Plant Cell Signaling Research Articles

Transcription regulation by biomolecular condensates.

Biomolecular condensates regulate transcription by dynamically compartmentalizing the transcription machinery. Classic models of transcription regulation focus on the recruitment and regulation of RNA polymerase II by the formation of complexes at the 1-10 nm length scale, which are driven by structured and stoichiometric interactions. These complexes are further organized into condensates at the 100-1,000 nm length scale, which are driven by dynamic multivalent interactions often involving domain-ligand pairs or intrinsically disordered regions. Regulation through condensate-mediated organization does not supersede the processes occurring at the 1-10 nm scale, but it provides regulatory mechanisms for promoting or preventing these processes in the crowded nuclear environment. Regulation of transcription by transcriptional condensates is involved in cell state transitions during animal and plant development, cell signalling and cellular responses to the environment. These condensate-mediated processes are dysregulated in developmental disorders, cancer and neurodegeneration. In this Review, we discuss the principles underlying the regulation of transcriptional condensates, their roles in physiology and their dysregulation in human diseases.

Regulating programmed cell death in plant cells: Intracellular acidification plays a pivotal role together with calcium signaling.

Programmed cell death (PCD) occurs in different tissues in response to a number of different signals in plant cells. Drawing from work in several different contexts, including root-cap cell differentiation, plant response to biotic and abiotic stress, and some self-incompatibility (SI) systems, the data suggest that, despite differences, there are underlying commonalities in the early decision-making stages of PCD. Here, we focus on how 2 cellular events, increased [Ca2+]cyt levels and cytosolic acidification, appear to act as early signals involved in regulating both developmental and stimulus-induced PCD in plant cells.

Requirement of two simultaneous environmental signals for activation of Arabidopsis ELIP2 promoter in response to high light, cold, and UV-B stresses

ABSTRACT Arabidopsis EARLY LIGH-INDUCIBLE PROTEIN 2 (ELIP2) is a chlorophyll- and carotenoid-binding protein and is involved in photoprotection under stress conditions. Because its expression is induced through high light, cold, or UV-B stressors, its mechanism of induction has been studied. It is known that a functional unit found in the promoter, which is composed of Element B and Element A, is required and sufficient for full activation by these stressors. In this study, the role of each element in the unit was analyzed by introducing weak mutations in each element as synthetic promoters in addition to intensive repeat constructs of each single element. The results suggest that a stressor like cold stress generates two parallel signals in plant cells, and they merge at the promoter region for the activation of ELIP2 expression, which constitutes an “AND” gate and has a potential to realize strong response with high specificity by an environmental trigger.

Phytohormone Strigolactone: Involvement in Guard Cell Signaling and Abiotic Stress Tolerance in Plants

Phytohormone Strigolactone: Involvement in Guard Cell Signaling and Abiotic Stress Tolerance in Plants

Exploring the connections between ER-based lipid metabolism and plasma membrane nanodomain signaling.

Recent advancements in our understanding of cell membrane dynamics have shed light on the importance of plasma membrane (PM) nanodomains in plant cell signaling. Nevertheless, many aspects of membrane nanodomains, including their regulatory mechanisms and biological functions, remain enigmatic. To address this knowledge gap, our review article proposes a novel perspective wherein signaling pathways target endoplasmic reticulum (ER)-based lipid metabolism to exert control over the formation and function of membrane nanodomains. Subsequently, these nanodomains reciprocate by influencing the localization and activity of signaling molecules at the PM. We place a specific emphasis on ER-based enzymatic reactions, given the ER's central role in membrane lipid biosynthesis and its capacity to directly impact PM lipid composition, particularly with regard to saturation levels - an essential determinant of nanodomain properties. The interplay among cell signaling, glycerolipid metabolism, and PM nanodomain may create feedforward/feedback loops that fine-tune cellular responses to developmental and environmental cues.

Genome-wide identification and stress response analysis of BcaCPK gene family in amphidiploid Brassica carinata.

Calcium-dependent protein kinases (CPKs) are crucial for recognizing and transmitting Ca2+ signals in plant cells, playing a vital role in growth, development, and stress response. This study aimed to identify and detect the potential roles of the CPK gene family in the amphidiploid Brassica carinata (BBCC, 2n = 34) using bioinformatics methods. Based on the published genomic information of B. carinata, a total of 123 CPK genes were identified, comprising 70 CPK genes on the B subgenome and 53 on the C subgenome. To further investigate the homologous evolutionary relationship between B. carinata and other plants, the phylogenetic tree was constructed using CPKs in B. carinata and Arabidopsis thaliana. The phylogenetic analysis classified 123 family members into four subfamilies, where gene members within the same subfamily exhibited similar conserved motifs. Each BcaCPK member possesses a core protein kinase domain and four EF-hand domains. Most of the BcaCPK genes contain 5 to 8 introns, and these 123 BcaCPK genes are unevenly distributed across 17 chromosomes. Among these BcaCPK genes, 120 replicated gene pairs were found, whereas only 8 genes were tandem duplication, suggesting that dispersed duplication mainly drove the family amplification. The results of the Ka/Ks analysis indicated that the CPK gene family of B. carinata was primarily underwent purification selection in evolutionary selection. The promoter region of most BcaCPK genes contained various stress-related cis-acting elements. qRT-PCR analysis of 12 selected CPK genes conducted under cadmium and salt stress at various points revealed distinct expression patterns among different family members in response to different stresses. Specifically, the expression levels of BcaCPK2.B01a, BcaCPK16.B02b, and BcaCPK26.B02 were down-regulated under both stresses, whereas the expression levels of other members were significantly up-regulated under at least one stress. This study systematically identified the BcaCPK gene family in B. carinata, which contributes to a better understanding the CPK genes in this species. The findings also serve as a reference for analyzing stress responses, particularly in relation to cadmium and salt stress in B. carinata.

Proteomic Analysis of Arachis hypogaea Seeds from Different Maturity Classes.

Physiological maturity impacts seed quality through various mechanisms including vigor, desiccation tolerance, dormancy induction, synthesis of raw materials (including seed storage proteins), and the reorganization of metabolisms. Peanut seed development can be classified into seven classes with four incremental stages per class. Based on the mesocarp color, the final three stages are commonly referred to as "orange", "brown", and "black". In 2017, freshly harvested pods from one genotype of runner market-type peanuts grown under conventional practices were obtained from the University of Georgia research facility. The pods were removed from the plant material and 'pod blasted' to reveal the mesocarp. After separation, the remainder of the pod outer layer was removed, and the seeds were segregated for proteomic analysis. The raw peanuts were analyzed by bottom-up LC-MS/MS proteomics, which was conducted by the Proteomics Resource Center at the Rockefeller University, to identify the significant protein composition differences in each maturity class. The proteomic data revealed differentially expressed proteins as a function of maturity class with multiple functions including plant defense, metabolism, cell signaling, nutrient accumulation, and packaging. Understanding the processes needed for seed maturation will enable peanut scientists to evaluate the traits needed for robust germination, hardiness of the seed in response to disease, and nutrient quality.

Phosphatidic acid formation and signaling in plant cells

This review conteins updated information on the structure, localization and regulation of phosphatidic acid (PA)-producing enzymes phospholipase D, phosphoinositide-specific and non-specific phospholipases C and diacylglycerol kinases is analyzed. The specific role of PA and PA-producing enzymes in plant stress signaling is discussed.

The function of sphingolipids in membrane trafficking and cell signaling in plants, in comparison with yeast and animal cells

Sphingolipids are essential membrane components involved in a wide range of cellular, developmental and signaling processes. Sphingolipids are so essential that knock-out mutation often leads to lethality. In recent years, conditional or weak allele mutants as well as the broadening of the pharmacological catalog allowed to decipher sphingolipid function more precisely in a less invasive way. This review intends to provide a discussion and point of view on the function of sphingolipids with a main focus on endomembrane trafficking, Golgi-mediated protein sorting, cell polarity, cell-to-cell communication and cell signaling at the plasma membrane. While our main angle is the plant field research, we will constantly refer to and compare with the advances made in the yeast and animal field. In this review, we will emphasize the role of sphingolipids not only as a membrane component, but also as a key player at a center of homeostatic regulatory networks involving direct or indirect interaction with other lipids, proteins and ion fluxes.

Green leaf volatiles co-opt proteins involved in molecular pattern signalling in plant cells.

The green leaf volatiles (GLVs) Z-3-hexen-1-ol (Z3-HOL) and Z-3-hexenyl acetate (Z3-HAC) are airborne infochemicals released from damaged plant tissues that induce defenses and developmental responses in receiver plants, but little is known about their mechanism of action. We found that Z3-HOL and Z3-HAC induce similar but distinctive physiological and signaling responses in tomato seedlings and cell cultures. In seedlings, Z3-HAC showed a stronger root growth inhibition effect than Z3-HOL. In cell cultures, the two GLVs induced distinct changes in MAP kinase (MAPK) activity and proton fluxes as well as rapid and massive changes in the phosphorylation status of proteins within 5 min. Many of these phosphoproteins are involved in reprogramming the proteome from cellular homoeostasis to stress and include pattern recognition receptors, a receptor-like cytoplasmic kinase, MAPK cascade components, calcium signaling proteinsand transcriptional regulators. These are well-known components of damage-associated molecular pattern (DAMP) signaling pathways. These rapid changes in the phosphoproteome may underly the activation of defense and developmental responses to GLVs. Our data provide further evidence that GLVs function like DAMPs and indicate that GLVs coopt DAMP signaling pathways.

Automated Real-Time Monitoring of Extracellular pH to Assess Early Plant Defense Signaling.

Extracellular alkalinization mediated by the inhibition of plasma membrane-located proton pumping ATPases hallmarks the initiation of defense signaling in plant cells. Early defense responses also include depolarization of the plasma membrane, increase in cytosolic Ca2+ concentration, and an oxidative burst. Together these early signaling events lead to the activation of plant immunity. The transient alkalinization response is triggered by well-studied pathogen-derived and plant endogenous elicitors, including, for example, bacterial flagellin, fungal chitin, and tomato systemin in both model and agronomic species. Employing cell suspension cultures, extracellular alkalinization can be easily assessed by measuring the elicitor-induced pH changes of the cultivating medium. Here, we provide a protocol for an improved alkalinization assay in a system which is able to simultaneously monitor multiple samples, and fully automatically transfer customizable real-time pH records. In this system flagellin, chitin and systemin elicit robust time- and dose-dependent responses, proving a powerful tool for assessing plant early defense signaling.

K+ and pH homeostasis in plant cells is controlled by a synchronized K+ /H+ antiport at the plasma and vacuolar membrane.

Stomatal movement involves ion transport across the plasma membrane (PM) and vacuolar membrane (VM) of guard cells. However, the coupling mechanisms of ion transporters in both membranes and their interplay with Ca2+ and pH changes are largely unclear. Here, we investigated transporter networks in tobacco guard cells and mesophyll cells using multiparametric live-cell ion imaging and computational simulations. K+ and anion fluxes at both, PM and VM, affected H+ and Ca2+ , as changes in extracellular KCl or KNO3 concentrations were accompanied by cytosolic and vacuolar pH shifts and changes in [Ca2+ ]cyt and the membrane potential. At both membranes, the K+ transporter networks mediated an antiport of K+ and H+ . By contrast, net transport of anions was accompanied by parallel H+ transport, with differences in transport capacity for chloride and nitrate. Guard and mesophyll cells exhibited similarities in K+ /H+ transport but cell type-specific differences in [H+ ]cyt and pH-dependent [Ca2+ ]cyt signals. Computational cell biology models explained mechanistically the properties of transporter networks and the coupling of transport across the PM and VM. Our integrated approach indicates fundamental principles of coupled ion transport at membrane sandwiches to control H+ /K+ homeostasis and points to transceptor-like Ca2+ /H+ -based ion signaling in plant cells.

Visualizing calcium-dependent signaling networks in plants

Calcium-dependent protein kinases (CDPKs) are a multigene protein kinase family that have key regulatory roles in plants. However, imaging CDPK signals in plant cells remains challenging. The recently developed genetically encoded CDPK-Förster resonance energy transfer (FRET) reporter developed by Liese et al. allows visualization of calcium (Ca2+)-dependent conformational changes during activation or inactivation of CDPKs, providing a powerful tool for real-time monitoring of calcium decoding in plants.

ROS and RNS production, subcellular localization, and signaling triggered by immunogenic danger signals.

Plants continuously monitor the environment to detect changing conditions and to properly respond, avoiding deleterious effects on their fitness and survival. An enormous number of cell surface and intracellular immune receptors are deployed to perceive danger signals associated with microbial infections. Ligand binding by cognate receptors represents the first essential event in triggering plant immunity and determining the outcome of the tissue invasion attempt. Reactive oxygen and nitrogen species (ROS/RNS) are secondary messengers rapidly produced in different subcellular localizations upon the perception of immunogenic signals. Danger signal transduction inside the plant cells involves cytoskeletal rearrangements as well as several organelles and interactions between them to activate key immune signaling modules. Such immune processes depend on ROS and RNS accumulation, highlighting their role as key regulators in the execution of the immune cellular program. In fact, ROS and RNS are synergic and interdependent intracellular signals required for decoding danger signals and for the modulation of defense-related responses. Here we summarize current knowledge on ROS/RNS production, compartmentalization, and signaling in plant cells that have perceived immunogenic danger signals.

Identification and expression analysis of MAPK cascade gene family in foxtail millet (Setaria italica)

ABSTRACT The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including Arabidopsis thaliana, Oryza sativa, and Triticum aestivum, but have not been identified in foxtail millet (Setaria italica). In this study, a total of 93 MAPK cascade genes, including 15 SiMAPKs, 10 SiMAPKKs and 68 SiMAPKKKs genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the SiMAPKs and SiMAPKKs into four subgroups, respectively, and the SiMAPKKKs into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most SiMAPKs and SiMAPKKs were changed under both exogenous hormone and abiotic stress treatments, with SiMAPK3 and SiMAPKK4–2 being induced under almost all treatments, while the expression of SiMAPKK5 was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet (Setaria italica).

Quantitative phosphoproteomics reveals novel roles of cAMP in plants.

3',5'-cyclic adenosine monophosphate (cAMP) is finally recognized as an essential signaling molecule in plants where cAMP-dependent processes include responses to hormones and environmental stimuli. To better understand the role of 3',5'-cAMP at the systems level, we have undertaken a phosphoproteomic analysis to elucidate the cAMP-dependent response of tobacco BY-2 cells. These cells overexpress a molecular "sponge" that buffers free intracellular cAMP level. The results show that, firstly, in vivo cAMP dampening profoundly affects the plant kinome and notably mitogen-activated protein kinases, receptor-like kinases, and calcium-dependent protein kinases, thereby modulating the cellular responses at the systems level. Secondly, buffering cAMP levels also affects mRNA processing through the modulation of the phosphorylation status of several RNA-binding proteins with roles in splicing, including many serine and arginine-rich proteins. Thirdly, cAMP-dependent phosphorylation targets appear to be conserved among plant species. Taken together, these findings are consistent with an ancient role of cAMP in mRNA processing and cellular programming and suggest that unperturbed cellular cAMP levels are essential for cellular homeostasis and signaling in plant cells.

Artificial microRNA-mediated resistance against Oman strain of tomato yellow leaf curl virus.

Tomato yellow leaf curl virus (TYLCV) is a global spreading begomovirus that is exerting a major restraint on global tomato production. In this transgenic approach, an RNA interference (RNAi)-based construct consisting of sequences of an artificial microRNA (amiRNA), a group of small RNA molecules necessary for plant cell development, signal transduction, and stimulus to biotic and abiotic disease was engineered targeting the AC1/Rep gene of the Oman strain of TYLCV-OM. The Rep-amiRNA constructs presented an effective approach in regulating the expression of the Rep gene against TYLCV as a silencing target to create transgenic Solanum lycopersicum L. plant tolerance against TYLCV infection. Molecular diagnosis by PCR followed by a Southern hybridization analysis were performed to confirm the effectiveness of agrobacterium-mediated transformation in T0/T1-transformed plants. A substantial decrease in virus replication was observed when T1 transgenic tomato plants were challenged with the TYLCV-OM infectious construct. Although natural resistance options against TYLCV infection are not accessible, the current study proposes that genetically transformed tomato plants expressing amiRNA could be a potential approach for engineering tolerance in plants against TYLCV infection and conceivably for the inhibition of viral diseases against different strains of whitefly-transmitted begomoviruses in Oman.

Super-Resolution Imaging of Plant Receptor-Like Kinases Uncovers Their Colocalization and Coordination with Nanometer Resolution.

Plant cell signaling often relies on the cellular organization of receptor-like kinases (RLKs) within membrane nanodomains to enhance signaling specificity and efficiency. Thus, nanometer-scale quantitative analysis of spatial organizations of RLKs could provide new understanding of mechanisms underlying plant responses to environmental stress. Here, we used stochastic optical reconstruction fluorescence microscopy (STORM) to quantify the colocalization of the flagellin-sensitive-2 (FLS2) receptor and the nanodomain marker, remorin, within Arabidopsis thaliana root hair cells. We found that recovery of FLS2 and remorin in the plasma membrane, following ligand-induced internalization by bacterial-flagellin-peptide (flg22), reached ~85% of their original membrane density after ~90 min. The pairs colocalized at the membrane at greater frequencies, compared with simulated randomly distributed pairs, except for directly after recovery, suggesting initial uncoordinated recovery followed by remorin and FLS2 pairing in the membrane. The purinergic receptor, P2K1, colocalized with remorin at similar frequencies as FLS2, while FLS2 and P2K1 colocalization occurred at significantly lower frequencies, suggesting that these RLKs mostly occupy distinct nanodomains. The chitin elicitor receptor, CERK1, colocalized with FLS2 and remorin at much lower frequencies, suggesting little coordination between CERK1 and FLS2. These findings emphasize STORM's capacity to observe distinct nanodomains and degrees of coordination between plant cell receptors, and their respective immune pathways.

Abscisic acid agonists suitable for optimizing plant water use.

Climate change and overexploitation of groundwater resources cause constraints on water demand for agriculture, thus threatening crop productivity. For future food security, there is an urgent need for crops of high water use efficiency combined with high crop productivity, i.e. having high water productivity. Highwater productivity means efficient biomass accumulation at reduced transpiration. Recent studies show that plants are able to optimize carbon uptake per water transpired with little or no trade-off in yield. The phytohormone abscisic acid (ABA) plays a pivotal role in minimizing leaf transpiration and mediating enhanced water productivity. Hence, ABA and more chemically stable ABA agonists have the potential to improve crop water productivity. Synthesis, screening, and identification of suitable ABA agonists are major efforts currently undertaken. In this study, we used yeast expressing the plant ABA signal pathway to prescreen ABA-related cyano cyclopropyl compounds (CCPs). The yeast analysis allowed testing the ABA agonists for general toxicity, efficient uptake, and specificity in regulating different ABA receptor complexes. Subsequently, promising ABA-mimics were analyzed in vitro for ligand-receptor interaction complemented by physiological analyses. Several CCPs activated ABA signaling in yeast and plant cells. CCP1, CCP2, and CCP5 were by an order of magnitude more efficient than ABA in minimizing transpiration of Arabidopsis plants. In a progressive drought experiment, CCP2 mediated an increase in water use efficiency superior to ABA without trade-offs in biomass accumulation.

The global dynamic of DNA methylation in response to heat stress revealed epigenetic mechanism of heat acclimation in Saccharina japonica.

Saccharina japonica is an ecologically and economically important kelp in cold-temperate regions. When it is cultivated on a large scale in the temperate and even subtropical zones, heat stress is a frequent abiotic stress. This study is the first attempt to reveal the regulatory mechanism of the response to heat stress from the perspective of DNA methylation in S. japonica. We firstly obtained the characteristics of variation in the methylome under heat stress, and observed that heat stress caused a slight increase in the overall methylation level and methylation rate, especially in the non-coding regions of the genome. Secondly, we noted that methylation was probably one of factors affecting the expression of genes, and that methylation within the gene body was positively correlated with the gene expression (rho=0.0784). Moreover, it was found that among the differentially expressed genes regulated by methylation, many genes were related to heat stress response, such as HSP gene family, genes of antioxidant enzymes, genes related to proteasome-ubiquitination pathway, and plant cell signaling pathways. This study demonstrated that DNA methylation is involved in regulating the response to heat stress, laying a foundation for studying the acclimation and adaptation of S. japonica to heat stress from an epigenetic perspective.