CTR1 phosphorylates the central regulator EIN2 to control ethylene hormone signaling from the ER membrane to the nucleus in Arabidopsis

The B'ζ subunit of protein phosphatase 2A negatively regulates ethylene signaling in Arabidopsis

Ethylene is a major plant hormone that regulates plant growth, development, and defense responses to biotic and abiotic stresses. The major pieces of the ethylene signaling pathway have been put together, although several details still need to be elucidated. For instance, the phosphorylation and dephosphorylation processes controlling the ethylene responses are poorly understood and need to be further explored. The type 2A protein phosphatase (PP2A) was suggested to play an important role in the regulation of ethylene biosynthesis, where the A1 subunit of PP2A was shown to be involved in the regulation of the rate-limiting enzyme of the ethylene biosynthetic pathway. However, whether other subunits of PP2A play roles in the ethylene signal transduction pathway is yet to be answered. In this study, we demonstrate that a B subunit, PP2A-B'ζ, positively regulates plant germination and seedling development, as a pp2a-b'ζ mutant is very sensitive to ethylene treatment. Furthermore, PP2A-B'ζ interacts with and stabilizes the kinase CTR1 (Constitutive Triple Response 1), a key enzyme in the ethylene signal transduction pathway, and like CTR1, PP2A-B'ζ negatively regulates ethylene signaling in plants.

The Euscaphis japonica genome and the evolution of malvids

Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the γ event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.

Modulation of the Tomato Rhizosphere Microbiome via Changes in Root Exudation Mediated by the Ethylene Receptor NR

Plant hormones have been recently shown to exert an indirect influence on the recruitment of plant-associated microbiomes. However, it remains unclear the extent to which the disruption of the ethylene (ET) signaling pathway affects the assembly and functioning of plant-root microbiomes. In this study, the Never-ripe tomato mutant (Nr) was profiled for differences compared to the wild type (control). Tomato plants were subjected to root exudate profiling and the characterization of bacterial and fungal communities. Compared to the control, Nr revealed differences in the composition of root exudates, including lower amounts of esculetin, gallic acid, L-fucose, eicosapentaenoic acid, and higher amounts of β-aldehyde. Interestingly, Nr significantly differed in the composition and functioning of the rhizosphere bacterial community. We also identified the taxa that occurred at relatively higher abundances in Nr, including the genus Lysobacter, which displayed a significant negative correlation with changes in eicosapentaenoic acid and esculetin, and a significant positive correlation with changes in β-aldehyde. Taken together, our study provides evidence that a mutation in the ET receptor exerts predictable changes in the root-associated microbial taxa of tomato plants. These indirect effects can potentially be explored towards new strategies to engineer beneficial plant microbiomes via targeted changes in plant genetics and physiology.

Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in Arabidopsis Seedlings upon Cold Exposure

Protein phosphorylation plays an important role in mediating signal transduction in cold response in plants. To better understand how plants sense and respond to the early temperature drop, we performed data-independent acquisition (DIA) method-based mass spectrometry analysis to profile the proteome and phosphoproteome of Arabidopsis seedlings upon cold stress in a time-course manner (10, 30 and 120 min of cold treatments). Our results showed the rapid and extensive changes at the phosphopeptide levels, but not at the protein abundance levels, indicating cold-mediated protein phosphorylation and dephosphorylation events. Alteration of over 1200 proteins at phosphopeptide levels were observed within 2 h of cold treatment, including over 140 kinases, over 40 transcriptional factors and over 40 E3 ligases, revealing the complexity of regulation of cold adaption. We summarized cold responsive phosphoproteins involved in phospholipid signaling, cytoskeleton reorganization, calcium signaling, and MAPK cascades. Cold-altered levels of 73 phosphopeptides (mostly novel cold-responsive) representing 62 proteins were validated by parallel reaction monitoring (PRM). In summary, this study furthers our understanding of the molecular mechanisms of cold adaption in plants and strongly supports that DIA coupled with PRM are valuable tools in uncovering early signaling events in plants.

6-Benzyladenine increasing subsequent waterlogging-induced waterlogging tolerance of summer maize by increasing hormone signal transduction

Summer maize is frequently subjected to waterlogging damage because of increased and variable rainfall during the growing season. The application of 6-benzyladenine (6-BA) can effectively mitigate the waterlogging effects on plant growth and increase the grain yield of waterlogged summer maize. However, the mechanisms underlying this process and the involvement of 6-BA in relevant signal transduction pathways remain unclear. In this study, we explored the effects of 6-BA on waterlogged summer maize using a phosphoproteomic technique to better understand the mechanism by which summer maize growth improves following waterlogging. Application of 6-BA inhibited the waterlogging-induced increase in abscisic acid (ABA) content and increased the phosphorylation levels of proteins involved in ABA signaling; accordingly, stomatal responsiveness to exogenous ABA increased. In addition, the application of 6-BA had a long-term effect on signal transduction pathways and contributed to rapid responses to subsequent stresses. Plants primed with 6-BA accumulated more ethylene and jasmonic acid in response to subsequent waterlogging; accordingly, leaf SPAD, antioxidase activity, and root traits improved by 6-BA priming. These results suggest that the effects of 6-BA on hormone signal transduction pathways are anamnestic, which enables plants to show faster or stronger defense responses to stress.

Cross-Tolerance and Autoimmunity as Missing Links in Abiotic and Biotic Stress Responses in Plants: A Perspective toward Secondary Metabolic Engineering

Plants employ a diversified array of defense activities when they encounter stress. Continuous activation of defense pathways that were induced by mutation or altered expression of disease resistance genes and mRNA surveillance mechanisms develop abnormal phenotypes. These plants show continuous defense genes' expression, reduced growth, and also manifest tissue damage by apoptosis. These macroscopic abrasions appear even in the absence of the pathogen and can be attributed to a condition known as autoimmunity. The question is whether it is possible to develop an autoimmune mutant that does not fetch yield and growth penalty and provides enhanced protection against various biotic and abiotic stresses via secondary metabolic pathways' engineering. This review is a discussion about the common stress-fighting mechanisms, how the concept of cross-tolerance instigates propitious or protective autoimmunity, and how it can be achieved by engineering secondary metabolic pathways.

Phosphoproteome analysis reveals the involvement of protein dephosphorylation in ethylene-induced corolla senescence in petunia

BACKGROUND

Senescence represents the last stage of flower development. Phosphorylation is the key posttranslational modification that regulates protein functions, and kinases may be more required than phosphatases during plant growth and development. However, little is known about global phosphorylation changes during flower senescence.

RESULTS

In this work, we quantitatively investigated the petunia phosphoproteome following ethylene or air treatment. In total, 2170 phosphosites in 1184 protein groups were identified, among which 2059 sites in 1124 proteins were quantified. To our surprise, treatment with ethylene resulted in 697 downregulated and only 117 upregulated phosphosites using a 1.5-fold threshold (FDR < 0.05), which showed that ethylene negatively regulates global phosphorylation levels and that phosphorylation of many proteins was not necessary during flower senescence. Phosphoproteome analysis showed that ethylene regulates ethylene and ABA signalling transduction pathways via phosphorylation levels. One of the major targets of ethylene-induced dephosphorylation is the plant mRNA splicing machinery, and ethylene treatment increases the number of alternative splicing events of precursor RNAs in petunia corollas.

CONCLUSIONS

Protein dephosphorylation could play an important role in ethylene-induced senescence, and ethylene treatment increased the number of AS precursor RNAs in petunia corollas.

Verticillium dahliae secretory effector PevD1 induces leaf senescence by promoting ORE1-mediated ethylene biosynthesis

Leaf senescence, the final stage of leaf development, is influenced by numerous internal and environmental signals. However, how biotic stresses such as pathogen infection regulate leaf senescence remains largely unclear. In this study, we found that the premature leaf senescence in Arabidopsis caused by the soil-borne vascular fungus Verticillium dahliae was impaired by disruption of a protein elicitor from V. dahliae 1 named PevD1. Constitutive or inducible overexpression of PevD1 accelerated Arabidopsis leaf senescence. Interestingly, a senescence-associated NAC transcription factor, ORE1, was targeted by PevD1. PevD1 could interact with and stabilize ORE1 protein by disrupting its interaction with the RING-type ubiquitin E3 ligase NLA. Mutation of ORE1 suppressed the premature senescence caused by overexpressing PevD1, whereas overexpression of ORE1 or PevD1 led to enhanced ethylene production and thereby leaf senescence. We showed that ORE1 directly binds the promoter of ACS6 and promotes its expression for mediating PevD1-induced ethylene biosynthesis. Loss-of-function of ACSs could suppress V. dahliae-induced leaf senescence in ORE1-overexpressing plants. Furthermore, we found thatPevD1 also interacts with Gossypium hirsutum ORE1 (GhORE1) and that virus-induced gene silencing of GhORE1 delays V. dahliae-triggered leaf senescence in cotton, indicating a possibly conserved mechanism in plants. Taken together, these results suggest that V. dahliae induces leaf senescence by secreting the effector PevD1 to manipulate the ORE1-ACS6 cascade, providing new insights into biotic stress-induced senescence in plants.

Novel Translational and Phosphorylation Modification Regulation Mechanisms of Tomato (Solanum lycopersicum) Fruit Ripening Revealed by Integrative Proteomics and Phosphoproteomics

The tomato is a research model for fruit-ripening, however, its fruit-ripening mechanism still needs more extensive and in-depth exploration. Here, using TMT and LC-MS, the proteome and phosphoproteome of AC⁺⁺ (wild type) and rin (ripening-inhibitor) mutant fruits were studied to investigate the translation and post-translational regulation mechanisms of tomato fruit-ripening. A total of 6141 proteins and 4011 phosphorylation sites contained quantitative information. One-hundred proteins were identified in both omics’ profiles, which were mainly found in ethylene biosynthesis and signal transduction, photosynthesis regulation, carotenoid and flavonoid biosynthesis, chlorophyll degradation, ribosomal subunit expression changes, MAPK pathway, transcription factors and kinases. The affected protein levels were correlated with their corresponding gene transcript levels, such as NAC-NOR, MADS-RIN, IMA, TAGL1, MADS-MC and TDR4. Changes in the phosphorylation levels of NAC-NOR and IMA were involved in the regulation of tomato fruit-ripening. Although photosynthesis was inhibited, there were diverse primary and secondary metabolic pathways, such as glycolysis, fatty acid metabolism, vitamin metabolism and isoprenoid biosynthesis, regulated by phosphorylation. These data constitute a map of protein—protein phosphorylation in the regulation of tomato fruit-ripening, which lays the foundation for future in-depth study of the sophisticated molecular mechanisms of fruit-ripening and provide guidance for molecular breeding.

Distinct Functions of Ethylene and ACC in the Basal Land Plant Marchantia polymorpha

Ethylene is a gaseous phytohormone involved in various physiological processes, including fruit ripening, senescence, root hair development and stress responses. Recent genomics studies have suggested that most homologous genes of ethylene biosynthesis and signaling are conserved from algae to angiosperms, whereas the function and biosynthesis of ethylene remain unknown in basal plants. Here, we examined the physiological effects of ethylene, an ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC) and an inhibitor of ethylene perception, silver thiosulfate (STS), in a basal land plant, Marchantia polymorpha. M. polymorpha plants biosynthesized ethylene, and treatment with high concentrations of ACC slightly promoted ethylene production. ACC remarkably suppressed the growth of thalli (vegetative organs) and rhizoids (root-hair-like cells), whereas exogenous ethylene slightly promoted thallus growth. STS suppressed thallus growth and induced ectopic rhizoid formation on the dorsal surface of thalli. Thus, ACC and ethylene have different effects on the vegetative growth of M. polymorpha. We generated single and double mutants of ACC synthase-like (ACSL) genes, MpACSL1 and MpACSL2. The mutants did not show obvious defects in thallus growth, ACC content and ethylene production, indicating that MpACSL genes are not essential for the vegetative growth and biosynthesis of ACC and ethylene. Gene expression analysis suggested the involvement of MpACSL1 and MpACSL2 in stress responses. Collectively, our results imply ethylene-independent function of ACC and the absence of ACC-mediated ethylene biosynthesis in M. polymorpha.

Soybean responds to phosphate starvation through reversible protein phosphorylation

Phosphorus (P) deficiency is considered as a major constraint on crop production. Although a set of adaptative strategies are extensively suggested in soybean (Glycine max) to phosphate (Pi) deprivation, molecular mechanisms underlying reversible protein phosphorylation in soybean responses to P deficiency remains largely unclear. In this study, isobaric tags for relative and absolute quantitation, combined with liquid chromatography and tandem mass spectrometry analysis was performed to identify differential phosphoproteins in soybean roots under Pi sufficient and deficient conditions. A total of 427 phosphoproteins were found to exhibit differential accumulations, with 213 up-regulated and 214 down-regulated. Among them, a nitrate reductase, GmNR4 exhibiting increased phosphorylation levels under low Pi conditions, was further selected to evaluate the effects of phosphorylation on its nitrate reductase activity and subcellular localization. Mutations of GmNR4 phosphorylation levels significantly influenced its activity in vitro, but not for its subcellular localization. Taken together, identification of differential phosphoproteins reveled the complex regulatory pathways for soybean adaptation to Pi starvation through reversible protein phosphorylation.

Sphingolipid Profile during Cotton Fiber Growth Revealed That a Phytoceramide Containing Hydroxylated and Saturated VLCFA Is Important for Fiber Cell Elongation

Cotton fiber is a single-celled seed trichrome that arises from the epidermis of the ovule’s outer integument. The fiber cell displays high polar expansion and thickens but not is disrupted by cell division. Therefore, it is an ideal model for studying the growth and development of plant cells. Sphingolipids are important components of membranes and are also active molecules in cells. However, the sphingolipid profile during fiber growth and the differences in sphingolipid metabolism at different developmental stages are still unclear. In this study, we detected that there were 6 classes and 95 molecular species of sphingolipids in cotton fibers by ultrahigh performance liquid chromatography-MS/MS (UHPLC-MS/MS). Among these, the phytoceramides (PhytoCer) contained the most molecular species, and the PhytoCer content was highest, while that of sphingosine-1-phosphate (S1P) was the lowest. The content of PhytoCer, phytoceramides with hydroxylated fatty acyls (PhytoCer-OHFA), phyto-glucosylceramides (Phyto-GluCer), and glycosyl-inositol-phospho-ceramides (GIPC) was higher than that of other classes in fiber cells. With the development of fiber cells, phytosphingosine-1-phosphate (t-S1P) and PhytoCer changed greatly. The sphingolipid molecular species Ceramide (Cer) d18:1/26:1, PhytoCer t18:1/26:0, PhytoCer t18:0/26:0, PhytoCer t18:1/h20:0, PhytoCer t18:1/h26:0, PhytoCer t18:0/h26:0, and GIPC t18:0/h16:0 were significantly enriched in 10-DPA fiber cells while Cer d18:1/20:0, Cer d18:1/22:0, and GIPC t18:0/h18:0 were significantly enriched in 20-DPA fiber cells, indicating that unsaturated PhytoCer containing hydroxylated and saturated very long chain fatty acids (VLCFA) play some role in fiber cell elongation. Consistent with the content analysis results, the related genes involved in long chain base (LCB) hydroxylation and unsaturation as well as VLCFA synthesis and hydroxylation were highly expressed in rapidly elongating fiber cells. Furthermore, the exogenous application of a potent inhibitor of serine palmitoyltransferase, myriocin, severely blocked fiber cell elongation, and the exogenous application of sphingosine antagonized the inhibition of myriocin for fiber elongation. Taking these points together, we concluded that sphingolipids play crucial roles in fiber cell elongation and SCW deposition. This provides a new perspective for further studies on the regulatory mechanism of the growth and development of cotton fiber cells.

Arabidopsis WRKY71 regulates ethylene-mediated leaf senescence by directly activating EIN2, ORE1 and ACS2 genes

Leaf senescence is a pivotal step in the last stage of the plant life cycle and is influenced by various external and endogenous cues. A series of reports have indicated the involvement of the WRKY transcription factors in regulating leaf senescence, but the molecular mechanisms and signaling pathways remain largely unclear. Here we provide evidence demonstrating that WRKY71 acts as a positive regulator of leaf senescence in Arabidopsis. WRKY71-1D, an overexpressor of WRKY71, exhibited early leaf senescence, while wrky71-1, the WRKY71 loss-of-function mutant, displayed delayed leaf senescence. Accordingly, a set of senescence-associated genes (SAGs) were substantially elevated in WRKY71-1D but markedly decreased in wrky71-1. Chromatin immunoprecipitation assays indicated that WRKY71 can bind directly to the promoters of SAG13 and SAG201. Transcriptome analysis suggested that WRKY71 might mediate multiple cues to accelerate leaf senescence, such as abiotic stresses, dark and ethylene. WRKY71 was ethylene inducible, and treatment with the ethylene precursor 1-amino-cyclopropane-1-carboxylic acid enhanced leaf senescence in WRKY71-1D but caused only a marginal delay in leaf senescence in wrky71-1. In vitro and in vivo assays demonstrated that WRKY71 can directly regulate ETHYLENE INSENSITIVE2 (EIN2) and ORESARA1 (ORE1), genes of the ethylene signaling pathway. Consistently, leaf senescence of WRKY71-1D was obviously retarded in the ein2-5 and nac2-1 mutants. Moreover, WRKY71 was also proved to interact with ACS2 in vitro and in vivo. Treatment with AgNO₃ and aminoethoxyvinylglycine and acs2-1 could greatly arrest the leaf senescence of WRKY71-1D. In conclusion, our data revealed that WRKY71 mediates ethylene signaling and synthesis to hasten leaf senescence in Arabidopsis.

Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato

Late blight caused by Phytophthora infestans is one of the most devastating diseases in potatoes and tomatoes. At present, several late blight resistance genes have been mapped and cloned. To better understand the transcriptome changes during the incompatible interaction process between R3a and Avr3a, in this study, after spraying DEX, the leaves of MM-R3a-Avr3a and MM-Avr3a transgenic plants at different time points were used for comparative transcriptome analysis. A total of 7,324 repeated DEGs were detected in MM-R3a-Avr3a plants at 2-h and 6-h, and 729 genes were differentially expressed at 6-h compared with 2-h. Only 1,319 repeated DEGs were found in MM-Avr3a at 2-h and 6-h, of which 330 genes have the same expression pattern. Based on GO, KEGG and WCGNA analysis of DEGs, the phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly up-regulated. Parts of the down-regulated DEGs were enriched in carbon metabolism and the photosynthesis process. Among these DEGs, most of the transcription factors, such as WRKY, MYB, and NAC, related to disease resistance or endogenous hormones SA and ET pathways, as well as PR, CML, SGT1 gene were also significantly induced. Our results provide transcriptome-wide insights into R3a and Avr3a-mediated incompatibility interaction.

Ethylene-induced stomatal closure is mediated via MKK1/3-MPK3/6 cascade to EIN2 and EIN3

Mitogen-activated protein kinases (MPKs) play essential roles in guard cell signaling, but whether MPK cascades participate in guard cell ethylene signaling and interact with hydrogen peroxide (H₂ O₂ ), nitric oxide (NO), and ethylene-signaling components remain unclear. Here, we report that ethylene activated MPK3 and MPK6 in the leaves of wild-type Arabidopsis thaliana as well as ethylene insensitive2 (ein2), ein3, nitrate reductase1 (nia1), and nia2 mutants, but this effect was impaired in ethylene response1 (etr1), nicotinamide adenine dinucleotide phosphate oxidase AtrbohF, mpk kinase1 (mkk1), and mkk3 mutants. By contrast, the constitutive triple response1 (ctr1) mutant had constitutively active MPK3 and MPK6. Yeast two-hybrid, bimolecular fluorescence complementation, and pull-down assays indicated that MPK3 and MPK6 physically interacted with MKK1, MKK3, and the C-terminal region of EIN2 (EIN2 CEND). mkk1, mkk3, mpk3, and mpk6 mutants had typical levels of ethylene-induced H₂ O₂ generation but impaired ethylene-induced EIN2 CEND cleavage and nuclear translocation, EIN3 protein accumulation, NO production in guard cells, and stomatal closure. These results show that the MKK1/3-MPK3/6 cascade mediates ethylene-induced stomatal closure by functioning downstream of ETR1, CTR1, and H₂ O₂ to interact with EIN2, thereby promoting EIN3 accumulation and EIN3-dependent NO production in guard cells.

The RING E3 ligase SDIR1 destabilizes EBF1/EBF2 and modulates the ethylene response to ambient temperature fluctuations in Arabidopsis

The gaseous phytohormone ethylene mediates numerous aspects of plant growth and development as well as stress responses. The F-box proteins EIN3-binding F-box protein 1 (EBF1) and EBF2 are key components that ubiquitinate and degrade the master transcription factors ethylene insensitive 3 (EIN3) and EIN3-like 1 (EIL1) in the ethylene response pathway. Notably, EBF1 and EBF2 themselves undergo the 26S proteasome-mediated proteolysis induced by ethylene and other stress signals. However, despite their importance, little is known about the mechanisms regulating the degradation of these proteins. Here, we show that a really interesting new gene (RING)-type E3 ligase, salt- and drought-induced ring finger 1 (SDIR1), positively regulates the ethylene response and promotes the accumulation of EIN3. Further analyses indicate that SDIR1 directly interacts with EBF1/EBF2 and targets them for ubiquitination and proteasome-dependent degradation. We show that SDIR1 is required for the fine tuning of the ethylene response to ambient temperature changes by mediating temperature-induced EBF1/EBF2 degradation and EIN3 accumulation. Thus, our work demonstrates that SDIR1 functions as an important modulator of ethylene signaling in response to ambient temperature changes, thereby enabling plant adaptation under fluctuating environmental conditions.

The transcription factor WRKY32 affects tomato fruit colour by regulating YELLOW FRUITED-TOMATO 1, a core component of ethylene signal transduction

Fruit quality in most fleshy fruit crops is fundamentally linked to ripening-associated traits, including changes in colour. In many climacteric fruits, including tomato (Solanum lycopersicum), the phytohormone ethylene plays a key role in regulating ripening. Previous map-based cloning of YELLOW FRUITED-TOMATO 1 (YFT1) revealed that it encodes the EIN2 protein, a core component in ethylene signal transduction. A YFT1 allele with a genetic lesion was found to be down-regulated in the yft1 tomato mutant that has a yellow fruit phenotype and perturbed ethylene signalling. Based on bioinformatic analysis, yeast one hybrid assays and electrophoretic mobility shift assays, we report that transcription factor WRKY32 regulates tomato fruit colour formation. WRKY32 binds to W-box and W-box-like motifs in the regulatory region of the YFT1 promoter and induces its expression. In tomato fruits of WRKY32-RNAi generated lines, ethylene signalling was reduced, leading to a suppression in ethylene emission, a delay in chromoplast development, decreased carotenoid accumulation, and a yellow fruit phenotype. These results provide new insights into the regulatory networks that govern tomato fruit colour formation via ethylene signal transduction.

EIN2-directed histone acetylation requires EIN3-mediated positive feedback regulation in response to ethylene

Ethylene is an important phytohormone with pleotropic roles in plant growth, development, and stress responses. ETHYLENE INSENSITIVE2 (EIN2) mediates the transduction of the ethylene signal from the endoplasmic reticulum membrane to the nucleus, where its C-terminus (EIN2-C) regulates histone acetylation to mediate transcriptional regulation by EIN3. However, no direct interaction between EIN2-C and EIN3 has been detected. To determine how EIN2-C and EIN3 act together, we followed a synthetic approach and engineered a chimeric EIN2-C with EIN3 DNA-binding activity but lacking its transactivation activity (EIN2C-EIN3DB). The overexpression of EIN2C-EIN3DB in either wild-type or in the ethylene-insensitive mutant ein3-1 eil1-1 led to a partial constitutive ethylene response. Chromatin immunoprecipitation sequencing showed that EIN2C-EIN3DB has DNA-binding activity, indicating that EIN3DB is functional in EIN2C-EIN3DB. Furthermore, native EIN3 protein levels determine EIN2C-EIN3DB binding activity and binding targets in a positive feedback loop by interacting with EIN2C-EIN3DB to form a heterodimer. Additionally, although EIN3 does not direct affect histone acetylation levels in the absence of EIN2, it is required for the ethylene-induced elevation of H3K14Ac and H3K23Ac in the presence of EIN2. Together, we reveal efficient and specific DNA-binding by dimerized EIN3 in the presence of ethylene to mediate positive feedback regulation, which is required for EIN2-directed elevation of histone acetylation to integrate into an EIN3-dependent transcriptional activation.

Essential Roles of the Linker Sequence Between Tetratricopeptide Repeat Motifs of Ethylene Overproduction 1 in Ethylene Biosynthesis

Ethylene Overproduction 1 (ETO1) is a negative regulator of ethylene biosynthesis. However, the regulation mechanism of ETO1 remains largely unclear. Here, a novel eto1 allele (eto1-16) was isolated with typical triple phenotypes due to an amino acid substitution of G480C in the uncharacterized linker sequence between the TPR1 and TPR2 motifs. Further genetic and biochemical experiments confirmed the eto1-16 mutation site. Sequence analysis revealed that G480 is conserved not only in two paralogs, EOL1 and EOL2, in Arabidopsis, but also in the homologous protein in other species. The glycine mutations (eto1-11, eto1-12, and eto1-16) do not influence the mRNA abundance of ETO1, which is reflected by the mRNA secondary structure similar to that of WT. According to the protein-protein interaction analysis, the abnormal root phenotype of eto1-16 might be caused by the disruption of the interaction with type 2 1-aminocyclopropane-1-carboxylic acid (ACC) synthases (ACSs) proteins. Overall, these data suggest that the linker sequence between tetratricopeptide repeat (TPR) motifs and the glycine in TPR motifs or the linker region are essential for ETO1 to bind with downstream mediators, which strengthens our knowledge of ETO1 regulation in balancing ACSs.

Post-translational Modifications of bZIP Transcription Factors in Abscisic Acid Signaling and Drought Responses

Under drought stress, plants have developed various mechanisms to survive in the reduced water supply, of which the regulation of stress-related gene expression is responsible for several transcription factors. The basic leucine zippers (bZIPs) are one of the largest and most diverse transcription factor families in plants. Among the 10 Arabidopsis bZIP groups, group A bZIP transcription factors function as a positive or negative regulator in ABA signal transduction and drought stress response. These bZIP transcription factors, which are involved in the drought response, have also been isolated in various plant species such as rice, pepper, potato, and maize. Recent studies have provided substantial evidence that many bZIP transcription factors undergo the post-translational modifications, through which the regulation of their activity or stability affects plant responses to various intracellular or extracellular stimuli. This review aims to address the modulation of the bZIP proteins in ABA signaling and drought responses through phosphorylation, ubiquitination and sumoylation.

Pathogen-inducible OsMPKK10.2-OsMPK6 cascade phosphorylates the Raf-like kinase OsEDR1 and inhibits its scaffold function to promote rice disease resistance

Mitogen-activated protein kinase (MAPK) cascades regulate a myriad of plant biological processes, including disease resistance. Plant genomes encode a large number of MAPK kinase kinases (MAPKKKs) that can be divided into two subfamilies, namely MEKK-like kinases and Raf-like kinases. Thus far, the functions of MEKK-like MAPKKKs have been relatively well characterized, but the roles of Raf-like MAPKKKs in plant MAPK cascades remain less understood. Here, we report the role of OsEDR1, a Raf-like MAPKKK, in the regulation of the MAPK cascade in rice response to the bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc). We found that OsEDR1 inhibits OsMPKK10.2 (a MAPK kinase) activity through physical interaction. Upon Xoc infection, OsMPKK10.2 is phosphorylated at S304 to activate OsMPK6 (a MAPK). Interestingly, activated OsMPK6 phosphorylates OsEDR1 at S861, which destabilizes OsEDR1 and thus releases the inhibition of OsMPKK10.2, leading to increased OsMPKK10.2 activity and enhanced resistance of rice plants to Xoc. Taken together, these results provide new insights into the functions of Raf-like kinases in the regulation of the MAPK cascade in plant immunity.

Comparative Metabolite and Gene Expression Analyses in Combination With Gene Characterization Revealed the Patterns of Flavonoid Accumulation During Cistus creticus subsp. creticus Fruit Development

Cistus creticus L. subsp. creticus (rockrose) is a shrub widespread in Greece and the Mediterranean basin and has been used in traditional medicine as herb tea for colds, for healing and digestive hitches, for the treatment of maladies, as perfumes, and for other purposes. Compounds from its flavonoid fraction have recently drawn attention due to antiviral action against influenza virus and HIV. Although several bioactive metabolites belonging to this group have been chemically characterized in the leaves, the genes involved in their biosynthesis in Cistus remain largely unknown. Flavonoid metabolism during C. creticus fruit development was studied by adopting comparative metabolomic and transcriptomic approaches. The present study highlights the fruit of C. creticus subsp. creticus as a rich source of flavonols, flavan-3-ols, and proanthocyanidins, all of which displayed a decreasing trend during fruit development. The majority of proanthocyanidins recorded in Cistus fruit are B-type procyanidins and prodelphinidins, while gallocatechin and catechin are the dominant flavan-3-ols. The expression patterns of biosynthetic genes and transcription factors were analyzed in flowers and throughout three fruit development stages. Flavonoid biosynthetic genes were developmentally regulated, showing a decrease in transcript levels during fruit maturation. A high degree of positive correlations between the content of targeted metabolites and the expression of biosynthetic genes indicated the transcriptional regulation of flavonoid biosynthesis during C. creticus fruit development. This is further supported by the high degree of significant positive correlations between the expression of biosynthetic genes and transcription factors. The results suggest that leucoanthocyanidin reductase predominates the biosynthetic pathway in the control of flavan-3-ol formation, which results in catechin and gallocatechin as two of the major building blocks for Cistus proanthocyanidins. Additionally, there is a decline in ethylene production rates during non-climacteric Cistus fruit maturation, which coincides with the downregulation of the majority of flavonoid- and ethylene-related biosynthetic genes and corresponding transcription factors as well as with the decline in flavonoid content. Finally, functional characterization of a Cistus flavonoid hydroxylase (F3'5'H) was performed for the first time.

The Molecular Basis of Age-Modulated Plant De Novo Root Regeneration Decline in Arabidopsis thaliana

Plants possess a regeneration capacity that enables them to survive after wounding. For example, detached Arabidopsis thaliana leaves are able to form adventitious roots from their cutting sites even in the absence of exogenous hormone supplements, as process termed de novo root regeneration (DNRR). Wounding rapidly induces auxin biosynthesis at the cutting sites and then elicits a signaling cascade to promote cell fate transitions and finally generate the adventitious roots. However, rooting rates in older plants are much lower than in younger leaf explants. In this review, we highlight the recent breakthroughs in the understanding of DNRR decay in older plants from at least two independent signaling routes: (i) via the accumulation of EIN3 protein in older plants, which directly suppresses expression of WUSCHEL RELATED HOMEOBOX (WOX) genes to inhibit rooting; (ii) the miR156-SPLs-AP2/ERFs pathway, which modulates root regeneration by reducing auxin biosynthesis.

The root growth reduction in response to mechanical stress involves ethylene-mediated microtubule reorganization and transmembrane receptor-mediated signal transduction in Arabidopsis

We found that mutations in a Ca²⁺-permeable mechanosensitive channel MCA1, an ethylene-regulated microtubule-associated protein WDL5, and a versatile co-receptor BAK1 affect root growth response to mechanical stress. Plant root tips exposed to mechanical impedance show a temporal reduction in the elongation growth. The process involves a transient Ca²⁺ increase in the cytoplasm followed by ethylene signaling. To dissect the molecular mechanisms underlying this response, we examined the root growth of a series of Arabidopsis mutants with potentially altered response to mechanical stress after transfer from vertical to horizontal plates that were covered by dialysis membrane as an impedance. Among the plant hormone-response mutants tested, the ethylene-insensitive mutant ein3 was confirmed to show no growth reduction after the transfer. The root growth reduction was attenuated in a mutant of MCA1 encoding a Ca²⁺-permeable mechanosensitive channel and that of WDL5 encoding an ethylene-regulated microtubule-associated protein. We also found that the growth reduction was enhanced in a mutant of BAK1 encoding a co-receptor that pairs with numerous leucine-rich repeat receptor kinases to modulate growth and immunity. These results suggest the root growth reduction in response to mechanical stress involves ethylene-mediated microtubule reorganization and also transmembrane receptor-mediated signal transduction.

The TOR-EIN2 axis mediates nuclear signalling to modulate plant growth

The evolutionarily conserved target of rapamycin (TOR) kinase acts as a master regulator that coordinates cell proliferation and growth by integrating nutrient, energy, hormone and stress signals in all eukaryotes^1,2. Research has focused mainly on TOR-regulated translation, but how TOR orchestrates the global transcriptional network remains unclear. Here we identify ethylene-insensitive protein 2 (EIN2), a central integrator^3-5 that shuttles between the cytoplasm and the nucleus, as a direct substrate of TOR in Arabidopsis thaliana. Glucose-activated TOR kinase directly phosphorylates EIN2 to prevent its nuclear localization. Notably, the rapid global transcriptional reprogramming that is directed by glucose-TOR signalling is largely compromised in the ein2-5 mutant, and EIN2 negatively regulates the expression of a wide range of target genes of glucose-activated TOR that are involved in DNA replication, cell wall and lipid synthesis and various secondary metabolic pathways. Chemical, cellular and genetic analyses reveal that cell elongation and proliferation processes that are controlled by the glucose-TOR-EIN2 axis are decoupled from canonical ethylene-CTR1-EIN2 signalling, and mediated by different phosphorylation sites. Our findings reveal a molecular mechanism by which a central signalling hub is shared but differentially modulated by diverse signalling pathways using distinct phosphorylation codes that can be specified by upstream protein kinases.

GENOMES UNCOUPLED1-independent retrograde signaling targets the ethylene pathway to repress photomorphogenesis

When germinating in the light, Arabidopsis (Arabidopsis thaliana) seedlings undergo photomorphogenic development, characterized by short hypocotyls, greening, and expanded cotyledons. Stressed chloroplasts emit retrograde signals to the nucleus that induce developmental responses and repress photomorphogenesis. The nuclear targets of these retrograde signals are not yet fully known. Here, we show that lincomycin-treated seedlings (which lack developed chloroplasts) show strong phenotypic similarities to seedlings treated with ethylene (ET) precursor 1-aminocyclopropane-1-carboxylic acid, as both signals inhibit cotyledon separation in the light. We show that the lincomycin-induced phenotype partly requires a functioning ET signaling pathway, but could not detect increased ET emissions in response to the lincomycin treatment. The two treatments show overlap in upregulated gene transcripts, downstream of transcription factors ETHYLENE INSENSITIVE3 and EIN3-LIKE1. The induction of the ET signaling pathway is triggered by an unknown retrograde signal acting independently of GENOMES UNCOUPLED1. Our data show how two apparently different stress responses converge to optimize photomorphogenesis.

Nucleocytoplasmic partitioning as a mechanism to regulate Arabidopsis signaling events

The nucleus is the site of transcription events - compartmentalization of transcription in eukaryotes allows for regulated access to chromatin. The nucleopore, a complex of many intrinsically disorder proteins, acts as the gatekeeper for nuclear entry and exit, and receptors for nuclear localization signals and nuclear export signals interact with both cargo and nucleopore components to facilitate this movement. Thus, regulated occlusion of the nuclear localization signal or nuclear export signal, tethering of proteins, or sequestration in biomolecular condensates can be used to regulate nucleocytoplasmic partitioning. In plants, regulated nucleocytoplasmic partitioning is a key mechanism to regulate signaling pathways, including those involved in various phytohormones, environmental stimuli, and pathogen responses.

Ethylene Signaling Facilitates Plant Adaption to Physical Barriers

The morphological changes are usually observed in the terrestrial plants to respond to physical barriers. The phytohormone ethylene plays an essential role in the morphological development of plants encountering exogenous mechanical impedance, which enables plants to grow optimally in response to physical barriers. Ethylene is shown to regulate these developmental processes directly or in concert with other phytohormones, especially auxin. In this mini review, the involvement of ethylene action in seedling emergence from the soil, root movement within the soil, and parasitic plant invasion of the host plant are described.

Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms

Ethylene is a gaseous hormone which plays important roles in both plant growth and development and stress responses. Based on studies in the dicot model plant species Arabidopsis, a linear ethylene signaling pathway has been established, according to which ethylene is perceived by ethylene receptors and transduced through CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) and ETHYLENE-INSENSITIVE 2 (EIN2) to activate transcriptional reprogramming. In addition to this canonical signaling pathway, an alternative ethylene receptor-mediated phosphor-relay pathway has also been proposed to participate in ethylene signaling. In contrast to Arabidopsis, rice, a monocot, grows in semiaquatic environments and has a distinct plant structure. Several novel regulators and/or mechanisms of the rice ethylene signaling pathway have recently been identified, indicating that the ethylene signaling pathway in rice has its own unique features. In this review, we summarize the latest progress and compare the conserved and divergent aspects of the ethylene signaling pathway between Arabidopsis and rice. The crosstalk between ethylene and other plant hormones is also reviewed. Finally, we discuss how ethylene regulates plant growth, stress responses and agronomic traits. These analyses should help expand our knowledge of the ethylene signaling mechanism and could further be applied for agricultural purposes.

RPW8.1 enhances the ethylene-signaling pathway to feedback-attenuate its mediated cell death and disease resistance in Arabidopsis

The Arabidopsis RESISTANCE TO POWDERY MILDEW 8.1 (RPW8.1) activates confined cell death and defense against different pathogens. However, the underlying regulatory mechanisms still remain elusive. Here, we show that RPW8.1 activates ethylene signaling that, in turn, negatively regulates RPW8.1 expression. RPW8.1 binds and stabilizes 1-aminocyclopropane-1-carboxylate oxidase 4 (ACO4), which may in part explain increased ethylene production and signaling in RPW8.1-expressing plants. In return, ACO4 and other key components of ethylene signaling negatively regulate RPW8.1-mediated cell death and disease resistance via suppressing RPW8.1 expression. Loss of function in ACO4, EIN2, EIN3 EIL1, ERF6, ERF016 or ORA59 increases RPW8.1-mediated cell death and defense response. By contrast, overexpression of EIN3 abolishes or significantly compromises RPW8.1-mediated cell death and disease resistance. Furthermore, ERF6, ERF016 and ORA59 appear to act as trans-repressors of RPW8.1, with OAR59 being able to directly bind to the RPW8.1 promoter. Taken together, our results have revealed a feedback regulatory circuit connecting RPW8.1 and the ethylene-signaling pathway, in which RPW8.1 enhances ethylene signaling, and the latter, in return, negatively regulates RPW8.1-mediated cell death and defense response via suppressing RPW8.1 expression to attenuate its defense activity.

Signal Integration in Plant Abiotic Stress Responses via Multistep Phosphorelay Signaling

Plants growing in any particular geographical location are exposed to variable and diverse environmental conditions throughout their lifespan. The multifactorial environmental pressure resulted into evolution of plant adaptation and survival strategies requiring ability to integrate multiple signals that combine to yield specific responses. These adaptive responses enable plants to maintain their growth and development while acquiring tolerance to a variety of environmental conditions. An essential signaling cascade that incorporates a wide range of exogenous as well as endogenous stimuli is multistep phosphorelay (MSP). MSP mediates the signaling of essential plant hormones that balance growth, development, and environmental adaptation. Nevertheless, the mechanisms by which specific signals are recognized by a commonly-occurring pathway are not yet clearly understood. Here we summarize our knowledge on the latest model of multistep phosphorelay signaling in plants and the molecular mechanisms underlying the integration of multiple inputs including both hormonal (cytokinins, ethylene and abscisic acid) and environmental (light and temperature) signals into a common pathway. We provide an overview of abiotic stress responses mediated via MSP signaling that are both hormone-dependent and independent. We highlight the mutual interactions of key players such as sensor kinases of various substrate specificities including their downstream targets. These constitute a tightly interconnected signaling network, enabling timely adaptation by the plant to an ever-changing environment. Finally, we propose possible future directions in stress-oriented research on MSP signaling and highlight its potential importance for targeted crop breeding.

Multi-Walled Carbon Nanotubes Can Promote Brassica napus L. and Arabidopsis thaliana L. Root Hair Development through Nitric Oxide and Ethylene Pathways

Here, we report that multi-walled carbon nanotubes (MWCNTs) can promote plant root hair growth in the species analyzed in this study; however, low and excessive concentrations of MWCNTs had no significant effect or even an inhibiting influence. Further results show that MWCNTs can enter rapeseed root cells. Meanwhile, nitrate reductase (NR)-dependent nitric oxide (NO) and ethylene syntheses, as well as root hair formation, were significantly stimulated by MWCNTs. Transcription of root hair growth-related genes were also modulated. The above responses were sensitive to the removal of endogenous NO or ethylene with a scavenger of NO or NO/ethylene synthesis inhibitors. Pharmacological and molecular evidence suggested that ethylene might act downstream of NR-dependent NO in MWCNTs-induced root hair morphogenesis. Genetic evidence in Arabidopsis further revealed that MWCNTs-triggered root hair growth was abolished in ethylene-insensitive mutants ein2-5 and ein3-1, and NR mutant nia1/2, but not in noa1 mutant. Further data placed NO synthesis linearly before ethylene production in root hair development triggered by MWCNTs. The above findings thus provide some insights into the molecular mechanism underlying MWCNTs control of root hair morphogenesis.

Sphingolipids in plants: a guidebook on their function in membrane architecture, cellular processes, and environmental or developmental responses

Sphingolipids are fundamental lipids involved in various cellular, developmental and stress-response processes. As such, they orchestrate not only vital molecular mechanisms of living cells but also act in diseases, thus qualifying as potential pharmaceutical targets. Sphingolipids are universal to eukaryotes and are also present in some prokaryotes. Some sphingolipid structures are conserved between animals, plants and fungi, whereas others are found only in plants and fungi. In plants, the structural diversity of sphingolipids, as well as their downstream effectors and molecular and cellular mechanisms of action, are of tremendous interest to both basic and applied researchers, as about half of all small molecules in clinical use originate from plants. Here, we review recent advances towards a better understanding of the biosynthesis of sphingolipids, the diversity in their structures as well as their functional roles in membrane architecture, cellular processes such as membrane trafficking and cell polarity, and cell responses to environmental or developmental signals.

TREE1-EIN3-mediated transcriptional repression inhibits shoot growth in response to ethylene

Ethylene is an important plant hormone that regulates plant growth, in which the master transcriptionactivator EIN3 (Ethylene Insensitive 3)-mediated transcriptional activation plays vital roles. However, the EIN3-mediated transcriptional repression in ethylene response is unknown. We report here that a Transcriptional Repressor of EIN3-dependent Ethylene-response 1 (TREE1) interacts with EIN3 to regulate transcriptional repression that leads to an inhibition of shoot growth in response to ethylene. Tissue-specific transcriptome analysis showed that most of the genes are down-regulated by ethylene in shoots, and a DNA binding motif was identified that is important for this transcriptional repression. TREE1 binds to the DNA motif to repress gene expression in an EIN3-dependent manner. Genetic validation demonstrated that repression of TREE1-targeted genes leads to an inhibition of shoot growth. Overall, this work establishes a mechanism by which transcriptional repressor TREE1 interacts with EIN3 to inhibit shoot growth via transcriptional repression in response to ethylene.

The fungal elicitor AsES requires a functional ethylene pathway to activate the innate immunity in strawberry

Acremonium strictum Elicitor Subtilisin (AsES) is a fungal elicitor that activates innate immunity, conferring disease resistance in strawberry (Fragaria × ananassa Duch.), Arabidopsis and other plant species. The aim of the present work was to evaluate the involvement of the ethylene (ET) signalling pathway in AsES-mediated immune response in strawberry. Ethylene production and expression of the genes responsible for ET synthesis, perception and response were measured after AsES treatment. ROS (H₂ O₂ ) accumulation and immunity induced by AsES were studied after ET perception was blocked by 1-methylcyclopropene (1-MCP). Biochemical and molecular results showed that AsES induced a marked increase in local and systemic biosynthesis of ET, both in a biphasic manner. Blocking of ET perception by 1-MCP prior to AsES induction reduced production of ROS (H₂ O₂ ) and prevented AsES from eliciting defence against fungal pathogens having different lifestyles, such as Botrytis cinerea (necrotrophic) and Colletotrichum acutatum (hemibiotrophic). These findings contribute to elucidate the mode of action of the novel elicitor subtilase, AsES, specifically regarding the role of ET signalling in the activation of plant innate immunity, in addition to the multitude of processes regulated by ET in plants.

Yellow-fruited phenotype is caused by 573 bp insertion at 5' UTR of YFT1 allele in yft1 mutant tomato

The yft1 tomato mutant has a yellow-fruited phenotype controlled by a recessive gene of YFT1 allele, which has been shown by map-based cloning to be a homolog of ETHYLENE INSENSITIVE 2 (EIN2). Genetic lesion of YFT1 allele in yft1 is attributed to a 573 bp DNA fragment (IF₅₇₃) insertion at 1,200 bp downstream of the transcription start site. Transcriptomic analysis revealed that YFT1 lesion resulted in 5,053 differentially expressed genes (DEGs) in yft1 pericarp compared with the M82 wild type cultivar. These were annotated as being involved in ethylene synthesis, chromoplast development, and carotenoid synthesis. The YFT1 lesion caused a reduction in its own transcript levels in yft1 and impaired ethylene emission and signal transduction, delayed chromoplast development and decreased carotenoid accumulation. The molecular mechanism underlying the downregulated YFT1 allele in yft1 was examined at both RNA and DNA levels. The IF₅₇₃ event appeared to introduce two negative regulatory sequences located at -272 to -173 bp and -172 to -73 bp in the YFT1 allele promoter, causing alterative splicing due to introduction of aberrant splicing sites, and breaking upstream open reading frames (uORF) structure in the 5'-UTR. Those results a new provided insight into molecular regulation of color formation in tomato fruit.

Ethylene signaling mediates host invasion by parasitic plants

Parasitic plants form a specialized organ, a haustorium, to invade host tissues and acquire water and nutrients. To understand the molecular mechanism of haustorium development, we performed a forward genetics screening to isolate mutants exhibiting haustorial defects in the model parasitic plant Phtheirospermum japonicum. We isolated two mutants that show prolonged and sometimes aberrant meristematic activity in the haustorium apex, resulting in severe defects on host invasion. Whole-genome sequencing revealed that the two mutants respectively have point mutations in homologs of ETHYLENE RESPONSE 1 (ETR1) and ETHYLENE INSENSITIVE 2 (EIN2), signaling components in response to the gaseous phytohormone ethylene. Application of the ethylene signaling inhibitors also caused similar haustorial defects, indicating that ethylene signaling regulates cell proliferation and differentiation of parasite cells. Genetic disruption of host ethylene production also perturbs parasite invasion. We propose that parasitic plants use ethylene as a signal to invade host roots.

Phytohormone signaling mechanisms and genetic methods for their modulation and detection

Phytohormones enable plants to regulate their development, growth and physiology according to the environmental requirements. Knowledge about the underlying signaling mechanisms, combined with the ability to pharmacologically or genetically manipulate phytohormone responses is steadily being incorporated into modern plant biology research and agriculture. This knowledge also enabled the development of genetically encoded phytohormone indicators that allow the tracking of spatiotemporal phytohormone dynamics and signaling processes in vivo. This review aims to provide an overview about core phytohormone signaling mechanisms, and about genetic tools for the manipulation and in vivo tracking of phytohormone actions.

No Home without Hormones: How Plant Hormones Control Legume Nodule Organogenesis

The establishment of symbiotic nitrogen fixation requires the coordination of both nodule development and infection events. Despite the evolution of a variety of anatomical structures, nodule organs serve a common purpose in establishing a localized area that facilitates efficient nitrogen fixation. As in all plant developmental processes, the establishment of a new nodule organ is regulated by plant hormones. During nodule initiation, regulation of plant hormone signaling is one of the major targets of symbiotic signaling. We review the role of major developmental hormones in the initiation of the nodule organ and argue that the manipulation of plant hormones is a key requirement for engineering nitrogen fixation in non-legumes as the basis for improved food security and sustainability.

ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm

Double digest restriction-site associated sequencing (ddRAD-seq) is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections. Using this methodology, we investigated the genomic diversity of a panel of 288 diverse tomato (Solanum lycopersicum L.) accessions enriched in 'da serbo' (called 'de penjar' in Spain) long shelf life (LSL) materials (152 accessions) mostly originating from Italy and Spain. The rest of the materials originate from different countries and include landraces for fresh consumption, elite cultivars, heirlooms, and breeding lines. Apart from their LSL trait, 'da serbo' landraces are of remarkable interest for their resilience. We identified 32,799 high-quality SNPs, which were used for model ancestry population structure and non-parametric hierarchical clustering. Six genetic subgroups were revealed, clearly separating most 'da serbo' landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on type and geographical provenance. Linkage disequilibrium (LD) in the collection decayed very rapidly within <5 kb. We then investigated SNPs showing contrasted minor frequency allele (MAF) in 'da serbo' materials, resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such as CTR1 and JAR1. Finally, a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits. Our findings suggest the presence of a genetic footprint of the 'da serbo' germplasm selected in the Mediterranean basin. Moreover, we provide novel insights on LSL 'da serbo' germplasm as a promising source of alleles for tolerance to stresses.

A CEP Peptide Receptor-Like Kinase Regulates Auxin Biosynthesis and Ethylene Signaling to Coordinate Root Growth and Symbiotic Nodulation in Medicago truncatula

Because of the large amount of energy consumed during symbiotic nitrogen fixation, legumes must balance growth and symbiotic nodulation. Both lateral roots and nodules form on the root system, and the developmental coordination of these organs under conditions of reduced nitrogen (N) availability remains elusive. We show that the Medicago truncatula COMPACT ROOT ARCHITECTURE2 (MtCRA2) receptor-like kinase is essential to promote the initiation of early symbiotic nodulation and to inhibit root growth in response to low N. C-TERMINALLY ENCODED PEPTIDE (MtCEP1) peptides can activate MtCRA2 under N-starvation conditions, leading to a repression of YUCCA2 (MtYUC2) auxin biosynthesis gene expression, and therefore of auxin root responses. Accordingly, the compact root architecture phenotype of cra2 can be mimicked by an auxin treatment or by overexpressing MtYUC2, and conversely, a treatment with YUC inhibitors or an MtYUC2 knockout rescues the cra2 root phenotype. The MtCEP1-activated CRA2 can additionally interact with and phosphorylate the MtEIN2 ethylene signaling component at Ser643 and Ser924, preventing its cleavage and thereby repressing ethylene responses, thus locally promoting the root susceptibility to rhizobia. In agreement with this interaction, the cra2 low nodulation phenotype is rescued by an ein2 mutation. Overall, by reducing auxin biosynthesis and inhibiting ethylene signaling, the MtCEP1/MtCRA2 pathway balances root and nodule development under low-N conditions.

Chromatin Regulation in the Response of Ethylene: Nuclear Events in Ethylene Signaling

Plant hormones, produced in response to environmental stimuli, regulate almost all aspects of plant growth and development. Ethylene is a gaseous plant hormone that plays pleotropic roles in plant growth, plant development, fruit ripening, stress responses, and pathogen defenses. After decades of research, the key components of ethylene signaling have been identified and characterized. Although the molecular mechanisms of the sensing of ethylene signal and the transduction of ethylene signaling have been studied extensively, how chromatin influences ethylene signaling and ethylene response is a new area of research. This review describes the current understanding of how chromatin modifications, specifically histone acetylation, regulate ethylene signaling and the ethylene response.

LcEIL2/3 are involved in fruitlet abscission via activating genes related to ethylene biosynthesis and cell wall remodeling in litchi

Fruit crops are subject to precocious fruit abscission, during which the phytohormone ethylene (ET) acts as a major positive regulator. However, the molecular basis of ET-induced fruit abscission remains poorly understood. Here, we show that two ETHYLENE INSENSITIVE 3-like (EIL) homologs in litchi, LcEIL2 and LcEIL3, play a role in ET-activated fruitlet abscission. LcEIL2/3 were significantly upregulated in the fruit abscission zone (AZ) during the ET-induced fruitlet abscission in litchi. The presence of LcEIL2/3 in wild-type Arabidopsis and ein3 eil1 mutants can accelerate the floral organ abscission. Moreover, the electrophoretic mobility shift assay and dual luciferase reporter analysis illustrated that LcEIL2/3 directly interacted with the gene promoters to activate the expression of cell wall remodeling genes LcCEL2/8 and LcPG1/2, and ET biosynthetic genes LcACS1/4/7 and LcACO2/3. Furthermore, we showed that LcPG1/2 were expressed in the floral abscission zone of Arabidopsis, and constitutive expression of LcPG2 in Arabidopsis promoted the floral organ abscission. In conclusion, we propose that LcEIL2/3 are involved in ET-induced fruitlet abscission via controlling expression of genes related to ET biosynthesis and cell wall remodeling in litchi.

Ethylene promotes seed iron storage during Arabidopsis seed maturation via ERF95 transcription factor

Because Iron (Fe) is an essential element, Fe storage in plant seeds is necessary for seedling establishment following germination. However, the mechanisms controlling seed Fe storage during seed development remain largely unknown. Here we reveal that an ERF95 transcription factor regulates Arabidopsis seed Fe accumulation. We show that expression of ERF95 increases during seed maturation, and that lack of ERF95 reduces seed Fe accumulation, consequently increasing sensitivity to Fe deficiency during seedling establishment. Conversely, overexpression of ERF95 has the opposite effects. We show that lack of ERF95 decreases abundance of FER1 messenger RNA in developing seed, which encodes Fe-sequestering ferritin. Accordingly, a fer1-1 loss-of-function mutation confers reduced seed Fe accumulation, and suppresses ERF95-promoted seed Fe accumulation. In addition, ERF95 binds to specific FER1 promoter GCC-boxes and transactivates FER1 expression. We show that ERF95 expression in maturing seed is dependent on EIN3, the master transcriptional regulator of ethylene signaling. While lack of EIN3 reduces seed Fe content, overexpression of ERF95 rescues Fe accumulation in the seed of ein3 loss-of-function mutant. Finally, we show that ethylene production increases during seed maturation. We conclude that ethylene promotes seed Fe accumulation during seed maturation via an EIN3-ERF95-FER1-dependent signaling pathway.

A repressor complex silencing ABA signaling in seeds?

Seed dormancy is induced primarily by abscisic acid (ABA) and maintained through elevated levels of ABA sensitivity in seeds. The core mechanisms of ABA-imposed seed dormancy are emerging, but it is still unclear how these blockages in seeds are eliminated during after-ripening, or what molecular events in imbibed seeds are responsible for the initial stages of germination induction. Some pieces of evidence suggest that a repressor complex, which potentially triggers seed germination through the suppression of ABA signaling components, might be present in seeds. The usual suspect, protein phosphatase 2C, which inactivates kinases and shuts down ABA signaling in the major dormancy pathway, is possibly associated with this complex. Other members, such as WD40 proteins and histone deacetylase subunits, homologs of which are found in the flowering repressor complex, perhaps constitute this complex in seeds. The repressor activity could counteract the dormancy mechanisms in an overwhelming manner, through well-coordinated inactivation and turnover of germination-suppressing transcription factors, which is probably accompanied by chromatin silencing and transcriptional repression of the transcription factor target genes. This review provides a perspective on a putative seed germination-inducing repressor complex, including its possible modes of action and upstream regulators.

Ethylene signaling in plants

Ethylene is a gaseous phytohormone and the first of this hormone class to be discovered. It is the simplest olefin gas and is biosynthesized by plants to regulate plant development, growth, and stress responses via a well-studied signaling pathway. One of the earliest reported responses to ethylene is the triple response. This response is common in eudicot seedlings grown in the dark and is characterized by reduced growth of the root and hypocotyl, an exaggerated apical hook, and a thickening of the hypocotyl. This proved a useful assay for genetic screens and enabled the identification of many components of the ethylene-signaling pathway. These components include a family of ethylene receptors in the membrane of the endoplasmic reticulum (ER); a protein kinase, called constitutive triple response 1 (CTR1); an ER-localized transmembrane protein of unknown biochemical activity, called ethylene-insensitive 2 (EIN2); and transcription factors such as EIN3, EIN3-like (EIL), and ethylene response factors (ERFs). These studies led to a linear model, according to which in the absence of ethylene, its cognate receptors signal to CTR1, which inhibits EIN2 and prevents downstream signaling. Ethylene acts as an inverse agonist by inhibiting its receptors, resulting in lower CTR1 activity, which releases EIN2 inhibition. EIN2 alters transcription and translation, leading to most ethylene responses. Although this canonical pathway is the predominant signaling cascade, alternative pathways also affect ethylene responses. This review summarizes our current understanding of ethylene signaling, including these alternative pathways, and discusses how ethylene signaling has been manipulated for agricultural and horticultural applications.

Comparative analysis of RNA-binding proteomes under Arabidopsis thaliana-Pst DC3000-PAMP interaction by orthogonal organic phase separation

RNA-binding proteins (RBPs) are pivotal participants in post-transcriptional gene regulation. They interact with RNA directly to perform several post-transcriptional RNA regulatory functions or direct metabolic processes. Despite the essential importance, the understanding of plant RBPs is elementary, which derives mainly from other kingdoms via bioinformatic extrapolation or mRNA-binding proteins captured through UV crosslinked method. Recently, orthogonal organic phase separation (OOPS) method for RBP identification has been used in mammals and Escherichia coli. And plentiful RBPs were enriched without molecular tagging or capture of polyadenylated RNA in an unbiased way. In our study, OOPS was conducted on Arabidopsis and 468 RBPs were discovered including 244 putative RBPs. There were 17 peroxidases in 232 RBPs with enzymatic activities. In addition, Arabidopsis thaliana-Pst DC3000-chitinpentaose interaction system was chosen to explore whether OOPS can be used to dig specific RBPs under special physiological conditions. Eighty-four differential RBPs in this system were found and some of them involved in reactive oxygen species (ROS) metabolic pathway. These results showed OOPS can be applied to plants successfully and would be a useful method to identify RBPomes and specific RBPs.

Uncertainty of EIN2Ser645/Ser924 Inactivation by CTR1-Mediated Phosphorylation Reveals the Complexity of Ethylene Signaling

ETHYLENE INSENSITIVE2 (EIN2) is a key component of ethylene signaling whose activity is inhibited upon phosphorylation of Ser⁶⁴⁵ and Ser⁹²⁴ by the Raf-like CONSTITUTIVE TRIPLE-RESPONSE 1 (CTR1) in the absence of ethylene. Ethylene prevents CTR1 activity and thus EIN2^{Ser645/Ser924} phosphorylation, and subcellular trafficking of a proteolytically cleaved EIN2 C terminus (EIN2-C) from the endoplasmic reticulum to the nucleus and processing bodies triggers ethylene signaling. Here, we report an unexpected complexity of EIN2-activated ethylene signaling. EIN2 activation in part requires ethylene in the absence of CTR1-mediated negative regulation. The ein2 mutant was complemented by the transgenes encoding EIN2, EIN2 variants with mutations that either prevent or mimic Ser⁶⁴⁵/Ser⁹²⁴ phosphorylation, or EIN2-C; and all the transgenic lines carrying these EIN2-derived transgenes responded to ethylene. Furthermore, we found that the fluorescence protein-tagged EIN2 and its variants were affected little by ethylene and exhibited similar subcellular distribution patterns: in the cytosolic particles and nuclear speckles. Of note, the subcellular localization patterns of EIN2 proteins fused with a fluorescence protein either at the N or C terminus were similar, whereas EIN2-C-YFP was primarily observed in the cytosol but not in the nucleus. Western blots and mass spectrum analyses suggested a high complexity of EIN2, which is likely proteolytically processed into multiple fragments. Our results suggested a nuclear localization of the full-length EIN2, weak association of the EIN2^{Ser645/Ser924} phosphorylation status and ethylene signaling, and the complexity of ethylene signaling caused by EIN2 and its proteolytic products in different subcellular compartments. We propose an alternative model to explain EIN2-activated ethylene signaling.

All Roads Lead to Auxin: Post-translational Regulation of Auxin Transport by Multiple Hormonal Pathways

Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.