefore, we generated transgenic Arabidopsis plants expressing MdGolS2. They showed higher galactinol and raffinose contents and increased tolerance to water deficit. Our results suggest that MdGolS2 is the major GolS responsible for RFO accumulation during apple dormancy, and these carbohydrates help to protect dormant buds against limited water supply.

The fructan syndrome: Evolutionary aspects and common themes among plants and microbes

Fructans are multifunctional fructose-based water soluble carbohydrates found in all biological kingdoms but not in animals. Most research has focused on plant and microbial fructans and has received a growing interest because of their practical applications. Nevertheless, the origin of fructan production, the so-called "fructan syndrome," is still unknown. Why fructans only occur in a limited number of plant and microbial species remains unclear. In this review, we provide an overview of plant and microbial fructan research with a focus on fructans as an adaptation to the environment and their role in (a)biotic stress tolerance. The taxonomical and biogeographical distribution of fructans in both kingdoms is discussed and linked (where possible) to environmental factors. Overall, the fructan syndrome may be related to water scarcity and differences in physicochemical properties, for instance, water retaining characteristics, at least partially explain why different fructan types with different branching levels are found in different species. Although a close correlation between environmental stresses and fructan production is quite clear in plants, this link seems to be missing in microbes. We hypothesize that this can be at least partially explained by differential evolutionary timeframes for plants and microbes, combined with potential redundancy effects.

Stress-Inducible Galactinol Synthase of Chickpea (CaGolS) is Implicated in Heat and Oxidative Stress Tolerance Through Reducing Stress-Induced Excessive Reactive Oxygen Species Accumulation

Raffinose family oligosaccharides (RFOs) participate in various aspects of plant physiology, and galactinol synthase (GolS; EC 2.4.1.123) catalyzes the key step of RFO biosynthesis. Stress-induced accumulation of RFOs, in particular galactinol and raffinose, has been reported in a few plants; however, their precise role and mechanistic insight in stress adaptation remain elusive. In the present study, we have shown that the GolS activity as well as galactinol and raffinose content are significantly increased in response to various abiotic stresses in chickpea. Transcriptional analysis indicated that the CaGolS1 and CaGolS2 genes are induced in response to different abiotic stresses. Interestingly, heat and oxidative stress preferentially induce CaGolS1 over CaGolS2. In silco analysis revealed several common yet distinct cis-acting regulatory elements in their 5'-upstream regulatory sequences. Further, in vitro biochemical analysis revealed that the CaGolS1 enzyme functions better in stressful conditions than the CaGolS2 enzyme. Finally, Arabidopsis transgenic plants constitutively overexpressing CaGolS1 or CaGolS2 exhibit not only significantly increased galactinol but also raffinose content, and display better growth responses than wild-type or vector control plants when exposed to heat and oxidative stress. Further, improved tolerance of transgenic lines is associated with reduced accumulation of reactive oxygen species (ROS) and consequent lipid peroxidation as compared with control plants. Collectively, our data imply that GolS enzyme activity and consequent galactinol and raffinose content are significantly increased in response to stresses to mitigate stress-induced growth inhibition by restricting excessive ROS accumulation and consequent lipid peroxidation in plants.

Angiosperm Plant Desiccation Tolerance: Hints from Transcriptomics and Genome Sequencing

Desiccation tolerance (DT) in angiosperms is present in the small group of resurrection plants and in seeds. DT requires the presence of protective proteins, specific carbohydrates, restructuring of membrane lipids, and regulatory mechanisms directing a dedicated gene expression program. Many components are common to resurrection plants and seeds; however, some are specific for resurrection plants. Understanding how each component contributes to DT is challenging. Recent transcriptome analyses and genome sequencing indicate that increased expression is essential of genes encoding protective components, recently evolved, species-specific genes and non-protein-coding RNAs. Modification and reshuffling of existing cis-regulatory promoter elements seems to play a role in the rewiring of regulatory networks required for increased expression of DT-related genes in resurrection species.

An integrative overview of the molecular and physiological responses of sugarcane under drought conditions

Drought is the main abiotic stress constraining sugarcane production. However, our limited understanding of the molecular mechanisms involved in the drought stress responses of sugarcane impairs the development of new technologies to increase sugarcane drought tolerance. Here, an integrated approach was performed to reveal the molecular and physiological changes in two closely related sugarcane cultivars, including the most extensively planted cultivar in Brazil (cv. RB867515), in response to moderate (-0.5 MPa) and severe (-1 MPa) drought stress at the transcriptional, translational, and posttranslational levels. The results show common and cultivar exclusive changes in specific genes related to photosynthesis, carbohydrate, amino acid, and phytohormone metabolism. The novel phosphoproteomics and redox proteomic analysis revealed the importance of posttranslational regulation mechanisms during sugarcane drought stress. The shift to soluble sugar, secondary metabolite production, and activation of ROS eliminating processes in response to drought tolerance were mechanisms exclusive to cv. RB867515, helping to explain the better performance and higher production of this cultivar under these stress conditions.

Unravelling early events in the Taphrina deformans-Prunus persica interaction: an insight into the differential responses in resistant and susceptible genotypes

Leaf peach curl is a devastating disease affecting leaves, flowers and fruits, caused by the dimorphic fungus Taphrina deformans. To gain insight into the mechanisms of fungus pathogenesis and plant responses, leaves of a resistant and two susceptible Prunus persica genotypes were inoculated with blastospores (yeast), and the infection was monitored during 120 h post inoculation (h.p.i.). Fungal dimorphism to the filamentous form and induction of reactive oxygen species (ROS), callose synthesis, cell death and defence compound production were observed independently of the genotype. Fungal load significantly decreased after 120 h.p.i. in the resistant genotype, while the pathogen tended to grow in the susceptible genotypes. Metabolic profiling revealed a biphasic re-programming of plant tissue in susceptible genotypes, with an initial stage co-incident with the yeast form of the fungus and a second when the hypha is developed. Transcriptional analysis of PRs and plant hormone-related genes indicated that pathogenesis-related (PR) proteins are involved in P. persica defence responses against T. deformans and that salicylic acid is induced in the resistant genotype. Conducted experiments allowed the elucidation of common and differential responses in susceptible versus resistant genotypes and thus allow us to construct a picture of early events during T. deformans infection.

Silencing of Soybean Raffinose Synthase Gene Reduced Raffinose Family Oligosaccharides and Increased True Metabolizable Energy of Poultry Feed

Soybean [Glycine max (L.) Merr.] is the number one oil and protein crop in the United States, but the seed contains several anti-nutritional factors that are toxic to both humans and livestock. RNA interference technology has become an increasingly popular technique in gene silencing because it allows for both temporal and spatial targeting of specific genes. The objective of this research is to use RNA-mediated gene silencing to down-regulate the soybean gene raffinose synthase 2 (RS2), to reduce total raffinose content in mature seed. Raffinose is a trisaccharide that is indigestible to humans and monogastric animals, and as monogastric animals are the largest consumers of soy products, reducing raffinose would improve the nutritional quality of soybean. An RNAi construct targeting RS2 was designed, cloned, and transformed to the soybean genome via Agrobacterium-mediated transformation. Resulting plants were analyzed for the presence and number of copies of the transgene by PCR and Southern blot. The efficiency of mRNA silencing was confirmed by real-time quantitative PCR. Total raffinose content was determined by HPLC analysis. Transgenic plant lines were recovered that exhibited dramatically reduced levels of raffinose in mature seed, and these lines were further analyzed for other phenotypes such as development and yield. Additionally, a precision-fed rooster assay was conducted to measure the true metabolizable energy (TME) in full-fat soybean meal made from the wild-type or transgenic low-raffinose soybean lines. Transgenic low-raffinose soy had a measured TME of 2,703 kcal/kg, an increase as compared with 2,411 kcal/kg for wild-type. As low digestible energy is a major limiting factor in the percent of soybean meal that can be used in poultry diets, these results may substantiate the use of higher concentrations of low-raffinose, full-fat soy in formulated livestock diets.

Cell culture media supplemented with raffinose reproducibly enhances high mannose glycan formation

Glycosylation plays a pivotal role in pharmacokinetics and protein physiochemical characteristics. In particular, effector functions including antibody-dependent cell-mediated cytotoxicity (ADCC) can be desired, and it has been described that high-mannose species exhibited enhanced ADCC. In this work we present the trisaccharide raffinose as a novel cell culture medium supplement to promote high mannose N-glycans in fed-batch cultures, which is sought after in the development of biosimilars to match the quality profile of the reference medicinal product (RMP) also. Up to six-fold increases of high mannose species were observed with increasing raffinose concentrations in the medium of shaken 96-deepwell plates and shake tubes when culturing two different CHO cell lines in two different media. The findings were confirmed in a pH-, oxygen- and CO₂-controlled environment in lab-scale 3.5-L bioreactors. To circumvent detrimental effects on cell growth and productivity at high raffinose concentrations, the media osmolality was adjusted to reach the same value independently of the supplement concentration. Interestingly, raffinose predominantly enhanced mannose 5 glycans, and to a considerably smaller degree, mannose 6. While the underlying mechanism is still not fully understood, minor effects on the nucleotide sugar levels have been observed and transcriptomics analysis revealed that raffinose supplementation altered the expression levels of a number of glycosylation related genes. Among many genes, galactosyltransferase was downregulated and sialyltransferase upregulated. Our results highlight the potential of cell culture medium supplementation to modulate product quality.

Impacts of leaf age and heat stress duration on photosynthetic gas exchange and foliar nonstructural carbohydrates in Coffea arabica

Given future climate predictions of increased temperature, and frequency and intensity of heat waves in the tropics, suitable habitat to grow ecologically, economically, and socially valuable Coffea arabica is severely threatened. We investigated how leaf age and heat stress duration impact recovery from heat stress in C. arabica. Treated plants were heated in a growth chamber at 49°C for 45 or 90 min. Physiological recovery was monitored in situ using gas exchange, chlorophyll fluorescence (the ratio of variable to maximum fluorescence, FV/FM), and leaf nonstructural carbohydrate (NSC) on mature and expanding leaves before and 2, 15, 25, and 50 days after treatment. Regardless of leaf age, the 90-min treatment resulted in greater FV/FM reduction 2 days after treatment and slower recovery than the 45-min treatment. In both treatments, photosynthesis of expanding leaves recovered more slowly than in mature leaves. Stomatal conductance (gs) decreased in expanding leaves but did not change in mature leaves. These responses led to reduced intrinsic water-use efficiency with increasing heat stress duration in both age classes. Based on a leaf energy balance model, aftereffects of heat stress would be exacerbated by increases in leaf temperature at low gs under full sunlight where C. arabica is often grown, but also under partial sunlight. Starch and total NSC content of the 45-min group significantly decreased 2 days after treatment and then accumulated 15 and 25 days after treatment coinciding with recovery of photosynthesis and FV/FM. In contrast, sucrose of the 90-min group accumulated at day 2 suggesting that phloem transport was inhibited. Both treatment group responses contrasted with control plant total NSC and starch, which declined with time associated with subsequent flower and fruit production. No treated plants produced flowers or fruits, suggesting that short duration heat stress can lead to crop failure.