Genome-wide identification and expression analysis of the cucumber PYL gene family

Abscisic acid (ABA) is a very important hormone in plants. It regulates growth and development of plants and plays an important role in biotic and abiotic stresses. The Pyrabactin resistance 1-like (PYR/PYL) proteins play a central role in ABA signal transduction pathways. The working system of PYL genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. Through bioinformatics, a total of 14 individual PYL genes were identified in Chinese long ‘9930’ cucumber. Fourteen PYL genes were distributed on six chromosomes of cucumber, and their encoded proteins predicted to be distributed in cytoplasm and nucleus. Based on the phylogenetic analysis, the PYL genes of cucumber, Arabidopsis, rice, apple, Brachypodium distachyon and soybeancould be classified into three groups. Genetic structures and conserved domains analysis revealed that CsPYL genes in the same group have similar exons and conserved domains. By predicting cis-elements in the promoters, we found that all CsPYL members contained hormone and stress-related elements. Additionally, the expression patterns of CsPYL genes were specific in tissues. Finally, we further examined the expression of 14 CsPYL genes under ABA, PEG, salt stress. The qRT-PCR results showed that most PYL gene expression levels were up-regulated. Furthermore, with different treatments about 3h, the relative expression of PYL8 was up-regulated and more than 20 times higher than 0h. It indicated that this gene may play an important role in abiotic stress.

A Transcriptome Analysis Revealing the New Insight of Green Light on Tomato Plant Growth and Drought Stress Tolerance

Light plays a pivotal role in plant growth, development, and stress responses. Green light has been reported to enhance plant drought tolerance via stomatal regulation. However, the mechanisms of green light-induced drought tolerance in plants remain elusive. To uncover those mechanisms, we investigated the molecular responses of tomato plants under monochromatic red, blue, and green light spectrum with drought and well-water conditions using a comparative transcriptomic approach. The results showed that compared with monochromatic red and blue light treated plants, green light alleviated the drought-induced inhibition of plant growth and photosynthetic capacity, and induced lower stomatal aperture and higher ABA accumulation in tomato leaves after 9 days of drought stress. A total of 3,850 differentially expressed genes (DEGs) was identified in tomato leaves through pairwise comparisons. Functional annotations revealed that those DEGs responses to green light under drought stress were enriched in plant hormone signal transduction, phototransduction, and calcium signaling pathway. The DEGs involved in ABA synthesis and ABA signal transduction both participated in the green light-induced drought tolerance of tomato plants. Compared with ABA signal transduction, more DEGs related to ABA synthesis were detected under different light spectral treatments. The bZIP transcription factor- HY5 was found to play a vital role in green light-induced drought responses. Furthermore, other transcription factors, including WRKY46 and WRKY81 might participate in the regulation of stomatal aperture and ABA accumulation under green light. Taken together, the results of this study might expand our understanding of green light-modulated tomato drought tolerance via regulating ABA accumulation and stomatal aperture.

ABA-induced cytoplasmic translocation of COP1 enhances ROS accumulation through the HY5-ABI5 pathway to modulate seed germination

Seed germination is a physiological process regulated by multiple factors. Abscisic acid (ABA) can inhibit seed germination to improve seedling survival under conditions of abiotic stress, and this process is often regulated by light signals. Constitutive Photomorphogenic 1 (COP1) is an upstream core repressor of light signals, and is involved in several ABA responses. Here, we demonstrate that COP1 is a negative regulator of the ABA-mediated inhibition of seed germination. Disruption of COP1 enhanced Arabidopsis seed sensitivity to ABA and increased ROS levels. In seeds, ABA induced the translocation of COP1 to the cytoplasm, resulting in enhanced ABA-induced ROS levels. Genetic evidence indicated that HY5 and ABI5 act downstream of COP1 in the ABA-mediated inhibition of seed germination. ABA-induced COP1 cytoplasmic localization increased HY5 and ABI5 protein levels in the nucleus, leading to increased expression of ABI5 target genes and ROS levels in seeds. Together, our results reveal that ABA-induced cytoplasmic translocation of COP1 activates the HY5-ABI5 pathway to promote the expression of ABA-responsive genes and the accumulation of ROS during ABA-mediated inhibition of seed germination. These findings enhance the role of COP1 in the ABA signal transduction pathway.

Integrative Identification of Crucial Genes Associated With Plant Hormone-Mediated Bud Dormancy in Prunus mume

Prunus mume is an important ornamental woody plant with winter-flowering property, which is closely related to bud dormancy. Despite recent scientific headway in deciphering the mechanism of bud dormancy in P. mume, the overall picture of gene co-expression regulating P. mume bud dormancy is still unclear. Here a total of 23 modules were screened by weighted gene co-expression network analysis (WGCNA), of which 12 modules were significantly associated with heteroauxin, abscisic acid (ABA), and gibberellin (GA), including GA1, GA3, and GA4. The yellow module, which was positively correlated with the content of ABA and negatively correlated with the content of GA, was composed of 1,426 genes, among which 156 transcription factors (TFs) were annotated with transcriptional regulation function. An enrichment analysis revealed that these genes are related to the dormancy process and plant hormone signal transduction. Interestingly, the expression trends of PmABF2 and PmABF4 genes, the core members of ABA signal transduction, were positively correlated with P. mume bud dormancy. Additionally, the PmSVP gene had attracted lots of attention because of its co-expression, function enrichment, and expression level. PmABF2, PmABF4, and PmSVP were the genes with a high degree of expression in the co-expression network, which was upregulated by ABA treatment. Our results provide insights into the underlying molecular mechanism of plant hormone-regulated dormancy and screen the hub genes involved in bud dormancy in P. mume.

Plant Copper Amine Oxidases: Key Players in Hormone Signaling Leading to Stress-Induced Phenotypic Plasticity

Polyamines are ubiquitous, low-molecular-weight aliphatic compounds, present in living organisms and essential for cell growth and differentiation. Copper amine oxidases (CuAOs) oxidize polyamines to aminoaldehydes releasing ammonium and hydrogen peroxide, which participates in the complex network of reactive oxygen species acting as signaling molecules involved in responses to biotic and abiotic stresses. CuAOs have been identified and characterized in different plant species, but the most extensive study on a CuAO gene family has been carried out in Arabidopsis thaliana. Growing attention has been devoted in the last years to the investigation of the CuAO expression pattern during development and in response to an array of stress and stress-related hormones, events in which recent studies have highlighted CuAOs to play a key role by modulation of a multilevel phenotypic plasticity expression. In this review, the attention will be focused on the involvement of different AtCuAOs in the IAA/JA/ABA signal transduction pathways which mediate stress-induced phenotypic plasticity events.

The Arabidopsis SMALL AUXIN UP RNA32 Protein Regulates ABA-Mediated Responses to Drought Stress

SMALL AUXIN UP-REGULATED RNAs (SAURs) are recognized as auxin-responsive genes involved in the regulation of abiotic stress adaptive growth. Among the growth-limiting factors, water-deficit condition significantly affects plant growth and development. The putative function of SAUR family member AtSAUR32 has the potential to diminish the negative impact of drought stress, but the exact function and mode of action remain unclear in Arabidopsis. In the current study, AtSAUR32 gene was cloned and functionally analyzed. AtSAUR32 localized to the plasma membrane and nucleus was dominantly expressed in roots and highly induced by abscisic acid and drought treatment at certain time points. The stomatal closure and seed germination of saur32 were less sensitive to ABA relative to AtSAUR32-overexpressed line (OE32-5) and wild type (WT). Moreover, the saur32 mutant under drought stress showed increased ion leakage while quantum yield of photosystem II (ΦPSII) and endogenous ABA accumulation were reduced, along with the expression pattern of ABA/stress-responsive genes compared with WT and the OE32-5 transgenic line. Additionally, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that AtSAUR32 interacted with clade-A PP2C proteins (AtHAI1 and AtAIP1) to regulate ABA sensitivity in Arabidopsis. Taken together, these results indicate that AtSAUR32 plays an important role in drought stress adaptation via mediating ABA signal transduction.

Role of ABA in Overcoming Environmental Stress: Sensing, Signaling and Crosstalk

The Abscisic Acid (ABA) is an isoprenoid phytohormone, regulating various physiological processes ranging from stomatal opening to protein storage. Moreover, it provides adaptation to drought, salt and cold stresses acts also as a signaling mediator during the plant’s adaptive response to environmental conditions. In addition, numbers of transcription factors are involved in regulating the expression of ABA responsive genes by interacting with their respective cis-acting elements. ABA signal transduction initiates signal perception by ABA receptors and transfer via downstream proteins, including protein kinases and phosphatases. Hence, for improvement in plants-stress-tolerance capacity, it is necessary to understand the mechanism behind it. On this ground, this article lightens the importance and also the role of ABA signaling with regard to various stresses as well as regulation of ABA biosynthetic pathway along with the transcription factors for stress tolerance.

Suppressed ABA signal transduction in the spike promotes sucrose use in the stem and reduces grain number in wheat under water stress

Water stress is a primary trigger for reducing grain number per spike in wheat during the reproductive period. However, under stress conditions, the responses of plant organs and the interactions between them at the molecular and physiological levels remain unclear. In this study, when water stress occurred at the young microspore stage, RNA-seq data indicated that the spike had 970 differentially expressed genes, while the stem, comprising the two internodes below the spike (TIS), had 382. Abscisic acid (ABA) signal transduction genes were down-regulated by water stress in both these tissues, although to a greater extent in the TIS than in the spike. A reduction in sucrose was observed, and was accompanied by increases in cell wall invertase (CWIN) and sucrose:sucrose 1-fructosyl-transferase (1-SST) activities. Hexose and fructan were increased in the TIS but decreased in the spike. ABA was increased in the spike and TIS, and showed significant positive correlation with CWIN and 1-SST activities in the TIS. Overall, our results suggest that water stress induces the conversion of sucrose to hexose by CWIN, and to fructan by 1-SST, due to increased down-regulation of ABA signal transduction related-genes in the TIS; this leads to deficient sucrose supply to the spike and a decrease in grain number.

Structural Basis for Negative Regulation of ABA Signaling by ROP11 GTPase

Abscisic acid (ABA) is an essential plant hormone responsible for plant development and stress responses. Recent structural and biochemical studies have identified the key components involved in ABA signaling cascade, including PYR/PYL/RCAR receptors, protein phosphatases PP2C, and protein kinases SnRK2. The plant-specific, Roh-like (ROPs) small GTPases are negative regulators of ABA signal transduction by interacting with PP2C, which can shut off “leaky” ABA signal transduction caused by constitutive activity of monomeric PYR/PYL/RCAR receptors. However, the structural basis for negative regulation of ABA signaling by ROP GTPases remain elusive. In this study, we have utilized large-scale coarse-grained (10.05 milliseconds) and all-atom molecular dynamics simulations and standard protein-protein binding free energy calculations to predict the complex structure of AtROP11 and phosphatase AtABI1. In addition, we have elucidated the detailed complex association pathway and identified the critical residue pairs in AtROP11 and AtABI1 for complex stability. Overall, this study has established a powerful framework of using large-scale molecular simulations to predict unknown protein complex structures and elucidated the molecular mechanism of the negative regulation of ABA signal transduction by small GTPases.

MAP3Kinase-dependent SnRK2-kinase activation is required for abscisic acid signal transduction and rapid osmotic stress response

Abiotic stresses, including drought and salinity, trigger a complex osmotic-stress and abscisic acid (ABA) signal transduction network. The core ABA signalling components are snf1-related protein kinase2s (SnRK2s), which are activated by ABA-triggered inhibition of type-2C protein-phosphatases (PP2Cs). SnRK2 kinases are also activated by a rapid, largely unknown, ABA-independent osmotic-stress signalling pathway. Here, through a combination of a redundancy-circumventing genetic screen and biochemical analyses, we have identified functionally-redundant MAPKK-kinases (M3Ks) that are necessary for activation of SnRK2 kinases. These M3Ks phosphorylate a specific SnRK2/OST1 site, which is indispensable for ABA-induced reactivation of PP2C-dephosphorylated SnRK2 kinases. ABA-triggered SnRK2 activation, transcription factor phosphorylation and SLAC1 activation require these M3Ks in vitro and in plants. M3K triple knock-out plants show reduced ABA sensitivity and strongly impaired rapid osmotic-stress-induced SnRK2 activation. These findings demonstrate that this M3K clade is required for ABA- and osmotic-stress-activation of SnRK2 kinases, enabling robust ABA and osmotic stress signal transduction.