A high-throughput method for screening Arabidopsis mutants with disordered abiotic stress-induced calcium signal

SCAB1 coordinates sequential Ca2+ and ABA signals during osmotic stress induced stomatal closure in Arabidopsis

Hyperosmotic stress caused by drought is a detrimental threat to plant growth and agricultural productivity due to limited water availability. Stomata are gateways of transpiration and gas exchange, the swift adjustment of stomatal aperture has a strong influence on plant drought resistance. Despite intensive investigations of stomatal closure during drought stress in past decades, little is known about how sequential signals are integrated during complete processes. Here, we discovered that the rapid Ca2+ signaling and subsequent abscisic acid (ABA) signaling contribute to the kinetics of both F-actin reorganizations and stomatal closure in Arabidopsis thaliana, while STOMATAL CLOSURE-RELATED ACTIN BINDING PROTEIN1 (SCAB1) is the molecular switch for this entire process. During the early stage of osmotic shock responses, swift elevated calcium signaling promotes SCAB1 phosphorylation through calcium sensors CALCIUM DEPENDENT PROTEIN KINASE3 (CPK3) and CPK6. The phosphorylation restrained the microfilament binding affinity of SCAB1, which bring about the F-actin disassembly and stomatal closure initiation. As the osmotic stress signal continued, both the kinase activity of CPK3 and the phosphorylation level of SCAB1 attenuated significantly. We further found that ABA signaling is indispensable for these attenuations, which presumably contributed to the actin filament reassembly process as well as completion of stomatal closure. Notably, the dynamic changes of SCAB1 phosphorylation status are crucial for the kinetics of stomatal closure. Taken together, our results support a model in which SCAB1 works as a molecular switch, and directs the microfilament rearrangement through integrating the sequentially generated Ca2+ and ABA signals during osmotic stress induced stomatal closure.

Phytochromes enhance SOS2-mediated PIF1 and PIF3 phosphorylation and degradation to promote Arabidopsis salt tolerance

Soil salinity is one of the most detrimental abiotic stresses affecting plant survival, and light is a core environmental signal regulating plant growth and responses to abiotic stress. However, how light modulates the plant's response to salt stress remains largely obscure. Here, we show that Arabidopsis (Arabidopsis thaliana) seedlings are more tolerant to salt stress in the light than in the dark, and that the photoreceptors phytochrome A (phyA) and phyB are involved in this tolerance mechanism. We further show that phyA and phyB physically interact with the salt tolerance regulator SALT OVERLY SENSITIVE2 (SOS2) in the cytosol and nucleus, and enhance salt-activated SOS2 kinase activity in the light. Moreover, SOS2 directly interacts with and phosphorylates PHYTOCHROME-INTERACTING FACTORS PIF1 and PIF3 in the nucleus. Accordingly, PIFs act as negative regulators of plant salt tolerance, and SOS2 phosphorylation of PIF1 and PIF3 decreases their stability and relieves their repressive effect on plant salt tolerance in both light and dark conditions. Together, our study demonstrates that photoactivated phyA and phyB promote plant salt tolerance by increasing SOS2-mediated phosphorylation and degradation of PIF1 and PIF3, thus broadening our understanding of how plants adapt to salt stress according to their dynamic light environment.

Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Sugar Beet to Salt Stress of Different Durations

Salinity is one of the most serious threats to agriculture worldwide. Sugar beet is an important sugar-yielding crop and has a certain tolerance to salt; however, the genome-wide dynamic response to salt stress remains largely unknown in sugar beet. In the present study, physiological and transcriptome analyses of sugar beet leaves and roots were compared under salt stress at five time points. The results showed that different salt stresses influenced phenotypic characteristics, leaf relative water content and root activity in sugar beet. The contents of chlorophyll, malondialdehyde (MDA), the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) were also affected by different salt stresses. Compared with control plants, there were 7391 and 8729 differentially expressed genes (DEGs) in leaves and roots under salt stress, respectively. A total of 41 hub genes related to salt stress were identified by weighted gene co-expression network analysis (WGCNA) from DEGs, and a transcriptional regulatory network based on these genes was constructed. The expression pattern of hub genes under salt stress was confirmed by qRT-PCR. In addition, the metabolite of sugar beet was compared under salt stress for 24 h. A total of 157 and 157 differentially accumulated metabolites (DAMs) were identified in leaves and roots, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that DEGs and DAMs act on the starch and sucrose metabolism, alpha-linolenic acid metabolism, phenylpropanoid biosynthesis and plant hormone signal transduction pathway. In this study, RNA-seq, WGCNA analysis and untargeted metabolomics were combined to investigate the transcriptional and metabolic changes of sugar beet during salt stress. The results provided new insights into the molecular mechanism of sugar beet response to salt stress, and also provided candidate genes for sugar beet improvement.

MDP25 mediates the fine-tuning of microtubule organization in response to salt stress

Microtubules are dynamic cytoskeleton structures playing fundamental roles in plant responses to salt stress. The precise mechanisms by which microtubule organization is regulated under salt stress are largely unknown. Here, we report that Arabidopsis thaliana MICROTUBULE-DESTABILIZING PROTEIN 25 (MDP25; also known as PLASMA MEMBRANE-ASSOCIATED CATION-BINDING PROTEIN 1 (PCaP1)) helps regulate microtubule organization. Under salt treatment, elevated cytosolic Ca²⁺ concentration caused MDP25 to partially dissociate from the plasma membrane, promoting microtubule depolymerization. When Ca²⁺ signaling was blocked by BAPTA-AM or LaCl₃ , microtubule depolymerization in wild-type and MDP25-overexpressing cells was slower, while there was no obvious change in mdp25 cells. Knockout of MDP25 improved microtubule reassembly and was conducive to microtubule integrity under long-term salt treatment and microtubule recovery after salt stress. Moreover, mdp25 seedlings exhibited a higher survival rate under salt stress. The presence microtubule-disrupting reagent oryzalin or microtubule-stabilizing reagent paclitaxel differentially affected the survival rates of different genotypes under salt stress. MDP25 promoted microtubule instability by affecting the catastrophe and rescue frequencies, shrinkage rate and time in pause phase at the microtubule plus-end and the depolymerization rate at the microtubule minus-end. These findings reveal a role for MDP25 in regulating microtubule organization under salt treatment by affecting microtubule dynamics.

GR24-mediated enhancement of salt tolerance and roles of H2O2 and Ca2+ in regulating this enhancement in cucumber

This study investigated the regulation of the exogenous strigolactone (SL) analog GR24 in enhancing the salt tolerance and the effects of calcium ion (Ca2+) and hydrogen peroxide (H2O2) on GR24's regulation effects in cucumber. The seedlings were sprayed with (1) distilled water (CK), (2) NaCl, (3) GR24, then NaCl, (4) GR24, then H2O2 scavenger, then NaCl, and (5) GR24, then Ca2+ blocker, then NaCl. The second true leaf was selected for biochemical assays. Under the salt stress, the exogenous GR24 maintained the ion balance, increased the activity of antioxidant enzymes, reduced the membrane lipid peroxidation, and increased the activities of catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX), accompanied by a decrease in relative conductivity, an increase in the proline content, and elevated gene expression levels of antioxidant enzymes, nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, calcium-dependent protein kinases (CDPKs), salt overly sensitive SOS1, CBL-interacting protein kinase 2 (CIPK2), and calcineurin B-like protein 3 (CBL3). Such protective effects triggered by GR24 were attenuated or almost abolished by ethylene glycol tetraacetic acid (EGTA), lanthanum chloride (LaCl3, Ca2+ channel blocker), diphenyleneiodonium (DPI, NADPH oxidase inhibitor), and dimethylthiourea (DMTU, hydroxyl radical scavenger). Our data suggest that exogenous GR24 is highly effective in alleviating salt-induced damages via modulating antioxidant capabilities and improving ionic homeostasis and osmotic balance and that H2O2 and Ca2+ are required for GR24-mediated enhancement of salt tolerance.

Screening for Arabidopsis mutants with altered Ca2+ signal response using aequorin-based Ca2+ reporter system

Environmental stimuli evoke transient increases of the cytosolic Ca²⁺ level. To identify upstream components of Ca²⁺ signaling, we have optimized two forward genetic screening systems based on Ca²⁺ reporter aequorin. AEQsig6 and AEQub plants were used for generating ethyl methanesulfonate (EMS)-mutagenized libraries. The AEQsig6 EMS-mutagenized library was preferably used to screen the mutants with reduced Ca²⁺ signal response due to its high effectiveness, while the AEQub EMS-mutagenized library was used for screening of the mutants with altered Ca²⁺ signal response.

For complete details on the use and execution of this protocol, please refer to Chen et al. (2020) and Zhu et al. (2013).

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Highly efficient systems for screening of Ca²⁺ signal mutants in Arabidopsis

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Step-by-step instructions to analyze Ca²⁺ signal response using Ca²⁺ reporter aequorin

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AEQsig6 system for identifying mutants impaired in shoot-based Ca²⁺ signaling

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FAS system for isolating tissue- or stimuli-specific Ca²⁺ responsive mutants

Overexpression of Cassava MeAnn2 Enhances the Salt and IAA Tolerance of Transgenic Arabidopsis

Annexins are a superfamily of soluble calcium-dependent phospholipid-binding proteins that have considerable regulatory effects in plants, especially in response to adversity and stress. The Arabidopsis thaliana AtAnn1 gene has been reported to play a significant role in various abiotic stress responses. In our study, the cDNA of an annexin gene highly similar to AtAnn1 was isolated from the cassava genome and named MeAnn2. It contains domains specific to annexins, including four annexin repeat sequences (I–IV), a Ca²⁺-binding sequence, Ca²⁺-independent membrane-binding-related tryptophan residues, and a salt bridge-related domain. MeAnn2 is localized in the cell membrane and cytoplasm, and it was found to be preferentially expressed in the storage roots of cassava. The overexpression of MeAnn2 reduced the sensitivity of transgenic Arabidopsis to various Ca²⁺, NaCl, and indole-3-acetic acid (IAA) concentrations. The expression of the stress resistance-related gene AtRD29B and auxin signaling pathway-related genes AtIAA4 and AtLBD18 in transgenic Arabidopsis was significantly increased under salt stress, while the Malondialdehyde (MDA) content was significantly lower than that of the control. These results indicate that the MeAnn2 gene may increase the salt tolerance of transgenic Arabidopsis via the IAA signaling pathway.

BONZAI Proteins Control Global Osmotic Stress Responses in Plants

Hyperosmotic stress caused by drought and salinity is a significant environmental threat that limits plant growth and agricultural productivity. Osmotic stress induces diverse responses in plants including Ca²⁺ signaling, accumulation of the stress hormone abscisic acid (ABA), reprogramming of gene expression, and altering of growth. Despite intensive investigation, no global regulators of all of these responses have been identified. Here, we show that the Ca²⁺-responsive phospholipid-binding BONZAI (BON) proteins are critical for all of these osmotic stress responses. A Ca²⁺-imaging-based forward genetic screen identified a loss-of-function bon1 mutant with a reduced cytosolic Ca²⁺ signal in response to hyperosmotic stress. The loss-of-function mutants of the BON1 gene family, bon1bon2bon3, are impaired in the induction of gene expression and ABA accumulation in response to osmotic stress. In addition, the bon mutants are hypersensitive to osmotic stress in growth inhibition. BON genes have been shown to negatively regulate plant immune responses mediated by intracellular immune receptor NLR genes including SNC1. We found that the defects of the bon mutants in osmotic stress responses were suppressed by mutations in the NLR gene SNC1 or the immunity regulator PAD4. Our findings indicate that NLR signaling represses osmotic stress responses and that BON proteins suppress NLR signaling to enable global osmotic stress responses in plants.

The nuclear transporter SAD2 plays a role in calcium- and H2 O2 -mediated cell death in Arabidopsis

In response to pathogens, plant cells exhibit a rapid increase in the intracellular calcium concentration and a burst of reactive oxygen species (ROS). The cytosolic increase in Ca²⁺ and the accumulation of ROS are critical for inducing programmed cell death (PCD), but the molecular mechanism is not fully understood. We screened an Arabidopsis mutant, sad2-5, which harbours a T-DNA insertion in the 18^th exon of the importin beta-like gene, SAD2. The H₂ O₂ -induced increase in the [Ca²⁺ ]_cyt of the sad2-5 mutant was greater than that of the wild type, and the sad2-5 mutant showed clear cell death phenotypes and abnormal H₂ O₂ accumulation under fumonisin-B1 (FB1) treatment. CaCl₂ could enhance the FB1-induced cell death of the sad2-5 mutant, whereas lanthanum chloride (LaCl₃ ), a broad-spectrum calcium channel blocker, could restore the FB1-induced PCD phenotype of sad2-5. The sad2-5 fbr11-1 double mutant exhibited the same FB1-insensitive phenotype as fbr11-1, which plays a critical role in novo sphingolipid synthesis, indicating that SAD2 works downstream of FBR11. These results suggest the important role of nuclear transporters in calcium- and ROS-mediated PCD response as well as provide an important theoretical basis for further analysis of the molecular mechanism of SAD2 function in PCD and for improvement of the resistance of crops to adverse environments.

The SOS2-SCaBP8 Complex Generates and Fine-Tunes an AtANN4-Dependent Calcium Signature under Salt Stress

Calcium signals act as universal second messengers that trigger many cellular processes in animals and plants, but how specific calcium signals are generated is not well understood. In this study, we determined that AtANN4, a putative calcium-permeable transporter, and its interacting proteins, SCaBP8 and SOS2, generate a calcium signal under salt stress, which initially activates the SOS pathway, a conserved mechanism that modulates ion homeostasis in plants under salt stress. After activation, SCaBP8 promotes the interaction of protein kinase SOS2 with AtANN4, which enhances its phosphorylation by SOS2. This phosphorylation of AtANN4 further increases its interaction with SCaBP8. Both the interaction with and phosphorylation of AtANN4 repress its activity and alter calcium transients and signatures in HEK cells and plants. Our results reveal how downstream targets are required to create a specific calcium signal via a negative feedback regulatory loop, thereby enhancing our understanding of the regulation of calcium signaling.

Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements

Plant phenomics offers unique opportunities to accelerate our understanding of gene function and plant response to different environments, and may be particularly useful for studying previously uncharacterized genes. One important type of poorly characterized genes is those derived from transposable elements (TEs), which have departed from a mobility-driven lifestyle to attain new adaptive roles for the host (exapted TEs). We used phenomics approaches, coupled with reverse genetics, to analyze T-DNA insertion mutants of both previously reported and novel protein-coding exapted TEs in the model plant Arabidopsis thaliana. We show that mutations in most of these exapted TEs result in phenotypes, particularly when challenged by abiotic stress. We built statistical multi-dimensional phenotypic profiles and compared them to wild-type and known stress responsive mutant lines for each particular stress condition. We found that these exapted TEs may play roles in responses to phosphate limitation, tolerance to high salt concentration, freezing temperatures, and arsenic toxicity. These results not only experimentally validate a large set of putative functional exapted TEs recently discovered through computational analysis, but also uncover additional novel phenotypes for previously well-characterized exapted TEs in A. thaliana.

MYB30 transcription factor regulates oxidative and heat stress responses through ANNEXIN-mediated cytosolic calcium signaling in Arabidopsis

Cytosolic calcium signaling is critical for regulating downstream responses in plants encountering unfavorable environmental conditions. In a genetic screen for Arabidopsis thaliana mutants defective in stress-induced cytosolic free Ca²⁺ ([Ca²⁺ ]_cyt ) elevations, we identified the R2R3-MYB transcription factor MYB30 as a regulator of [Ca²⁺ ]_cyt in response to H₂ O₂ and heat stresses. Plants lacking MYB30 protein exhibited greater elevation of [Ca²⁺ ]_cyt in response to oxidative and heat stimuli. Real-time reverse transcription-polymerase chain reaction (RT-PCR) results indicated that the expression of a number of ANNEXIN (ANN) genes, which encode Ca²⁺ -regulated membrane-binding proteins modulating cytosolic calcium signatures, were upregulated in myb30 mutants. Further analysis showed that MYB30 bound to the promoters of ANN1 and ANN4 and repressed their expression. myb30 mutants were sensitive to methyl viologen (MV) and heat stresses. The H₂ O₂ - and heat-induced abnormal [Ca²⁺ ]_cyt in myb30 was dependent on the function of ANN proteins. Moreover, the MV and heat sensitivity of myb30 was suppressed in mutants lacking ANN function or by application of LaCl₃ , a calcium channel blocker. These results indicate that MYB30 regulates oxidative and heat stress responses through calcium signaling, which is at least partially mediated by ANN1 and ANN4.

The Glycosyltransferase QUA1 Regulates Chloroplast-Associated Calcium Signaling During Salt and Drought Stress in Arabidopsis

Cytoplasmic Ca2+ ([Ca2+]cyt) elevation induced by various signals is responsible for appropriate downstream responses. Through a genetic screen of Arabidopsis thaliana mutants defective in stress-induced [Ca2+]cyt elevation, the glycosyltransferase QUASIMODO1 (QUA1) was identified as a regulator of [Ca2+]cyt in response to salt stress. Compared with the wild type, the qua1-4 mutant exhibited a dramatically greater increase in [Ca2+]cyt under NaCl treatment. Functional analysis showed that QUA1 is a novel chloroplast protein that regulates cytoplasmic Ca2+ signaling. QUA1 was detected in chloroplast thylakoids, and the qua1-4 mutant exhibited irregularly stacked grana. The observed greater increase in [Ca2+]cyt was inhibited upon recovery of chloroplast function in the qua1-4 mutant. Further analysis showed that CAS, a thylakoid-localized calcium sensor, also displayed irregularly stacked grana, and the chloroplasts of the qua1-4 cas-1 double mutant were similar to those of cas-1 plants. In QUA1-overexpressing plants, the protein level of CAS was decreased, and CAS was readily degraded under osmotic stress. When CAS was silenced in the qua1-4 mutant, the large [Ca2+]cyt increase was blocked, and the higher expression of PLC3 and PLC4 was suppressed. Under osmotic stress, the qua1-4 mutant showed an even greater elevation in [Ca2+]cyt and was hypersensitive to drought stress. However, this sensitivity was inhibited when the increase in [Ca2+]cyt was repressed in the qua1-4 mutant. Collectively, our data indicate that QUA1 may function in chloroplast-dependent calcium signaling under salt and drought stresses. Additionally, CAS may function downstream of QUA1 to mediate these processes.

Enlightenment on the aequorin-based platform for screening Arabidopsis stress sensory channels related to calcium signaling

Free calcium ions (Ca(2+)) are an important signal molecule in response to a large array of external stimuli encountered by plants. Using the aequorin-based Ca(2+) recording system, tremendous progress has been made in understanding the Ca(2+) responses to biotic or abiotic stresses in dicotyledonous Arabidopsis. However, due to the lack of a similar detection system, little information has been obtained from the monocotyledonous rice (Oryza sativa). Recombinant aequorin has been introduced into rice, and the Ca(2+) responses to NaCl and H2O2 in rice roots were characterized. Although rice calcium signal sensor research has just started, the transgenic rice expressing aequorin provides a good platform to study rice adapted to different environmental conditions.

Measuring spatial and temporal Ca2+ signals in Arabidopsis plants

Developmental and environmental cues induce Ca(2+) fluctuations in plant cells. Stimulus-specific spatial-temporal Ca(2+) patterns are sensed by cellular Ca(2+) binding proteins that initiate Ca(2+) signaling cascades. However, we still know little about how stimulus specific Ca(2+) signals are generated. The specificity of a Ca(2+) signal may be attributed to the sophisticated regulation of the activities of Ca(2+) channels and/or transporters in response to a given stimulus. To identify these cellular components and understand their functions, it is crucial to use systems that allow a sensitive and robust recording of Ca(2+) signals at both the tissue and cellular levels. Genetically encoded Ca(2+) indicators that are targeted to different cellular compartments have provided a platform for live cell confocal imaging of cellular Ca(2+) signals. Here we describe instructions for the use of two Ca(2+) detection systems: aequorin based FAS (film adhesive seedlings) luminescence Ca(2+) imaging and case12 based live cell confocal fluorescence Ca(2+) imaging. Luminescence imaging using the FAS system provides a simple, robust and sensitive detection of spatial and temporal Ca(2+) signals at the tissue level, while live cell confocal imaging using Case12 provides simultaneous detection of cytosolic and nuclear Ca(2+) signals at a high resolution.

The actin-related Protein2/3 complex regulates mitochondrial-associated calcium signaling during salt stress in Arabidopsis

Microfilament and Ca(2+) dynamics play important roles in stress signaling in plants. Through genetic screening of Arabidopsis thaliana mutants that are defective in stress-induced increases in cytosolic Ca(2+) ([Ca(2+)]cyt), we identified Actin-Related Protein2 (Arp2) as a regulator of [Ca(2+)]cyt in response to salt stress. Plants lacking Arp2 or other proteins in the Arp2/3 complex exhibited enhanced salt-induced increases in [Ca(2+)]cyt, decreased mitochondria movement, and hypersensitivity to salt. In addition, mitochondria aggregated, the mitochondrial permeability transition pore opened, and mitochondrial membrane potential Ψm was impaired in the arp2 mutant, and these changes were associated with salt-induced cell death. When opening of the enhanced mitochondrial permeability transition pore was blocked or increases in [Ca(2+)]cyt were prevented, the salt-sensitive phenotype of the arp2 mutant was partially rescued. These results indicate that the Arp2/3 complex regulates mitochondrial-dependent Ca(2+) signaling in response to salt stress.

Plant calcium-permeable channels

Experimental and modeling breakthroughs will help establish the genetic identities of plant calcium channels.

Aequorin-based luminescence imaging reveals stimulus- and tissue-specific Ca2+ dynamics in Arabidopsis plants

Calcium ion is a versatile second messenger for diverse cell signaling in response to developmental and environmental cues. The specificity of Ca(2+)-mediated signaling is defined by stimulus-elicited Ca(2+) signature and downstream decoding processes. Here, an Aequorin-based luminescence recording system was developed for monitoring Ca(2+) in response to various stimuli in Arabidopsis. With the simple, highly sensitive, and robust Ca(2+) recording, this system revealed stimulus- and tissue-specific Ca(2+) signatures in seedlings. Cellular Ca(2+) dynamics and relationship to Aequorin-based Ca(2+) recording were explored using a GFP-based Ca(2+) indicator, which suggested that a synchronous cellular Ca(2+) signal is responsible for cold-induced Ca(2+) response in seedlings, whereas asynchronous Ca(2+) oscillation contributes to osmotic stress-induced Ca(2+) increase in seedlings. The optimized recording system would be a powerful tool for the identification and characterization of novel components in Ca(2+)-mediated stress-signaling pathways.