An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response

Integrating multi-omics data reveals energy and stress signaling activated by abscisic acid in Arabidopsis

Phytohormones are essential signaling molecules regulating various processes in growth, development, and stress responses. Genetic and molecular studies, especially using Arabidopsis thaliana (Arabidopsis), have discovered many important players involved in hormone perception, signal transduction, transport, and metabolism. Phytohormone signaling pathways are extensively interconnected with other endogenous and environmental stimuli. However, our knowledge of the huge and complex molecular network governed by a hormone remains limited. Here we report a global overview of downstream events of an abscisic acid (ABA) receptor, REGULATORY COMPONENTS OF ABA RECEPTOR (RCAR) 6 (also known as PYRABACTIN RESISTANCE 1 [PYR1]-LIKE [PYL] 12), by integrating phosphoproteomic, proteomic and metabolite profiles. Our data suggest that the RCAR6 overexpression constitutively decreases the protein levels of its coreceptors, namely clade A protein phosphatases of type 2C, and activates sucrose non-fermenting-1 (SNF1)-related protein kinase 1 (SnRK1) and SnRK2, the central regulators of energy and ABA signaling pathways. Furthermore, several enzymes in sugar metabolism were differentially phosphorylated and expressed in the RCAR6 line, and the metabolite profile revealed altered accumulations of several organic acids and amino acids. These results indicate that energy- and water-saving mechanisms mediated by the SnRK1 and SnRK2 kinases, respectively, are under the control of the ABA receptor-coreceptor complexes.

Sucrose-associated SnRK1a1-mediated phosphorylation of Opaque2 modulates endosperm filling in maize

During maize endosperm filling, sucrose not only serves as a source of carbon skeletons for storage-reserve synthesis but also acts as a stimulus to promote this process. However, the molecular mechanisms underlying sucrose and endosperm filling are poorly understood. In this study, we found that sucrose promotes the expression of endosperm-filling hub gene Opaque2 (O2), coordinating with storage-reserve accumulation. We showed that the protein kinase SnRK1a1 can attenuate O2-mediated transactivation, but sucrose can release this suppression. Biochemical assays revealed that SnRK1a1 phosphorylates O2 at serine 41 (S41), negatively affecting its protein stability and transactivation ability. We observed that mutation of SnRK1a1 results in larger seeds with increased kernel weight and storage reserves, while overexpression of SnRK1a1 causes the opposite effect. Overexpression of the native O2 (O2-OE), phospho-dead (O2-SA), and phospho-mimetic (O2-SD) variants all increased 100-kernel weight. Although O2-SA seeds exhibit smaller kernel size, they have higher accumulation of starch and proteins, resulting in larger vitreous endosperm and increased test weight. O2-SD seeds display larger kernel size but unchanged levels of storage reserves and test weight. O2-OE seeds show elevated kernel dimensions and nutrient storage, like a mixture of O2-SA and O2-SD seeds. Collectively, our study discovers a novel regulatory mechanism of maize endosperm filling. Identification of S41 as a SnRK1-mediated phosphorylation site in O2 offers a potential engineering target for enhancing storage-reserve accumulation and yield in maize.

ABI5 binding proteins: key players in coordinating plant growth and development

During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants' morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants' growth and development.

DOMAIN OF UNKNOWN FUNCTION581-9 negatively regulates SnRK1 kinase activity

In plants, sucrose nonfermenting 1 (SNF1)-related protein kinase 1 (SnRK1) is a key energy sensor that orchestrates large-scale transcriptional reprograming to maintain cellular homeostasis under energy deficit. SnRK1 activity is under tight negative control, although the exact mechanisms leading to its activation are not well understood. We show that the Arabidopsis (Arabidopsis thaliana) DOMAIN OF UNKNOWN FUNCTION (DUF581) protein DUF581-9/FCS-like zinc finger 3 binds to the catalytic SnRK1.1 α subunit (KIN10) to inhibit its activation by geminivirus rep-interacting kinase (GRIK)-dependent T-loop phosphorylation. Overexpression of DUF581-9 in Arabidopsis dampens SnRK1 signaling and interferes with adaptation to dark-induced starvation. The presence of DUF581-9 significantly reduced SnRK1 activity in protoplasts and in vitro. This was accompanied by a reduction in T175 T-loop phosphorylation and also diminished KIN10 auto-phosphorylation. Furthermore, DUF581-9 reduced binding of the upstream activating kinase GRIK2 to KIN10, explaining the reduced KIN10 T-loop phosphorylation. Ectopically expressed DUF581-9 protein was rapidly turned over by the proteasome when Arabidopsis plants were subjected to starvation treatment, likely releasing its inhibitory activity on the SnRK1 complex. Taken together, our results support a model in which DUF581-9 negatively regulates SnRK1 activity under energy sufficient conditions. Turnover of the protein provides a rapid way for SnRK1 activation under energy deficit without the need of de novo protein synthesis.

The Time-Resolved Salt Stress Response of Dunaliella tertiolecta-A Comprehensive System Biology Perspective

Algae-driven processes, such as direct CO2 fixation into glycerol, provide new routes for sustainable chemical production in synergy with greenhouse gas mitigation. The marine microalgae Dunaliella tertiolecta is reported to accumulate high amounts of intracellular glycerol upon exposure to high salt concentrations. We have conducted a comprehensive, time-resolved systems biology study to decipher the metabolic response of D. tertiolecta up to 24 h under continuous light conditions. Initially, due to a lack of reference sequences required for MS/MS-based protein identification, a high-quality draft genome of D. tertiolecta was generated. Subsequently, a database was designed by combining the genome with transcriptome data obtained before and after salt stress. This database allowed for detection of differentially expressed proteins and identification of phosphorylated proteins, which are involved in the short- and long-term adaptation to salt stress, respectively. Specifically, in the rapid salt adaptation response, proteins linked to the Ca2+ signaling pathway and ion channel proteins were significantly increased. While phosphorylation is key in maintaining ion homeostasis during the rapid adaptation to salt stress, phosphofructokinase is required for long-term adaption. Lacking β-carotene, synthesis under salt stress conditions might be substituted by the redox-sensitive protein CP12. Furthermore, salt stress induces upregulation of Calvin-Benson cycle-related proteins.

SnRK1 kinase-mediated phosphorylation of transcription factor bZIP39 regulates sorbitol metabolism in apple

Sorbitol is a major photosynthate produced in leaves and transported through the phloem of apple (Malus domestica) and other tree fruits in Rosaceae. Sorbitol stimulates its own metabolism, but the underlying molecular mechanism remains unknown. Here, we show that sucrose nonfermenting 1 (SNF1)-related protein kinase 1 (SnRK1) is involved in regulating the sorbitol-responsive expression of both SORBITOL DEHYDROGENASE 1 (SDH1) and ALDOSE-6-PHOSPHATE REDUCTASE (A6PR), encoding 2 key enzymes in sorbitol metabolism. SnRK1 expression is increased by feeding of exogenous sorbitol but decreased by sucrose. SnRK1 interacts with and phosphorylates the basic leucine zipper (bZIP) transcription factor bZIP39. bZIP39 binds to the promoters of both SDH1 and A6PR and activates their expression. Overexpression of SnRK1 in 'Royal Gala' apple increases its protein level and activity, upregulating transcript levels of both SDH1 and A6PR without altering the expression of bZIP39. Of all the sugars tested, sorbitol is the only 1 that stimulates SDH1 and A6PR expression, and this stimulation is blocked by RNA interference (RNAi)-induced repression of either SnRK1 or bZIP39. These findings reveal that sorbitol acts as a signal regulating its own metabolism via SnRK1-mediated phosphorylation of bZIP39, which integrates sorbitol signaling into the SnRK1-mediated sugar signaling network to modulate plant carbohydrate metabolism.

The changing landscape of agriculture: role of precision breeding in developing smart crops

Food plants play a crucial role in human survival, providing them essential nutrients. However, traditional breeding methods have not been able to keep up with the demands of the growing population. The improvement of food plants aims to increase yield, quality, and resistance to biotic and abiotic stresses. With CRISPR/Cas9, researchers can identify and edit key genes conferring desirable qualities in agricultural plants, including increased yield, enhanced product quality attributes, and increased tolerance to biotic and abiotic challenges. These modifications have enabled the creation of "smart crops" that exhibit rapid climatic adaptation, resistance to extreme weather conditions and high yield and quality. The use of CRISPR/Cas9 combined with viral vectors or growth regulators has made it possible to produce more efficient modified plants with certain conventional breeding methods. However, ethical and regulatory aspects of this technology must be carefully considered. Proper regulation and application of genome editing technology can bring immense benefits to agriculture and food security. This article provides an overview of genetically modified genes and conventional as well as emerging tools, including CRISPR/Cas9, that have been utilized to enhance the quality of plants/fruits and their products. The review also discusses the challenges and prospects associated with these techniques.

Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis

Plant functioning and responses to abiotic stresses largely involve regulations at the transcriptomic level via complex interactions of signal molecules, signaling cascades, and regulators. Nevertheless, all the signaling networks involved in responses to abiotic stresses have not yet been fully established. The in-depth analysis of transcriptomes in stressed plants has become a relevant state-of-the-art methodology to study these regulations and signaling pathways that allow plants to cope with or attempt to survive abiotic stresses. The plant science and molecular biology community has developed databases about genes, proteins, protein-protein interactions, protein-DNA interactions and ontologies, which are valuable sources of knowledge for deciphering such regulatory and signaling networks. The use of these data and the development of bioinformatics tools help to make sense of transcriptomic data in specific contexts, such as that of abiotic stress signaling, using functional biological approaches. The aim of this chapter is to present and assess some of the essential online tools and resources that will allow novices in bioinformatics to decipher transcriptomic data in order to characterize the cellular processes and functions involved in abiotic stress responses and signaling. The analysis of case studies further describes how these tools can be used to conceive signaling networks on the basis of transcriptomic data. In these case studies, particular attention was paid to the characterization of abiotic stress responses and signaling related to chemical and xenobiotic stressors.

Fast Identification of In Vivo Protein Phosphorylation Events Using Transient Expression in Leaf Mesophyll Protoplasts and Phos-tagTM SDS-PAGE

Phosphorylation/dephosphorylation is a key posttranslational mechanism for signal transduction and amplification. Several techniques exist for assessing protein phosphorylation status, but each has its own drawbacks. The fast, straightforward, and low-tech approach described here uses transient overexpression of peptide-tagged proteins in Arabidopsis leaf mesophyll protoplasts and immunoblotting with Phos-tag™ SDS-PAGE and commercial anti-tag antibodies. We illustrate this with two relevant examples related to the SnRK1 protein kinase, which mediates metabolic stress signaling: Arabidopsis thaliana SnRK1 activation by T-loop (auto-)phosphorylation and SnRK1 phosphorylation of the Arabidopsis RAV1 transcription factor, which is involved in seed germination and early seedling development.

Compartmentalization, a key mechanism controlling the multitasking role of the SnRK1 complex

SNF1-related protein kinase 1 (SnRK1), the plant ortholog of mammalian AMP-activated protein kinase/fungal (yeast) Sucrose Non-Fermenting 1 (AMPK/SNF1), plays a central role in metabolic responses to reduced energy levels in response to nutritional and environmental stresses. SnRK1 functions as a heterotrimeric complex composed of a catalytic α- and regulatory β- and βγ-subunits. SnRK1 is a multitasking protein involved in regulating various cellular functions, including growth, autophagy, stress response, stomatal development, pollen maturation, hormone signaling, and gene expression. However, little is known about the mechanism whereby SnRK1 ensures differential execution of downstream functions. Compartmentalization has been recently proposed as a new key mechanism for regulating SnRK1 signaling in response to stimuli. In this review, we discuss the multitasking role of SnRK1 signaling associated with different subcellular compartments.

Long-Chain Acyl-CoA Synthetases Promote Poplar Resistance to Abiotic Stress by Regulating Long-Chain Fatty Acid Biosynthesis

Long-chain acyl-CoA synthetases (LACSs) catalyze fatty acids (FAs) to form fatty acyl-CoA thioesters, which play essential roles in FA and lipid metabolisms and cuticle wax biosynthesis. Although LACSs from Arabidopsis have been intensively studied, the characterization and function of LACSs from poplar are unexplored. Here, 10 poplar PtLACS genes were identified from the poplar genome and distributed to eight chromosomes. A phylogenetic tree indicated that PtLACSs are sorted into six clades. Collinearity analysis and duplication events demonstrated that PtLACSs expand through segmental replication events and experience purifying selective pressure during the evolutionary process. Expression patterns revealed that PtLACSs have divergent expression changes in response to abiotic stress. Interaction proteins and GO analysis could enhance the understanding of putative interactions among protein and gene regulatory networks related to FA and lipid metabolisms. Cluster networks and long-chain FA (LCFA) and very long-chain FA (VLCFA) content analysis revealed the possible regulatory mechanism in response to drought and salt stresses in poplar. The present study provides valuable information for the functional identification of PtLACSs in response to abiotic stress metabolism in poplar.

Mechanisms Regulating Energy Homeostasis in Plant Cells and Their Potential to Inspire Electrical Microgrids Models

In this paper, the main features of systems that are required to flexibly modulate energy states of plant cells in response to environmental fluctuations are surveyed and summarized. Plant cells possess multiple sources (chloroplasts and mitochondria) to produce energy that is consumed to drive many processes, as well as mechanisms that adequately provide energy to the processes with high priority depending on the conditions. Such energy-providing systems are tightly linked to sensors that monitor the status of the environment and inside the cell. In addition, plants possess the ability to efficiently store and transport energy both at the cell level and at a higher level. Furthermore, these systems can finely tune the various mechanisms of energy homeostasis in plant cells in response to the changes in environment, also assuring the plant survival under adverse environmental conditions. Electrical power systems are prone to the effects of environmental changes as well; furthermore, they are required to be increasingly resilient to the threats of extreme natural events caused, for example, by climate changes, outages, and/or external deliberate attacks. Starting from this consideration, similarities between energy-related processes in plant cells and electrical power grids are identified, and the potential of mechanisms regulating energy homeostasis in plant cells to inspire the definition of new models of flexible and resilient electrical power grids, particularly microgrids, is delineated. The main contribution of this review is surveying energy regulatory mechanisms in detail as a reference and helping readers to find useful information for their work in this research field.

ABI5 binding protein2 inhibits ABA responses during germination without ABA-INSENSITIVE5 degradation

Overexpression of ABA-INSENSITIVE5 binding proteins (AFPs) results in extreme ABA resistance of seeds and failure to acquire desiccation tolerance, at least in part through effects on chromatin modification. We tested the hypothesis that AFPs promote germination in Arabidopsis (Arabidopsis thaliana) by also functioning as adapters for E3 ligases that ubiquitinate ABI5, leading to its degradation. Interactions between AFPs and two well-characterized classes of E3 ligases targeting ABI5, DWD HYPERSENSITIVE TO ABA (DWA)s and KEEP ON GOING, were analyzed by yeast two-hybrid, bimolecular fluorescence complementation, and genetic assays. Although weak direct interactions were detected between AFPs and E3 ligases, loss of function for these E3 ligases did not impair ABA-resistance conferred by overexpression of the YFP-AFP2 fusion. Comparison of ABI5 and AFP2 levels in these lines showed that AFP2 accumulation increased during germination, but that ABI5 degradation followed germination, demonstrating that AFP2 overexpression reduces ABA sensitivity, thereby permitting germination prior to ABI5 degradation. Surprisingly, AFP2 overexpression in the dwa1 dwa2 mutant background produced the unusual combination of extreme ABA resistance and desiccation tolerance, creating an opportunity to separate the underlying biochemical characteristics of ABA sensitivity and desiccation tolerance. Our quantitative proteomics analysis identified at least three-fold more differentially accumulated seed proteins than previous studies. Comparison of dry seed proteomes of wild-type or dwa1 dwa2 mutants with or without AFP2 overexpression allowed us to separate and refine the changes in protein accumulation patterns associated with desiccation tolerance independently of ABA sensitivity, or vice versa, to a subset of cold-induced and defense stress-responsive proteins and signaling regulators.

CBF4/DREB1D represses XERICO to attenuate ABA, osmotic and drought stress responses in Arabidopsis

Water stress can severely impact plant growth, productivity and yield. Consequently, plants have evolved various strategies through which they can respond and adapt to their environment. XERICO (XER) is a stress-responsive RING E3 ubiquitin ligase that modulates abscisic acid (ABA) levels and promotes drought tolerance when overexpressed. To better understand the biological role of XER in stress responses, we characterized a xer-1 hypomorphic mutant and a CRISPR/Cas9-induced xer-2 null mutant in Arabidopsis. Both xer mutant alleles exhibited increased drought sensitivity, supporting the results from overexpression studies. Furthermore, we discovered that both xer mutants have greater stomatal indices and that XER is expressed in epidermal cells, indicating that XER functions in the epidermis to repress stomatal development. To explore XER spatiotemporal and stress-dependent regulation, we conducted a yeast one-hybrid screen and found that CBF4/DREB1D associates with the XER 5' untranslated region (5'-UTR). We generated three cbf4 null mutants with CRISPR/Cas9 and showed that CBF4 negatively regulates ABA responses, promotes stomatal development and reduces drought tolerance, in contrast to the roles shown for XER. CBF4 is induced by ABA and osmotic stress, and localizes to the nucleus where it downregulates XER expression via the DRE element in its 5'-UTR. Lastly, genetic interaction studies confirmed that xer is epistatic to cbf4 in stomatal development and in ABA, osmotic and drought stress responses. We propose that the repression of XER by CBF4 functions to attenuate ABA signaling and stress responses to maintain a balance between plant growth and survival under adverse environmental conditions.

Regulatory Mechanism of the Constitutive Photomorphogenesis 9 Signalosome Complex in Response to Abiotic Stress in Plants

The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a highly conserved protein complex that regulates signaling pathways in plants under abiotic stress. We discuss the potential molecular mechanisms of CSN under abiotic stress, including oxidative stress with reactive oxygen species signaling, salt stress with jasmonic acid, gibberellic acid, and abscisic acid signaling, high-temperature stress with auxin signaling, and optical radiation with DNA damage and repair response. We conclude that CSN likely participates in affecting antioxidant biosynthesis and hormone signaling by targeting receptors, kinases, and transcription factors in response to abiotic stress, which potentially provides valuable information for engineering stress-tolerant crops.

S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response

Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5' leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.

Phosphorylation of RAV1/2 by KIN10 is essential for transcriptional activation of CAT6/7, which underlies oxidative stress response in cassava

Related to ABI3/VP1 (RAV) transcription factors have important roles in plant stress responses; however, it is unclear whether RAVs regulates oxidative stress response in cassava (Manihot esculenta). In this study, we report that MeRAV1/2 positively regulate oxidative stress resistance and catalase (CAT) activity in cassava. Consistently, RNA sequencing (RNA-seq) identifies three MeCATs that are differentially expressed in MeRAV1/2-silenced cassava leaves. Interestingly, MeCAT6 and MeCAT7 are identified as direct transcriptional targets of MeRAV1/2 via binding to their promoters. In addition, protein kinase MeKIN10 directly interacts with MeRAV1/2 to phosphorylate them at Ser45 and Ser44 residues, respectively, to promote their direct transcriptional activation on MeCAT6 and MeCAT7. Site mutation of MeRAV1S45A or MeRAV2S44A has no significant effect on the activities of MeCAT6 and MeCAT7 promoters or on oxidative stress resistance. In summary, this study demonstrates that the phosphorylation of MeRAV1/2 by MeKIN10 is essential for its direct transcriptional activation of MeCAT6/7 in response to oxidative stress.

Identification of resurrection genes from the transcriptome of dehydrated and rehydrated Selaginella tamariscina

Selaginella tamariscina is a lycophyta species that survives under extremely dry conditions via the mechanism of resurrection. This phenomenon involves the regulation of numerous genes that play vital roles in desiccation tolerance and subsequent rehydration. To identify resurrection-related genes, we analyzed the transcriptome between dehydration conditions and rehydration conditions of S. tamariscina. The de novo assembly generated 124,417 transcripts with an average size of 1,000 bp and 87,754 unigenes. Among these genes, 1,267 genes and 634 genes were up and down regulated by rehydration compared to dehydration. To understand gene function, we annotated Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The unigenes encoding early light-inducible protein (ELIP) were down-regulated, whereas pentatricopeptide repeat-containing protein (PPR), late embryogenesis abundant proteins (LEA), sucrose nonfermenting protein (SNF), trehalose phosphate phosphatase (TPP), trehalose phosphate synthase (TPS), and ABC transporter G family (ABCG) were significantly up-regulated in response to rehydration conditions by differentially expressed genes (DEGs) analysis. Several studies provide evidence that these genes play a role in stress environment. The ELIP and PPR genes are involved in chloroplast protection during dehydration and rehydration. LEA, SNF, and trehalose genes are known to be oxidant scavengers that protect the cell structure from the deleterious effect of drought. TPP and TPS genes were found in the starch and sucrose metabolism pathways, which are essential sugar-signaling metabolites regulating plant metabolism and other biological processes. ABC-G gene interacts with abscisic acid (ABA) phytohormone in the stomata opening during stress conditions. Our findings provide valuable information and candidate resurrection genes for future functional analysis aimed at improving the drought tolerance of crop plants.

The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis

Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H₂O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO₂ concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.

SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants

The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5' RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.

Anno genominis XX: 20 years of Arabidopsis genomics

Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.

Imperative role of sugar signaling and transport during drought stress responses in plants

Cellular sugar status is essentially maintained during normal growth conditions but is impacted negatively during various environmental perturbations. Drought presents one such unfavorable environmental cue that hampers the photosynthetic fixation of carbon into sugars and affects their transport by lowering the cellular osmotic potential. The transport of cellular sugar is facilitated by a specific set of proteins known as sugar transporters. These transporter proteins are the key determinant of influx/ efflux of various sugars and their metabolite intermediates that support the plant growth and developmental process. Abiotic stress and especially drought stress-mediated injury results in reprogramming of sugar distribution across the cellular and subcellular compartments. Here, we have reviewed the imperative role of sugar accumulation, signaling, and transport under typical and atypical stressful environments. We have discussed the physiological effects of drought on sugar accumulation and transport through different transporter proteins involved in monosaccharide and disaccharide sugar transport. Further, we have illustrated sugar-mediated signaling and regulation of sugar transporter proteins along with the overall crosstalk of this signaling with the phytohormone module of abiotic stress response under osmotic stress. Overall, the present review highlights the critical role of sugar transport, distribution and signaling in plants under drought stress conditions.

Aging, stress, and senescence in plants: what can biological diversity teach us?

Aging, stress, and senescence in plants are interconnected processes that determine longevity. We focus here on compiling and discussing our current knowledge on the mechanisms of development that long-lived perennial plants have evolved to prevent and delay senescence. Clonal and nonclonal perennial herbs of various life forms and longevities will be particularly considered to illustrate what biological diversity can teach us about aging as a universal phenomenon. Source-sink relations and redox signaling will also be discussed as examples of regulatory mechanisms of senescence at the organ level. Whether or not effective mechanisms that biological diversity has evolved to completely prevent the wear and tear of aging will be applicable to human aging in the near future ultimately depends on ethical aspects.

SnRK1α1 Antagonizes Cell Death Induced by Transient Overexpression of Arabidopsis thaliana ABI5 Binding Protein 2 (AFP2)

Plants are continuously exposed to environmental stressors. They have thus evolved complex signaling pathways to govern responses to a variety of stimuli. The hormone abscisic acid (ABA) has been implicated in modulating both abiotic and biotic stress responses in plants. ABI5 Binding Proteins (AFPs) are a family of negative regulators of bZIP transcription factors of the AREB/ABF family, which promote ABA responses. AFP2 interacts with Snf1-Related protein Kinase 1 (SnRK1), which belongs to a highly conserved heterotrimeric kinase complex that is activated to re-establish energy homeostasis following stress. However, the role of this interaction is currently unknown. Here, we show that transient overexpression of Arabidopsis thaliana AFP2 in Nicotiana benthamiana leaves induces cell death (CD). Using truncated AFP2 constructs, we demonstrate that CD induction by AFP2 is dependent on the EAR domain. Co-expression of the catalytic subunit SnRK1α1, but not SnRK1α2, rescues AFP2-induced CD. Overexpression of SnRK1α1 has little effect on AFP2 protein level and does not affect AFP2 subcellular localization. Our results show that a high level of AFP2 is detrimental for cell function and that SnRK1α1 antagonizes AFP2-induced CD most likely through a mechanism that does not involve AFP2 protein degradation or a change in subcellular localization.