Physiological and Molecular Processes Associated with Long Duration of ABA Treatment

Alternative splicing as a driver of natural variation in abscisic acid response

Abscisic acid (ABA) is a crucial player in plant responses to the environment. It accumulates under stress, activating downstream signaling to implement molecular responses that restore homeostasis. Natural variance in ABA sensitivity remains barely understood, and the ABA pathway has been mainly studied at the transcriptional level, despite evidence that posttranscriptional regulation, namely, via alternative splicing, contributes to plant stress tolerance. Here, we identified the Arabidopsis accession Kn-0 as less sensitive to ABA than the reference Col-0, as shown by reduced effects of the hormone on seedling establishment, root branching, and stomatal closure, as well as by decreased induction of ABA marker genes. An in-depth comparative transcriptome analysis of the ABA response in the two variants revealed lower expression changes and fewer genes affected for the least ABA-sensitive ecotype. Notably, Kn-0 exhibited reduced levels of the ABA-signaling SnRK2 protein kinases and lower basal expression of ABA-reactivation genes, consistent with our finding that Kn-0 contains less endogenous ABA than Col-0. ABA also markedly affected alternative splicing, primarily intron retention, with Kn-0 being less responsive regarding both the number and magnitude of alternative splicing events, particularly exon skipping. We find that alternative splicing introduces a more ecotype-specific layer of ABA regulation and identify ABA-responsive splicing changes in key ABA pathway regulators that provide a functional and mechanistic link to the differential sensitivity of the two ecotypes. Our results offer new insight into the natural variation of ABA responses and corroborate a key role for alternative splicing in implementing ABA-mediated stress responses.

Excised leaves show limited and species-specific effects on photosynthetic parameters across crop functional types

Photosynthesis is increasingly becoming a recognized target for crop improvement. Phenotyping photosynthesis-related traits on field-grown material is a key bottleneck to progress here due to logistical barriers and short measurement days. Many studies attempt to overcome these challenges by phenotyping excised leaf material in the laboratory. To date there are no demonstrated examples of the representative nature of photosynthesis measurements performed on excised leaves relative to attached leaves in crops. Here, we tested whether standardized leaf excision on the day prior to phenotyping affected a range of common photosynthesis-related traits across crop functional types using tomato (C3 dicot), barley (C3 monocot), and maize (C4 monocot). Potentially constraining aspects of leaf physiology that could be predicted to impair photosynthesis in excised leaves, namely leaf water potential and abscisic acid accumulation, were not different between attached and excised leaves. We also observed non-significant differences in spectral reflectance and chlorophyll fluorescence traits between the treatments across the three species. However, we did observe some significant differences between traits associated with gas exchange and photosynthetic capacity across all three species. This study represents a useful reference for those who perform measurements of this nature and the differences reported should be considered in associated experimental design and statistical analyses.

Biochemical Response and Gene Expression to Water Deficit of Croatian Grapevine Cultivars (Vitis vinifera L.) and a Specimen of Vitis sylvestris

The biochemical response and gene expression in different grapevine cultivars to water deficit are still not well understood. In this study, we investigated the performance of four traditional Croatian Vitis vinifera L. cultivars ('Plavac mali crni', 'Istrian Malvasia', 'Graševina', and 'Tribidrag'), and one wild (Vitis vinifera subsp. sylvestris) genotype exposed to water deficit (WD) for nine days under semi-controlled conditions in the greenhouse. Sampling for biochemical and gene expression analyses was performed at days six and nine from the beginning of WD treatment. The WD affected the accumulation of metabolites with a significant increase in abscisic acid (ABA), salicylic acid (SA), and proline in the leaves of the stressed genotypes when the WD continued for nine days. Lipid peroxidation (MDA) was not significantly different from that of the control plants after six days of WD, whereas it was significantly lower (297.40 nmol/g dw) in the stressed plants after nine days. The cultivar 'Istrian Malvasia' responded rapidly to the WD and showed the highest and earliest increase in ABA levels (1.16 ng mg-1 dw, i.e., 3.4-fold increase compared to control). 'Graševina' differed significantly from the other genotypes in SA content at both time points analyzed (six and nine days, 47.26 and 49.63 ng mg-1 dw, respectively). Proline level increased significantly under WD (up to 5-fold at day nine), and proline variation was not genotype driven. The expression of aquaporin genes (TIP2;1 and PIP2;1) was down-regulated in all genotypes, coinciding with the accumulation of ABA. The gene NCED1 (9-cis-epoxycarotenoid dioxygenase) related to ABA was up-regulated in all genotypes under stress conditions and served as a reliable marker of drought stress. This work suggests that the stress response in metabolite synthesis and accumulation is complex, treatment- and genotype-dependent.

D, Olivo M, Urano D. Classification of Plant Endogenous States Using Machine Learning-Derived Agricultural Indices

Leaf color patterns vary depending on leaf age, pathogen infection, and environmental and nutritional stresses; thus, they are widely used to diagnose plant health statuses in agricultural fields. The visible-near infrared-shortwave infrared (VIS-NIR-SWIR) sensor measures the leaf color pattern from a wide spectral range with high spectral resolution. However, spectral information has only been employed to understand general plant health statuses (e.g., vegetation index) or phytopigment contents, rather than pinpointing defects of specific metabolic or signaling pathways in plants. Here, we report feature engineering and machine learning methods that utilize VIS-NIR-SWIR leaf reflectance for robust plant health diagnostics, pinpointing physiological alterations associated with the stress hormone, abscisic acid (ABA). Leaf reflectance spectra of wild-type, ABA2-overexpression, and deficient plants were collected under watered and drought conditions. Drought- and ABA-associated normalized reflectance indices (NRIs) were screened from all possible pairs of wavelength bands. Drought associated NRIs showed only a partial overlap with those related to ABA deficiency, but more NRIs were associated with drought due to additional spectral changes within the NIR wavelength range. Interpretable support vector machine classifiers built with 20 NRIs predicted treatment or genotype groups with an accuracy greater than those with conventional vegetation indices. Major selected NRIs were independent from leaf water content and chlorophyll content, 2 well-characterized physiological changes under drought. The screening of NRIs, streamlined with the development of simple classifiers, serves as the most efficient means of detecting reflectance bands that are highly relevant to characteristics of interest.

Global Proteome Profiling Revealed the Adaptive Reprogramming of Barley Flag Leaf to Drought and Elevated Temperature

Plants, as sessile organisms, have developed sophisticated mechanisms to survive in changing environments. Recent advances in omics approaches have facilitated the exploration of plant genomes; however, the molecular mechanisms underlying the responses of barley and other cereals to multiple abiotic stresses remain largely unclear. Exposure to stress stimuli affects many proteins with regulatory and protective functions. In the present study, we employed liquid chromatography coupled with high-resolution mass spectrometry to identify stress-responsive proteins on the genome-wide scale of barley flag leaves exposed to drought, heat, or both. Profound alterations in the proteome of genotypes with different flag leaf sizes were found. The role of stress-inducible proteins was discussed and candidates underlying the universal stress response were proposed, including dehydrins. Moreover, the putative functions of several unknown proteins that can mediate responses to stress stimuli were explored using Pfam annotation, including calmodulin-like proteins. Finally, the confrontation of protein and mRNA abundances was performed. A correlation network between transcripts and proteins performance revealed several components of the stress-adaptive pathways in barley flag leaf. Taking the findings together, promising candidates for improving the tolerance of barley and other cereals to multivariate stresses were uncovered. The presented proteomic landscape and its relationship to transcriptomic remodeling provide novel insights for understanding the molecular responses of plants to environmental cues.

SlERF.J2 reduces chlorophyll accumulation and inhibits chloroplast biogenesis and development in tomato leaves

Chlorophyll metabolism and chloroplast biogenesis in tomato (Solanum lycopersicum) leaves contribute to photosynthesis; however, their molecular mechanisms are poorly understood. In this study, we found that overexpression of SlERF.J2 (ethylene transcription factor) resulted in a decrease in leaf chlorophyll content and reduced accumulation of starch and soluble sugar. The slerf.j2 knockout mutant showed no apparent change. Further observation of tissue sections and transmission electron microscopy (TEM) showed that SlERF.J2 was involved in chlorophyll accumulation and chloroplast formation. RNA-seq of mature SlERF.J2-OE leaves showed that many genes involved in chlorophyll biosynthesis and chloroplast formation were significantly downregulated compared with those in WT leaves. Genome global scanning of the ERF TF binding site combined with RNA-seq differential gene expression and qRT-PCR detection analysis showed that COP1 was a potential target gene of SlERF.J2. Tobacco transient expression technology, a dual-luciferase reporter system and Y1H technology were employed to verify that SlERF.J2 could bind to the COP1 promoter. Notably, overexpression of SlERF.J2 in Nr mutants resulted in impaired chloroplast biogenesis and development. Taken together, our findings demonstrated that SlERF.J2 plays an essential role in chlorophyll accumulation and chloroplast formation, laying a foundation for enhancing plant photosynthesis.

Terpenoid Transport in Plants: How Far from the Final Picture?

Contrary to the biosynthetic pathways of many terpenoids, which are well characterized and elucidated, their transport inside subcellular compartments and the secretion of reaction intermediates and final products at the short- (cell-to-cell), medium- (tissue-to-tissue), and long-distance (organ-to-organ) levels are still poorly understood, with some limited exceptions. In this review, we aim to describe the state of the art of the transport of several terpene classes that have important physiological and ecological roles or that represent high-value bioactive molecules. Among the tens of thousands of terpenoids identified in the plant kingdom, only less than 20 have been characterized from the point of view of their transport and localization. Most terpenoids are secreted in the apoplast or stored in the vacuoles by the action of ATP-binding cassette (ABC) transporters. However, little information is available regarding the movement of terpenoid biosynthetic intermediates from plastids and the endoplasmic reticulum to the cytosol. Through a description of the transport mechanisms of cytosol- or plastid-synthesized terpenes, we attempt to provide some hypotheses, suggestions, and general schemes about the trafficking of different substrates, intermediates, and final products, which might help develop novel strategies and approaches to allow for the future identification of terpenoid transporters that are still uncharacterized.

Transcriptome profiling disclosed the effect of single and combined drought and heat stress on reprogramming of genes expression in barley flag leaf

Despite numerous studies aimed at unraveling the genetic background of barley's response to abiotic stress, the modulation of the transcriptome induced by combinatorial drought and increased temperature remains largely unrecognized. Very limited studies were done, especially on the flag leaf, which plays an important role in grain filling in cereals. In the present study, transcriptome profiles, along with chlorophyll fluorescence parameters and yield components, were compared between barley genotypes with different flag leaf sizes under single and combined drought and heat stress. High-throughput mRNA sequencing revealed 2,457 differentially expressed genes, which were functionally interpreted using Gene Ontology term enrichment analysis. The transcriptomic signature under double stress was more similar to effects caused by drought than by elevated temperature; it was also manifested at phenotypic and chlorophyll fluorescence levels. Both common and stress-specific changes in transcript abundance were identified. Genes regulated commonly across stress treatments, determining universal stress responses, were associated, among others, with responses to drought, heat, and oxidative stress. In addition, changes specific to the size of the flag leaf blade were found. Our study allowed us to identify sets of genes assigned to various processes underlying the response to drought and heat, including photosynthesis, the abscisic acid pathway, and lipid transport. Genes encoding LEA proteins, including dehydrins and heat shock proteins, were especially induced by stress treatments. Some association between genetic composition and flag leaf size was confirmed. However, there was no general coincidence between SNP polymorphism of genotypes and differential expression of genes induced by stress factors. This research provided novel insight into the molecular mechanisms of barley flag leaf that determine drought and heat response, as well as their co-occurrence.

The Role of ABA in the Interaction between Citrus Fruit and Penicillium digitatum

Abscisic acid (ABA) protects citrus fruit against Penicillium digitatum infection. The global mechanisms involved in the role of ABA in the P. digitatum-citrus fruit interaction are unknown. Here, we determine the transcriptome differences between the Navelate (Citrus sinensis (L.) Osbeck) orange and its ABA-deficient mutant Pinalate, which is less resistant to infection. Low ABA levels may affect both the constitutive mechanisms that protect citrus fruit against P. digitatum and early responses to infection. The repression of terpenoid, phenylpropanoid and glutation metabolism; of oxidation-reduction processes; and of processes related to the defense response to fungus and plant hormone signal transduction may be one part of the constitutive defense reduced in the mutant against P. digitatum. Our results also provide potential targets for developing P. digitatum-citrus fruit-resistant varieties. Of those up-regulated by ABA, a thaumatin protein and a bifunctional inhibitor/LTP, which are relevant in plant immunity, were particularly remarkable. It is also worth highlighting chlorophyllase 1 (CLH1), induced by infection in Pinalate, and the OXS3 gene, which was down-regulated by ABA, because the absence of OXS3 activates ABA-responsive genes in plants.

E3 ligase BRUTUS Is a Negative Regulator for the Cellular Energy Level and the Expression of Energy Metabolism-Related Genes Encoded by Two Organellar Genomes in Leaf Tissues

E3 ligase BRUTUS (BTS), a putative iron sensor, is expressed in both root and shoot tissues in seedlings of Arabidopsis thaliana. The role of BTS in root tissues has been well established. However, its role in shoot tissues has been scarcely studied. Comparative transcriptome analysis with shoot and root tissues revealed that BTS is involved in regulating energy metabolism by modulating expression of mitochondrial and chloroplast genes in shoot tissues. Moreover, in shoot tissues of bts-1 plants, levels of ADP and ATP and the ratio of ADP/ATP were greatly increased with a concomitant decrease in levels of soluble sugar and starch. The decreased starch level in bts-1 shoot tissues was restored to the level of shoot tissues of wild-type plants upon vanadate treatment. Through this study, we expand the role of BTS to regulation of energy metabolism in the shoot in addition to its role of iron deficiency response in roots.

Cytosolic and Nucleosolic Calcium-Regulated Molecular Networks in Response to Long-Term Treatment with Abscisic Acid and Methyl Jasmonate in Arabidopsis thaliana

Calcium acts as a universal secondary messenger that transfers developmental cues and stress signals for gene expression and adaptive growth. A prior study showed that abiotic stresses induce mutually independent cytosolic Ca²⁺ ([Ca²⁺]_cyt) and nucleosolic Ca²⁺ ([Ca²⁺]_nuc) increases in Arabidopsis thaliana root cells. However, gene expression networks deciphering [Ca²⁺]_cyt and [Ca²⁺]_nuc signalling pathways remain elusive. Here, using transgenic A. thaliana to selectively impair abscisic acid (ABA)- or methyl jasmonate (MeJA)-induced [Ca²⁺]_cyt and [Ca²⁺]_nuc increases, we identified [Ca²⁺]_cyt- and [Ca²⁺]_nuc-regulated ABA- or MeJA-responsive genes with a genome oligo-array. Gene co-expression network analysis revealed four Ca²⁺ signal-decoding genes, CAM1, CIPK8, GAD1, and CPN20, as hub genes co-expressed with Ca²⁺-regulated hormone-responsive genes and hormone signalling genes. Luciferase complementation imaging assays showed interactions among CAM1, CIPK8, and GAD1; they also showed interactions with several proteins encoded by Ca²⁺-regulated hormone-responsive genes. Furthermore, CAM1 and CIPK8 were required for MeJA-induced stomatal closure; they were associated with ABA-inhibited seed germination. Quantitative reverse transcription polymerase chain reaction analysis showed the unique expression pattern of [Ca²⁺]-regulated hormone-responsive genes in cam1, cipk8, and gad1. This comprehensive understanding of distinct Ca²⁺ and hormonal signalling will allow the application of approaches to uncover novel molecular foundations for responses to developmental and stress signals in plants.

Long-term abscisic acid promotes golden2-like1 degradation through constitutive photomorphogenic 1 in a light intensity-dependent manner to suppress chloroplast development

Abiotic stress, a serious threat to plants, occurs for extended periods in nature. Abscisic acid (ABA) plays a critical role in abiotic stress responses in plants. Therefore, stress responses mediated by ABA have been studied extensively, especially in short-term responses. However, long-term stress responses mediated by ABA remain largely unknown. To elucidate the mechanism by which plants respond to prolonged abiotic stress, we used long-term ABA treatment that activates the signalling against abiotic stress such as dehydration and investigated mechanisms underlying the responses. Long-term ABA treatment activates constitutive photomorphogenic 1 (COP1). Active COP1 mediates the ubiquitination of golden2-like1 (GLK1) for degradation, contributing to lowering expression of photosynthesis-associated genes such as glutamyl-tRNA reductase (HEMA1) and protochlorophyllide oxidoreductase A (PORA), resulting in the suppression of chloroplast development. Moreover, COP1 activation and GLK1 degradation upon long-term ABA treatment depend on light intensity. Additionally, plants with COP1 mutation or exposed to higher light intensity were more sensitive to salt stress. Collectively, our results demonstrate that long-term treatment of ABA leads to activation of COP1 in a light intensity-dependent manner for GLK1 degradation to suppress chloroplast development, which we propose to constitute a mechanism of balancing normal growth and stress responses upon the long-term abiotic stress.

The Plastid-Localized AtFtsHi3 Pseudo-Protease of Arabidopsis thaliana Has an Impact on Plant Growth and Drought Tolerance

While drought severely affects plant growth and crop production, the molecular mechanisms of the drought response of plants remain unclear. In this study, we demonstrated for the first time the effect of the pseudo-protease AtFtsHi3 of Arabidopsis thaliana on overall plant growth and in drought tolerance. An AtFTSHi3 knock-down mutant [ftshi3-1(kd)] displayed a pale-green phenotype with lower photosynthetic efficiency and Darwinian fitness compared to wild type (Wt). An observed delay in seed germination of ftshi3-1(kd) was attributed to overaccumulation of abscisic acid (ABA); ftshi3-1(kd) seedlings showed partial sensitivity to exogenous ABA. Being exposed to similar severity of soil drying, ftshi3-1(kd) was drought-tolerant up to 20 days after the last irrigation, while wild type plants wilted after 12 days. Leaves of ftshi3-1(kd) contained reduced stomata size, density, and a smaller stomatic aperture. During drought stress, ftshi3-1(kd) showed lowered stomatal conductance, increased intrinsic water-use efficiency (WUEi), and slower stress acclimation. Expression levels of ABA-responsive genes were higher in leaves of ftshi3-1(kd) than Wt; DREB1A, but not DREB2A, was significantly upregulated during drought. However, although ftshi3-1(kd) displayed a drought-tolerant phenotype in aboveground tissue, the root-associated bacterial community responded to drought.

GmLCLs negatively regulate ABA perception and signalling genes in soybean leaf dehydration response

The circadian clock allows plants to actively adapt to daily environmental changes through temporal regulation of physiological traits. In response to drought stress, circadian oscillators gate ABA signalling, but the molecular mechanisms remain unknown, especially in crops. Here, we investigated the role of soybean circadian oscillators GmLCLa1, GmLCLa2, GmLCLb1 and GmLCLb2 in leaf water stress response. Under dehydration stress, the GmLCL quadruple mutant had decreased leaf water loss. We found that the dehydration treatment delayed the peak expression of GmLCL genes by 4 hr. In addition, the circadian clock in hairy roots also responded to ABA, which led to a free-running rhythm with shortened period. Importantly, in the gmlclq quadruple mutant, diurnal expression phases of several circadian-regulated ABA receptor, ABA catabolism and ABA signalling-related genes were shifted significantly to daytime. Moreover, in the gmlclq mutant leaf, expression of GmPYL17, GmCYP707A, GmABI2 and GmSnRK2s was increased under water dehydration stress. In summary, our results show that GmLCLs act as negative regulators of ABA signalling in leaves during dehydration response.

Chloride as a macronutrient increases water-use efficiency by anatomically driven reduced stomatal conductance and increased mesophyll diffusion to CO2

Chloride (Cl- ) has been recently described as a beneficial macronutrient, playing specific roles in promoting plant growth and water-use efficiency (WUE). However, it is still unclear how Cl- could be beneficial, especially in comparison with nitrate (NO3- ), an essential source of nitrogen that shares with Cl- similar physical and osmotic properties, as well as common transport mechanisms. In tobacco plants, macronutrient levels of Cl- specifically reduce stomatal conductance (gs ) without a concomitant reduction in the net photosynthesis rate (AN ). As stomata-mediated water loss through transpiration is inherent in the need of C3 plants to capture CO2 , simultaneous increase in photosynthesis and WUE is of great relevance to achieve a sustainable increase in C3 crop productivity. Our results showed that Cl- -mediated stimulation of larger leaf cells leads to a reduction in stomatal density, which in turn reduces gs and water consumption. Conversely, Cl- improves mesophyll diffusion conductance to CO2 (gm ) and photosynthetic performance due to a higher surface area of chloroplasts exposed to the intercellular airspace of mesophyll cells, possibly as a consequence of the stimulation of chloroplast biogenesis. A key finding of this study is the simultaneous improvement of AN and WUE due to macronutrient Cl- nutrition. This work identifies relevant and specific functions in which Cl- participates as a beneficial macronutrient for higher plants, uncovering a sustainable approach to improve crop yield.