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

Nuclear pyruvate dehydrogenase complex regulates histone acetylation and transcriptional regulation in the ethylene response

Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprograming, in which EIN2-C-directed regulation of histone acetylation is the first key step for chromatin to perceive ethylene signaling. But how the nuclear acetyl coenzyme A (acetyl CoA) is produced to ensure the ethylene-mediated histone acetylation is unknown. Here we report that ethylene triggers the accumulation of the pyruvate dehydrogenase complex (PDC) in the nucleus to synthesize nuclear acetyl CoA to regulate ethylene response. PDC is identified as an EIN2-C nuclear partner, and ethylene triggers its nuclear accumulation. Mutations in PDC lead to an ethylene hyposensitivity that results from the reduction of histone acetylation and transcription activation. Enzymatically active nuclear PDC synthesizes nuclear acetyl CoA for EIN2-C-directed histone acetylation and transcription regulation. These findings uncover a mechanism by which PDC-EIN2 converges the mitochondrial enzyme-mediated nuclear acetyl CoA synthesis with epigenetic and transcriptional regulation for plant hormone response.

How chromatin senses plant hormones

Plant hormones activate receptors, initiating intracellular signaling pathways. Eventually, hormone-specific transcription factors become active in the nucleus, facilitating hormone-induced transcriptional regulation. Chromatin plays a fundamental role in the regulation of transcription, the process by which genetic information encoded in DNA is converted into RNA. The structure of chromatin, a complex of DNA and proteins, directly influences the accessibility of genes to the transcriptional machinery. The different signaling pathways and transcription factors involved in the transmission of information from the receptors to the nucleus have been readily explored, but not so much for the specific mechanisms employed by the cell to ultimately instruct the chromatin changes necessary for a fast and robust transcription activation, specifically for plant hormone responses. In this review, we will focus on the advancements in understanding how chromatin receives plant hormones, facilitating the changes necessary for fast, robust, and specific transcriptional regulation.

Factors Influencing Seed Dormancy and Germination and Advances in Seed Priming Technology

Seed dormancy and germination play pivotal roles in the agronomic traits of plants, and the degree of dormancy intuitively affects the yield and quality of crops in agricultural production. Seed priming is a pre-sowing seed treatment that enhances and accelerates germination, leading to improved seedling establishment. Seed priming technologies, which are designed to partially activate germination, while preventing full seed germination, have exerted a profound impact on agricultural production. Conventional seed priming relies on external priming agents, which often yield unstable results. What works for one variety might not be effective for another. Therefore, it is necessary to explore the internal factors within the metabolic pathways that influence seed physiology and germination. This review unveils the underlying mechanisms of seed metabolism and germination, the factors affecting seed dormancy and germination, as well as the current seed priming technologies that can result in stable and better germination.

Nuclear Pyruvate Dehydrogenase Complex Regulates Histone Acetylation and Transcriptional Regulation in the Ethylene Response

Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprograming, in which EIN2-C-directed regulation of histone acetylation is the first key-step for chromatin to perceive ethylene signaling. But how the nuclear acetyl coenzyme A (acetyl CoA) is produced to ensure the ethylene-mediated histone acetylation is unknown. Here we report that ethylene triggers the accumulation of the pyruvate dehydrogenase complex (PDC) in the nucleus to synthesize nuclear acetyl CoA to regulate ethylene response. PDC is identified as an EIN2-C nuclear partner, and ethylene triggers its nuclear accumulation. Mutations in PDC lead to an ethylene-hyposensitivity that results from the reduction of histone acetylation and transcription activation. Enzymatically active nuclear PDC synthesize nuclear acetyl CoA for EIN2-C-directed histone acetylation and transcription regulation. These findings uncover a mechanism by which PDC-EIN2 converges the mitochondrial enzyme mediated nuclear acetyl CoA synthesis with epigenetic and transcriptional regulation for plant hormone response.

Ethylene inhibits photosynthesis via temporally distinct responses in tomato plants

Ethylene is a volatile plant hormone that regulates many developmental processes and responses toward (a)biotic stress. Studies have shown that high levels of ethylene repress vegetative growth in many important crops, including tomato (Solanum lycopersicum), possibly by inhibiting photosynthesis. We investigated the temporal effects of ethylene on young tomato plants using an automated ethylene gassing system to monitor the physiological, biochemical, and molecular responses through time course RNA-seq of a photosynthetically active source leaf. We found that ethylene evokes a dose-dependent inhibition of photosynthesis, which can be characterized by 3 temporally distinct phases. The earliest ethylene responses that marked the first phase and occurred a few hours after the start of the treatment were leaf epinasty and a decline in stomatal conductance, which led to lower light perception and CO2 uptake, respectively, resulting in a rapid decline of soluble sugar levels (glucose, fructose). The second phase of the ethylene effect was marked by low carbohydrate availability, which modulated plant energy metabolism to adapt by using alternative substrates (lipids and proteins) to fuel the TCA cycle. Long-term continuous exposure to ethylene led to the third phase, characterized by starch and chlorophyll breakdown, which further inhibited photosynthesis, leading to premature leaf senescence. To reveal early (3 h) ethylene-dependent regulators of photosynthesis, we performed a ChIP-seq experiment using anti-ETHYLENE INSENSITIVE 3-like 1 (EIL1) antibodies and found several candidate transcriptional regulators. Collectively, our study revealed a temporal sequence of events that led to the inhibition of photosynthesis by ethylene and identified potential transcriptional regulators responsible for this regulation.

Histone dynamics responding to internal and external cues underlying plant development

Plants necessitate a refined coordination of growth and development to effectively respond to external triggers for survival and successful reproduction. This intricate harmonization of plant developmental processes and adaptability hinges on significant alterations within their epigenetic landscapes. In this review, we first delve into recent strides made in comprehending underpinning the dynamics of histones, driven by both internal and external cues. We encapsulate the prevailing working models through which cis/trans elements navigate the acquisition and removal of histone modifications, as well as the substitution of histone variants. As we look ahead, we anticipate that delving deeper into the dynamics of epigenetic regulation at the level of individual cells or specific cell types will significantly enrich our comprehension of how plant development unfolds under the influence of internal and external cues. Such exploration holds the potential to provide unprecedented resolution in understanding the orchestration of plant growth and development.

LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes

Ethylene signaling has been indicated as a potential positive regulator of plant warm ambient temperature response but its underlying molecular mechanisms are largely unknown. Here, we show that LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. We found that the presence of warm ambient temperature activates ethylene signaling through EIN2 and EIN3, leading to an interaction between LHP1 and accumulated EIN2-C to co-regulate a subset of LHP1-bound genes marked by H3K27me3 and H3K4me3 bivalency. Furthermore, we demonstrate that INO80 is recruited to bivalent genes by interacting with EIN2-C and EIN3, promoting H3K4me3 enrichment and facilitating transcriptional activation in response to warm ambient temperature. Together, our findings illustrate a novel mechanism wherein ethylene signaling orchestrates LHP1 and INO80 to regulate warm ambient temperature response through activating specific bivalent genes in Arabidopsis.

Endoribonuclease DNE1 Promotes Ethylene Response by Modulating EBF1/2 mRNA Processing in Arabidopsis

The gaseous phytohormone ethylene plays a crucial role in plant growth, development, and stress responses. In the ethylene signal transduction cascade, the F-box proteins EIN3-BINDING F-BOX 1 (EBF1) and EBF2 are identified as key negative regulators governing ethylene sensitivity. The translation and processing of EBF1/2 mRNAs are tightly controlled, and their 3' untranslated regions (UTRs) are critical in these regulations. However, despite their significance, the exact mechanisms modulating the processing of EBF1/2 mRNAs remain poorly understood. In this work, we identified the gene DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1), which encodes an endoribonuclease and is induced by ethylene treatment, as a positive regulator of ethylene response. The loss of function mutant dne1-2 showed mild ethylene insensitivity, highlighting the importance of DNE1 in ethylene signaling. We also found that DNE1 colocalizes with ETHYLENE INSENSITIVE 2 (EIN2), the core factor manipulating the translation of EBF1/2, and targets the P-body in response to ethylene. Further analysis revealed that DNE1 negatively regulates the abundance of EBF1/2 mRNAs by recognizing and cleaving their 3'UTRs, and it also represses their translation. Moreover, the dne1 mutant displays hypersensitivity to 1,4-dithiothreitol (DTT)-induced ER stress and oxidative stress, indicating the function of DNE1 in stress responses. This study sheds light on the essential role of DNE1 as a modulator of ethylene signaling through regulation of EBF1/2 mRNA processing. Our findings contribute to the understanding of the intricate regulatory process of ethylene signaling and provide insights into the significance of ribonuclease in stress responses.

DNA methylation remodeled amino acids biosynthesis regulates flower senescence in carnation (Dianthus caryophyllus)

Dynamic DNA methylation regulatory networks are involved in many biological processes. However, how DNA methylation patterns change during flower senescence and their relevance with gene expression and related molecular mechanism remain largely unknown. Here, we used whole genome bisulfite sequencing to reveal a significant increase of DNA methylation in the promoter region of genes during natural and ethylene-induced flower senescence in carnation (Dianthus caryophyllus L.), which was correlated with decreased expression of DNA demethylase gene DcROS1. Silencing of DcROS1 accelerated while overexpression of DcROS1 delayed carnation flower senescence. Moreover, among the hypermethylated differentially expressed genes during flower senescence, we identified two amino acid biosynthesis genes, DcCARA and DcDHAD, with increased DNA methylation and reduced expression in DcROS1 silenced petals, and decreased DNA methylation and increased expression in DcROS1 overexpression petals, accompanied by decreased or increased amino acids content. Silencing of DcCARA and DcDHAD accelerates carnation flower senescence. We further showed that adding corresponding amino acids could largely rescue the senescence phenotype of DcROS1, DcCARA and DcDHAD silenced plants. Our study not only demonstrates an essential role of DcROS1-mediated remodeling of DNA methylation in flower senescence but also unravels a novel epigenetic regulatory mechanism underlying DNA methylation and amino acid biosynthesis during flower senescence.

Histone acetyltransferase HAF2 associates with PDC to control H3K14ac and H3K23ac in ethylene response

Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprogramming, in which EIN2-C-directed regulation of histone acetylation is the first key-step for chromatin to perceive ethylene signaling. However, the histone acetyltransferase in this process remains unknown. Here, we identified histone acetyltransferase HAF2, and mutations in HAF2 confer plants with ethylene insensitivity. Furthermore, we found that HAF2 interacts with EIN2-C in response to ethylene. Biochemical assays demonstrated that the bromodomain of HAF2 binds to H3K14ac and H3K23ac peptides with a distinct affinity for H3K14ac; the HAT domain possesses acetyltransferase catalytic activity for H3K14 and H3K23 acetylation, with a preference for H3K14. ChIP-seq results provide additional evidence supporting the role of HAF2 in regulating H3K14ac and H3K23ac levels in response to ethylene. Finally, our findings revealed that HAF2 co-functions with pyruvate dehydrogenase complex (PDC) to regulate H3K14ac and H3K23ac in response to ethylene in an EIN2 dependent manner. Overall, this research reveals that HAF2 as a histone acetyltransferase that forms a complex with EIN2-C and PDC, collectively governing histone acetylation of H3H14ac and H3K23ac, preferentially for H3K14 in response to ethylene.

GERDH: an interactive multi-omics database for cross-species data mining in horticultural crops

Horticultural plants contribute immensely to the quality of human's life. The rapid development of omics studies on horticultural plants has resulted in large volumes of valuable growth- and development-related data. Genes that are essential for growth and development are highly conserved in evolution. Cross-species data mining reduces the impact of species heterogeneity and has been extensively used for conserved gene identification. Owing to the lack of a comprehensive database for cross-species data mining using multi-omics data from all horticultural plant species, the current resources in this field are far from satisfactory. Here, we introduce GERDH (https://dphdatabase.com), a database platform for cross-species data mining among horticultural plants, based on 12 961 uniformly processed publicly available omics libraries from more than 150 horticultural plant accessions, including fruits, vegetables and ornamental plants. Important and conserved genes that are essential for a specific biological process can be obtained by cross-species analysis module with interactive web-based data analysis and visualization. Moreover, GERDH is equipped with seven online analysis tools, including gene expression, in-species analysis, epigenetic regulation, gene co-expression, enrichment/pathway and phylogenetic analysis. By interactive cross-species analysis, we identified key genes contributing to postharvest storage. By gene expression analysis, we explored new functions of CmEIN3 in flower development, which was validated by transgenic chrysanthemum analysis. We believe that GERDH will be a useful resource for key gene identification and will allow for omics big data to be more available and accessible to horticultural plant community members.

An insertion of transposon in DcNAP inverted its function in the ethylene pathway to delay petal senescence in carnation (Dianthus caryophyllus L.)

Petal senescence is the final stage of flower development. Transcriptional regulation plays key roles in this process. However, whether and how post-transcriptional regulation involved is still largely unknown. Here, we identified an ethylene-induced NAC family transcription factor DcNAP in carnation (Dianthus caryophyllus L.). One allele, DcNAP-dTdic1, has an insertion of a dTdic1 transposon in its second exon. The dTdic1 transposon disrupts the structure of DcNAP and causes alternative splicing, which transcribes multiple domain-deleted variants (DcNAP2 and others). Conversely, the wild type allele DcNAP transcribes DcNAP1 encoding an intact NAC domain. Silencing DcNAP1 delays and overexpressing DcNAP1 accelerates petal senescence in carnation, while silencing and overexpressing DcNAP2 have the opposite effects, respectively. Further, DcNAP2 could interact with DcNAP1 and interfere the binding and activation activity of DcNAP1 to the promoters of its downstream target ethylene biosynthesis genes DcACS1 and DcACO1. Lastly, ethylene signalling core transcriptional factor DcEIL3-1 can activate the expression of DcNAP1 and DcNAP2 in the same way by binding their promoters. In summary, we discovered a novel mechanism by which DcNAP regulates carnation petal senescence at the post-transcriptional level. It may also provide a useful strategy to manipulate the NAC domains of NAC transcription factors for crop genetic improvement.

Multiplex CRISPR-Cas9 knockout of EIL3, EIL4, and EIN2L advances soybean flowering time and pod set

BACKGROUND

Ethylene inhibitor treatment of soybean promotes flower bud differentiation and early flowering, suggested that there is a close relationship between ethylene signaling and soybean growth and development. The short-lived ETHYLENE INSENSITIVE2 (EIN2) and ETHYLENE INSENSITIVE3 (EIN3) proteins play central roles in plant development. The objective of this study was carried out gene editing of EIL family members in soybeans and to examine the effects on soybean yield and other markers of growth.

METHODS AND RESULTS

By editing key-node genes in the ethylene signaling pathway using a multi-sgRNA-in-one strategy, we obtained a series of gene edited lines with variable edit combinations among 15 target genes. EIL3, EIL4, and EIN2L were editable genes favored by the T0 soybean lines. Pot experiments also show that the early flowering stage R1 of the EIL3, EIL4, and EIN2L triple mutant was 7.05 d earlier than that of the wild-type control. The yield of the triple mutant was also increased, being 1.65-fold higher than that of the control. Comparative RNA-seq revealed that sucrose synthase, AUX28, MADS3, type-III polyketide synthase A/B, ABC transporter G family member 26, tetraketide alpha-pyrone reductase, and fatty acyl-CoA reductase 2 may be involved in regulating early flowering and high-yield phenotypes in triple mutant soybean plants.

CONCLUSION

Our results provide a scientific basis for genetic modification to promote the development of earlier-flowering and higher-yielding soybean cultivars.

A truncated ETHYLENE INSENSITIVE3-like protein, GhLYI, regulates senescence in cotton

Numerous endogenous and environmental signals regulate the intricate and highly orchestrated process of plant senescence. Ethylene (ET), which accumulates as senescence progresses, is a major promoter of leaf senescence. The master transcription activator ETHYLENE INSENSITIVE3 (EIN3) activates the expression of a wide range of downstream genes during leaf senescence. Here, we found that a unique EIN3-LIKE 1 (EIL1) gene, cotton LINT YIELD INCREASING (GhLYI), encodes a truncated EIN3 protein in upland cotton (Gossypium hirsutum L.) that functions as an ET signal response factor and a positive regulator of senescence. Ectopic expression or overexpression of GhLYI accelerated leaf senescence in both Arabidopsis (Arabidopsis thaliana) and cotton. Cleavage under targets and tagmentation (CUT&Tag) analyses revealed that SENESCENCE-ASSOCIATED GENE 20 (SAG20) was a target of GhLYI. Electrophoretic mobility shift assay (EMSA), yeast 1-hybrid (Y1H), and dual-luciferase transient expression assay confirmed that GhLYI directly bound the promoter of SAG20 to activate its expression. Transcriptome analysis revealed that transcript levels of a series of senescence-related genes, SAG12, NAC-LIKE, ACTIVATED by APETALA 3/PISTILLATA (NAP/ANAC029), and WRKY53, are substantially induced in GhLYI overexpression plants compared with wild-type (WT) plants. Virus-induced gene silencing (VIGS) preliminarily confirmed that knockdown of GhSAG20 delayed leaf senescence. Collectively, our findings provide a regulatory module involving GhLYI-GhSAG20 in controlling senescence in cotton.

Arabidopsis EIN2 represses ABA responses during germination and early seedling growth by inactivating HLS1 protein independently of the canonical ethylene pathway

The signaling pathways for the phytohormones ethylene and abscisic acid (ABA) have antagonistic effects on seed germination and early seedling establishment. However, the underlying molecular mechanisms remain unclear. In Arabidopsis thaliana, ETHYLENE INSENSITIVE 2 (EIN2) localizes to the endoplasmic reticulum (ER); although its biochemical function is unknown, it connects the ethylene signal with the key transcription factors EIN3 and EIN3-LIKE 1 (EIL1), leading to the transcriptional activation of ethylene-responsive genes. In this study, we uncovered an EIN3/EIL1-independent role for EIN2 in regulating the ABA response. Epistasis analysis demonstrated that this distinct role of EIN2 in the ABA response depends on HOOKLESS 1 (HLS1), the putative histone acetyltransferase acting as a positive regulator of ABA responses. Protein interaction assays supported a direct physical interaction between EIN2 and HLS1 in vitro and in vivo. Loss of EIN2 function resulted in an alteration of HLS1-mediated histone acetylation at the ABA-INSENSITIVE 3 (ABI3) and ABI5 loci, which promotes gene expression and the ABA response during seed germination and early seedling growth, indicating that the EIN2-HLS1 module contributes to ABA responses. Our study thus revealed that EIN2 modulates ABA responses by repressing HLS1 function, independently of the canonical ethylene pathway. These findings shed light on the intricate regulatory mechanisms underling the antagonistic interactions between ethylene and ABA signaling, with significant implications for our understanding of plant growth and development.

A translational regulator MHZ9 modulates ethylene signaling in rice

Ethylene plays essential roles in rice growth, development and stress adaptation. Translational control of ethylene signaling remains unclear in rice. Here, through analysis of an ethylene-response mutant mhz9, we identified a glycine-tyrosine-phenylalanine (GYF) domain protein MHZ9, which positively regulates ethylene signaling at translational level in rice. MHZ9 is localized in RNA processing bodies. The C-terminal domain of MHZ9 interacts with OsEIN2, a central regulator of rice ethylene signaling, and the N-terminal domain directly binds to the OsEBF1/2 mRNAs for translational inhibition, allowing accumulation of transcription factor OsEIL1 to activate the downstream signaling. RNA-IP seq and CLIP-seq analyses reveal that MHZ9 associates with hundreds of RNAs. Ribo-seq analysis indicates that MHZ9 is required for the regulation of ~ 90% of genes translationally affected by ethylene. Our study identifies a translational regulator MHZ9, which mediates translational regulation of genes in response to ethylene, facilitating stress adaptation and trait improvement in rice.

The role of ethylene in plant temperature stress response

Temperature influences the seasonal growth and geographical distribution of plants. Heat or cold stress occur when temperatures exceed or fall below the physiological optimum ranges, resulting in detrimental and irreversible damage to plant growth, development, and yield. Ethylene is a gaseous phytohormone with an important role in plant development and multiple stress responses. Recent studies have shown that, in many plant species, both heat and cold stress affect ethylene biosynthesis and signaling pathways. In this review, we summarize recent advances in understanding the role of ethylene in plant temperature stress responses and its crosstalk with other phytohormones. We also discuss potential strategies and knowledge gaps that need to be adopted and filled to develop temperature stress-tolerant crops by optimizing ethylene response.

The ethylene-responsive transcription factor PpERF9 represses PpRAP2.4 and PpMYB114 via histone deacetylation to inhibit anthocyanin biosynthesis in pear

Ethylene induces anthocyanin biosynthesis in most fruits, including apple (Malus domestica) and plum (Prunus spp.). By contrast, ethylene inhibits anthocyanin biosynthesis in pear (Pyrus spp.), but the underlying molecular mechanism remains unclear. In this study, we identified and characterized an ethylene-induced ETHYLENE RESPONSE FACTOR (ERF) transcription factor, PpETHYLENE RESPONSE FACTOR9 (PpERF9), which functions as a transcriptional repressor. Our analyses indicated PpERF9 can directly inhibit expression of the MYB transcription factor gene PpMYB114 by binding to its promoter. Additionally, PpERF9 inhibits the expression of the transcription factor gene PpRELATED TO APETALA2.4 (PpRAP2.4), which activates PpMYB114 expression, by binding to its promoter, thus forming a PpERF9-PpRAP2.4-PpMYB114 regulatory circuit. Furthermore, PpERF9 interacts with the co-repressor PpTOPLESS1 (PpTPL1) via EAR motifs to form a complex that removes the acetyl group on histone H3 and maintains low levels of acetylated H3 in the PpMYB114 and PpRAP2.4 promoter regions. The resulting suppressed expression of these 2 genes leads to decreased anthocyanin biosynthesis in pear. Collectively, these results indicate that ethylene inhibits anthocyanin biosynthesis by a mechanism that involves PpERF9-PpTPL1 complex-mediated histone deacetylation of PpMYB114 and PpRAP2.4. The data presented herein will be useful for clarifying the relationship between chromatin status and hormone signaling, with implications for plant biology research.

Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation

Petal senescence is controlled by a complex regulatory network. Epigenetic regulation like histone modification influences chromatin state and gene expression. However, the involvement of histone methylation in regulating petal senescence remains poorly understood. Here, we found that the trimethylation of histone H3 at Lysine 4 (H3K4me3) is increased during ethylene-induced petal senescence in carnation (Dianthus caryophyllus L.). H3K4me3 levels were positively associated with the expression of transcription factor DcWRKY75, ethylene biosynthetic genes 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (DcACS1), and ACC oxidase (DcACO1), and senescence associated genes (SAGs) DcSAG12 and DcSAG29. Further, we identified that carnation ARABIDOPSIS HOMOLOG OF TRITHORAX1 (DcATX1) encodes a histone lysine methyltransferase which can methylate H3K4. Knockdown of DcATX1 delayed ethylene-induced petal senescence in carnation, which was associated with the down-regulated expression of DcWRKY75, DcACO1, and DcSAG12, whereas overexpression of DcATX1 exhibited the opposite effects. DcATX1 promoted the transcription of DcWRKY75, DcACO1, and DcSAG12 by elevating the H3K4me3 levels within their promoters. Overall, our results demonstrate that DcATX1 is a H3K4 methyltransferase that promotes the expression of DcWRKY75, DcACO1, DcSAG12 and potentially other downstream target genes by regulating H3K4me3 levels, thereby accelerating ethylene-induced petal senescence in carnation. This study further indicates that epigenetic regulation is important for plant senescence processes.

The mutual regulation between DcEBF1/2 and DcEIL3-1 is involved in ethylene induced petal senescence in carnation (Dianthus caryophyllus L.)

Carnation (Dianthus caryophyllus L.) is a respiratory climacteric flower, comprising one of the most important cut flowers that is extremely sensitive to plant hormone ethylene. Ethylene signaling core transcription factor DcEIL3-1 plays a key role in ethylene induced petal senescence in carnation. However, how the dose of DcEIL3-1 is regulated in the carnation petal senescence process is still not clear. Here, we screened out two EBF (EIN3 Binding F-box) genes, DcEBF1 and DcEBF2, which showed quick elevation by ethylene treatment according to the ethylene induced carnation petal senescence transcriptome. Silencing of DcEBF1 and DcEBF2 accelerated, whereas overexpression of DcEBF1 and DcEBF2 delayed, ethylene induced petal senescence in carnation by influencing DcEIL3-1 downstream target genes but not DcEIL3-1 itself. Furthermore, DcEBF1 and DcEBF2 interact with DcEIL3-1 to degrade DcEIL3-1 via an ubiquitination pathway in vitro and in vivo. Finally, DcEIL3-1 binds to the promoter regions of DcEBF1 and DcEBF2 to activate their expression. In conclusion, the present study reveals the mutual regulation between DcEBF1/2 and DcEIL3-1 during ethylene induced petal senescence in carnation, which not only expands our understanding about ethylene signal regulation network in the carnation petal senescence process, but also provides potential targets with respect to breeding a cultivar of long-lived cut carnation.

Ethylene-mediated regulation of coleoptile elongation in rice seedlings

Rice is an important food crop in the world and the study of its growth and plasticity has a profound influence on sustainable development. Ethylene modulates multiple agronomic traits of rice as well as abiotic and biotic stresses during its lifecycle. It has diverse roles, depending on the organs, developmental stages and environmental conditions. Compared to Arabidopsis (Arabidopsis thaliana), rice ethylene signalling pathway has its own unique features due to its special semiaquatic living environment and distinct plant structure. Ethylene signalling and responses are part of an intricate network in crosstalk with internal and external factors. This review will summarize the current progress in the mechanisms of ethylene-regulated coleoptile growth in rice, with a special focus on ethylene signaling and interaction with other hormones. Insights into these molecular mechanisms may shed light on ethylene biology and should be beneficial for the genetic improvement of rice and other crops.

BBX7 interacts with BBX8 to accelerate flowering in chrysanthemum

The quantitative control of FLOWERING LOCUS T (FT) activation is important for the floral transition in flowering plants. However, the flowering regulation mechanisms in the day-neutral, summer-flowering chrysanthemum plant remain unclear. In this study, the chrysanthemum BBX7 homolog CmBBX7 was isolated and its flowering function was identified. The expression of CmBBX7 showed a diurnal rhythm and CmBBX7 exhibited higher expression levels than CmBBX8. Overexpression of CmBBX7 in transgenic chrysanthemum accelerated flowering, whereas lines transfected with a chimeric repressor (pSRDX-CmBBX7) exhibited delayed flowering. Yeast single hybridization, luciferase, electrophoretic mobility shift, and chromatin immunoprecipitation assays showed that CmBBX7 directly targets CmFTL1. In addition, we found that CmBBX7 and CmBBX8 interact to positively regulate the expression of CmFTL1 through binding to its promoter. Collectively, these results highlight CmBBX7 as a key cooperator in the BBX8-FT module to control chrysanthemum flowering.

The involvement of Ein3-binding F-box protein PbrEBF3 in regulating ethylene signaling during Cuiguan pear fruit ripening

Ein3-binding F-box (EBF) proteins have been determined to modulate ethylene response processes by regulating EIN3/EIL protein degradation in Arabidopsis and tomato. However, the function of pear PbrEBFs in ethylene-dependent responses during fruit ripening remains unclear. In this study, PbrEBF1, PbrEBF2, and PbrEBF3 display contrasting expression patterns in response to ethylene and 1-MCP treatment. PbrEBF3 displayed potential fruit ripening-associated function in a transient expression experiment. Yeast two-hybrid (Y2H) and Firefly luciferase complementation imaging (LCI) assays indicated that PbrEBF3 interacts with PbrEIL1, PbrEIL2, and PbrEIL3 proteins. In turn, the transcription of PbrEBF3 is directly regulated by PbrEILs via a feedback loop. PbrEILs trigger a transcriptional cascade of PbrERF24 and finally affect ethylene synthesis. Overall, PbrEBF3 plays a central role in pear fruit ripening through mediation of the ethylene signaling pathway.

Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity

Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.

Databases and prospects of dynamic gene regulation in eukaryotes: A mini review

In eukaryotes, dynamic regulation enables DNA polymerases to catalyze a variety of RNA products in spatial and temporal patterns. Dynamic gene expression is regulated by transcription factors (TFs) and epigenetics (DNA methylation and histone modification). The applications of biochemical technology and high-throughput sequencing enhance the understanding of mechanisms of these regulations and affected genomic regions. To provide a searchable platform for retrieving such metadata, numerous databases have been developed based on the integration of genome-wide maps (e.g., ChIP-seq, whole-genome bisulfite sequencing, RNA-seq, ATAC-seq, DNase-seq, and MNase-seq data) and functionally genomic annotation. In this mini review, we summarize the main functions of TF-related databases and outline the prevalent approaches used in inferring epigenetic regulations, their associated genes, and functions. We review the literature on crosstalk between TF and epigenetic regulation and the properties of non-coding RNA regulation, which are challenging topics that promise to pave the way for advances in database development.

The transcription factors DcHB30 and DcWRKY75 antagonistically regulate ethylene-induced petal senescence in carnation (Dianthus caryophyllus)

Although numerous transcription factors with antagonistic activities have been shown to contribute to growth and development, whether and how they regulate senescence in plants is largely unknown. In this study, we investigated the role of antagonistic transcription factors in petal senescence in carnation (Dianthus caryophyllus), one of the most common types of ethylene-sensitive cut flowers produced worldwide. We identified DcHB30 that encodes a ZF-HD transcription factor that is down-regulated in ethylene-treated petal transcriptomes. We found that silencing DcHB30 accelerated ethylene-induced petal senescence and that DcHB30 physically interacts with DcWRKY75, a positive regulator of ethylene-induced petal senescence. Phenotypic characterization and molecular evidence indicated that DcHB30 and DcWRKY75 competitively regulate the expression of their co-targeted genes DcACS1, DcACO1, DcSAG12, and DcSAG29 by reciprocally inhibiting the DNA-binding activity of each other on the gene promoters. This transcriptional regulation mechanism demonstrates that these transcription factors serve as positive and negative regulators in ethylene-induced petal senescence in carnation. Thus, our study provides insights into how antagonizing transcription factors regulate plant senescence.

Phosphorylation status of Bβ subunit acts as a switch to regulate the function of phosphatase PP2A in ethylene-mediated root growth inhibition

The various combinations and regulations of different subunits of phosphatase PP2A holoenzymes underlie their functional complexity and importance. However, molecular mechanisms governing the assembly of PP2A complex in response to external or internal signals remain largely unknown, especially in Arabidopsis thaliana. We found that the phosphorylation status of Bβ of PP2A acts as a switch to regulate the activity of PP2A. In the absence of ethylene, phosphorylated Bβ leads to an inactivation of PP2A; the substrate EIR1 remains to be phosphorylated, preventing the EIR1-mediated auxin transport in epidermis, leading to normal root growth. Upon ethylene treatment, the dephosphorylated Bβ mediates the formation of the A2-C4-Bβ protein complex to activate PP2A, resulting in the dephosphorylation of EIR1 to promote auxin transport in epidermis of elongation zone, leading to root growth inhibition. Altogether, our research revealed a novel molecular mechanism by which the dephosphorylation of Bβ subunit switches on PP2A activity to dephosphorylate EIR1 to establish EIR1-mediated auxin transport in the epidermis in elongation zone for root growth inhibition in response to ethylene.

FoCupin1, a Cupin_1 domain-containing protein, is necessary for the virulence of Fusarium oxysporum f. sp. cubense tropical race 4

Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is an important soilborne fungal pathogen that causes the most devastating banana disease. Effectors secreted by microbes contribute to pathogen virulence on host plants in plant-microbe interactions. However, functions of Foc TR4 effectors remain largely unexplored. In this study, we characterized a novel cupin_1 domain-containing protein (FoCupin1) from Foc TR4. Sequence analysis indicated that the homologous proteins of FoCupin1 in phytopathogenic fungi were evolutionarily conserved. Furthermore, FoCupin1 could suppress BAX-mediated cell death and significantly downregulate the expression of defense-related genes in tobacco by using the Agrobacterium-mediated transient expression system. FoCupin1 was highly induced in the early stage of Foc TR4 infection. The deletion of FoCupin1 gene did not affect Foc TR4 growth and conidiation. However, FoCupin1 deletion significantly reduced Foc TR4 virulence on banana plants, which was further confirmed by biomass assay. The expression of the defense-related genes in banana was significantly induced after inoculation with FoCupin1 mutants. These results collectively indicate FoCupin1 is a putative effector protein that plays an essential role in Foc TR4 pathogenicity. These findings suggest a novel role for cupin_1 domain-containing proteins and deepen our understanding of effector-mediated Foc TR4 pathogenesis.

Ethylene Insensitive 3-Like 2 is a Brassicaceae-specific transcriptional regulator involved in fine-tuning ethylene responses in Arabidopsis thaliana

Ethylene signaling directs a pleiotropy of developmental processes in plants. In Arabidopsis, ethylene signaling converges at the master transcription factor Ethylene Insensitive 3 (EIN3), which has five homologs, EIN3-like 1-5 (EIL1-EIL5). EIL1 is most fully characterized and operates similarly to EIN3, while EIL3-5 are not involved in ethylene signaling. EIL2 remains less investigated. Our phylogenetic analysis revealed that EIL2 homologs have only been retrieved in the Brassicaceae family, suggesting that EIL2 diverged to have specific functions in the mustard family. By characterizing eil2 mutants, we found that EIL2 is involved in regulating ethylene-specific developmental processes in Arabidopsis thaliana, albeit in a more subtle way compared with EIN3/EIL1. EIL2 steers ethylene-triggered hypocotyl elongation in light-grown seedlings and is involved in lateral root formation. Furthermore, EIL2 takes part in regulating flowering time as eil2 mutants flower on average 1 d earlier and have fewer leaves. A pEIL2:EIL2:GFP translational reporter line revealed that EIL2 protein abundance is restricted to the stele of young developing roots. EIL2 expression, and not EIL2 protein stability, is regulated by ethylene in an EIN3/EIL1-dependent way. Despite EIL2 taking part in several developmental processes, the precise upstream and downstream regulation of this ethylene- and Brassicaceae-specific transcription factor remains to be elucidated.

Histone deacetylase AtSRT2 regulates salt tolerance during seed germination via repression of vesicle-associated membrane protein 714 (VAMP714) in Arabidopsis

Salt tolerance during seed germination is essential for seedling establishment under salt stress. Sirtuin-like proteins, NAD⁺ -dependent histone deacetylases, are involved in plant responses to abiotic stresses; however, the regulatory mechanism remains unknown. We elucidated the mechanism underlying AtSRT2 (a sirtuin-like protein)-mediated regulation of salt tolerance during seed germination in Arabidopsis. The AtSRT2 mutant srt2 exhibited significantly reduced seed germination percentages under salt stress; its targets were identified via chromatin immunoprecipitation coupled with ultra-high-throughput parallel DNA sequencing (ChIP-Seq) assay. Epistasis analysis was performed to identify AtSRT2-related pathways. Overexpression of SRT2.7, an AtSRT2 splice variant, rescued the salt-sensitive phenotype of mutant srt2. AtSRT2 histone deacetylation activity was important for salt tolerance during seed germination. The acetylation level of histone H4K8 locus in srt2-1 increased significantly under salt treatment. Vesicle-associated membrane protein 714 (VAMP714), a negative regulator of hydrogen peroxide (H₂ O₂ )-containing vesicle trafficking in cells, was identified as a target of AtSRT2. AtSRT2 regulated histone acetylation in the promoter region of VAMP714 and inhibited VAMP714 transcription under salt treatment. Seed germination percentage of double-mutant srt2-1vamp714 was close to that of single-mutant vamp714, and higher than that of single-mutant srt2 under salt stress. Hydrogen peroxide content and DNA damage increased after salt treatment in srt2 during seed germination. AtSRT2 regulates salt tolerance during seed germination through VAMP714 in Arabidopsis.

Dynamic roles and intricate mechanisms of ethylene in epidermal hair development in Arabidopsis and cotton

Ethylene affects many aspects of plant growth and development, including root hairs and trichomes growth in Arabidopsis, as well as fiber development in cotton, though the underlying mechanism is unclear. In this article, we update the research progress associated with the main genes in ethylene biosynthesis and signaling pathway, and we propose a clear ethylene pathway based on genome-wide identification of homologues in cotton. Expression pattern analysis using transcriptome data revealed that some candidate genes may contribute to cotton fiber development through the ethylene pathway. Moreover, we systematically summarized the effects of ethylene on the development of epidermal hair and the underlying regulatory mechanisms in Arabidopsis. Based on the knowledge of ethylene-promoted cell differentiation, elongation, and development in different tissues or plants, we advised a possible regulatory network for cotton fiber development with ethylene as the hub. Importantly, we emphasized the roles of ethylene as an important node in regulating cotton vegetative growth, and stress resistance, and suggested utilizing multiple methods to subtly modify ethylene synthesis or signaling in a tissue or spatiotemporal-specific manner to clarify its exact effect on architecture, adaptability of the plant, and fiber development, paving the way for basic research and genetic improvement of the cotton crop.

Ethylene precisely regulates anthocyanin synthesis in apple via a module comprising MdEIL1, MdMYB1, and MdMYB17

Ethylene regulates anthocyanin synthesis in ripening apple fruit via the antagonistic activities of the R2R3-MYB repressors and activators. However, the molecular mechanism underlying this process remains unknown. In this study, ethylene significantly induced the expression of the R2R3-MYB gene MdMYB17 in apple fruit. Moreover, MdMYB17 was revealed to be an important repressor of anthocyanin synthesis. Specifically, MdMYB17 binds directly to the promoters of the ethylene-induced genes MdMYB1 and MdEIL1, which encode positive regulators of anthocyanin synthesis, and represses their expression. Additionally, MdMYB1 and MdEIL1 bind to the MdMYB17 promoter to activate its expression. Thus, MdMYB17, MdMYB1, and MdEIL1 form a regulatory module that controls the expression of the corresponding genes. MdMYB17 interacts with MdEIL1. The interaction between MdMYB17 and MdEIL1 attenuates the regulatory effects of MdMYB17 on MdMYB1 and MdEIL1 as well as the regulatory effects of MdEIL1 on MdMYB17. Overall, our results reveal the molecular mechanisms by which MdMYB17, MdMYB1, and MdEIL1 finely mediate ethylene-regulated anthocyanin synthesis in apple fruit.

DcWRKY75 promotes ethylene induced petal senescence in carnation (Dianthus caryophyllus L.)

Carnation (Dianthus caryophyllus L.) is one of the most important and typical ethylene sensitive cut flowers worldwide, although how ethylene influences the petal senescence process in carnation remains largely unknown. Here, we screened out one of the key transcription factors, DcWRKY75, using a constructed ethylene induced petal senescence transcriptome in carnation and found that it shows quick induction by ethylene treatment. Silencing of DcWRKY75 delays ethylene induced petal senescence in carnation. Molecular evidence confirms that DcWRKY75 can bind to the promoter regions of two main ethylene biosynthetic genes (DcACS1 and DcACO1) and a couple of senescence associated genes (DcSAG12 and DcSAG29) to activate their expression. Furthermore, we show that DcWRKY75 is a direct target gene of DcEIL3-1, which is a homolog of the ethylene signaling core transcription factor EIN3 in Arabidopsis. DcEIL3-1 can physically interact with DcWRKY75 and silencing of DcEIL3-1 also delays ethylene induced petal senescence in carnation and inhibits the ethylene induced expression of DcWRKY75 and its target genes. The present study demonstrates that the transcriptional regulation network is vitally important for ethylene induced petal senescence process in carnation and potentially in other ethylene sensitive cut flowers.

Modulation of Organogenesis and Somatic Embryogenesis by Ethylene: An Overview

Ethylene is a plant hormone controlling physiological and developmental processes such as fruit maturation, hairy root formation, and leaf abscission. Its effect on regeneration systems, such as organogenesis and somatic embryogenesis (SE), has been studied, and progress in molecular biology techniques have contributed to unveiling the mechanisms behind its effects. The influence of ethylene on regeneration should not be overlooked. This compound affects regeneration differently, depending on the species, genotype, and explant. In some species, ethylene seems to revert recalcitrance in genotypes with low regeneration capacity. However, its effect is not additive, since in genotypes with high regeneration capacity this ability decreases in the presence of ethylene precursors, suggesting that regeneration is modulated by ethylene. Several lines of evidence have shown that the role of ethylene in regeneration is markedly connected to biotic and abiotic stresses as well as to hormonal-crosstalk, in particular with key regeneration hormones and growth regulators of the auxin and cytokinin families. Transcriptional factors of the ethylene response factor (ERF) family are regulated by ethylene and strongly connected to SE induction. Thus, an evident connection between ethylene, stress responses, and regeneration capacity is markedly established. In this review the effect of ethylene and the way it interacts with other players during organogenesis and somatic embryogenesis is discussed. Further studies on the regulation of ERF gene expression induced by ethylene during regeneration can contribute to new insights on the exact role of ethylene in these processes. A possible role in epigenetic modifications should be considered, since some ethylene signaling components are directly related to histone acetylation.